%0 Journal Article %J Cell %D 2024 %T The CARD8 inflammasome dictates HIV/SIV pathogenesis and disease progression. %A Wang, Qiankun %A Clark, Kolin M %A Tiwari, Ritudhwaj %A Raju, Nagarajan %A Tharp, Gregory K %A Jeffrey Rogers %A R. Alan Harris %A Raveendran, Muthuswamy %A Bosinger, Steven E %A Burdo, Tricia H %A Silvestri, Guido %A Shan, Liang %K Animals %K CARD Signaling Adaptor Proteins %K CD4-Positive T-Lymphocytes %K Disease Progression %K HIV %K HIV Infections %K Humans %K Inflammasomes %K Mice %K Neoplasm Proteins %K Simian Acquired Immunodeficiency Syndrome %K Simian Immunodeficiency Virus %K Viremia %X

While CD4 T cell depletion is key to disease progression in people living with HIV and SIV-infected macaques, the mechanisms underlying this depletion remain incompletely understood, with most cell death involving uninfected cells. In contrast, SIV infection of "natural" hosts such as sooty mangabeys does not cause CD4 depletion and AIDS despite high-level viremia. Here, we report that the CARD8 inflammasome is activated immediately after HIV entry by the viral protease encapsulated in incoming virions. Sensing of HIV protease activity by CARD8 leads to rapid pyroptosis of quiescent cells without productive infection, while T cell activation abolishes CARD8 function and increases permissiveness to infection. In humanized mice reconstituted with CARD8-deficient cells, CD4 depletion is delayed despite high viremia. Finally, we discovered loss-of-function mutations in CARD8 from "natural hosts," which may explain the peculiarly non-pathogenic nature of these infections. Our study suggests that CARD8 drives CD4 T cell depletion during pathogenic HIV/SIV infections.

%B Cell %V 187 %P 1223-1237.e16 %8 2024 Feb 29 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/38428396?dopt=Abstract %R 10.1016/j.cell.2024.01.048 %0 Journal Article %J Nat Biotechnol %D 2024 %T Characterization and visualization of tandem repeats at genome scale. %A Dolzhenko, Egor %A English, Adam %A Dashnow, Harriet %A De Sena Brandine, Guilherme %A Mokveld, Tom %A Rowell, William J %A Karniski, Caitlin %A Kronenberg, Zev %A Danzi, Matt C %A Cheung, Warren A %A Bi, Chengpeng %A Farrow, Emily %A Wenger, Aaron %A Chua, Khi Pin %A Martínez-Cerdeño, Verónica %A Bartley, Trevor D %A Jin, Peng %A Nelson, David L %A Züchner, Stephan %A Pastinen, Tomi %A Quinlan, Aaron R %A Fritz J Sedlazeck %A Eberle, Michael A %X

Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate full-length sequences and methylation of TRs, there is still a need for computational methods to profile TRs across the genome. Here we introduce the Tandem Repeat Genotyping Tool (TRGT) and an accompanying TR database. TRGT determines the consensus sequences and methylation levels of specified TRs from PacBio HiFi sequencing data. It also reports reads that support each repeat allele. These reads can be subsequently visualized with a companion TR visualization tool. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 98.38%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all expansions while also identifying methylation signals and mosaicism and providing finer repeat length resolution than existing methods. Additionally, we released a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes.

%B Nat Biotechnol %8 2024 Jan 02 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/38168995?dopt=Abstract %R 10.1038/s41587-023-02057-3 %0 Journal Article %J Hum Mol Genet %D 2024 %T Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases. %A Brock, Daniel C %A Wang, Meng %A Hussain, Hafiz Muhammad Jafar %A Rauch, David E %A Marra, Molly %A Pennesi, Mark E %A Yang, Paul %A Everett, Lesley %A Ajlan, Radwan S %A Colbert, Jason %A Porto, Fernanda Belga Ottoni %A Matynia, Anna %A Gorin, Michael B %A Koenekoop, Robert K %A Lopez, Irma %A Sui, Ruifang %A Zou, Gang %A Yumei Li %A Rui Chen %X

Inherited retinal diseases (IRDs) are a group of rare genetic eye conditions that cause blindness. Despite progress in identifying genes associated with IRDs, improvements are necessary for classifying rare autosomal dominant (AD) disorders. AD diseases are highly heterogenous, with causal variants being restricted to specific amino acid changes within certain protein domains, making AD conditions difficult to classify. Here, we aim to determine the top-performing in-silico tools for predicting the pathogenicity of AD IRD variants. We annotated variants from ClinVar and benchmarked 39 variant classifier tools on IRD genes, split by inheritance pattern. Using area-under-the-curve (AUC) analysis, we determined the top-performing tools and defined thresholds for variant pathogenicity. Top-performing tools were assessed using genome sequencing on a cohort of participants with IRDs of unknown etiology. MutScore achieved the highest accuracy within AD genes, yielding an AUC of 0.969. When filtering for AD gain-of-function and dominant negative variants, BayesDel had the highest accuracy with an AUC of 0.997. Five participants with variants in NR2E3, RHO, GUCA1A, and GUCY2D were confirmed to have dominantly inherited disease based on pedigree, phenotype, and segregation analysis. We identified two uncharacterized variants in GUCA1A (c.428T>A, p.Ile143Thr) and RHO (c.631C>G, p.His211Asp) in three participants. Our findings support using a multi-classifier approach comprised of new missense classifier tools to identify pathogenic variants in participants with AD IRDs. Our results provide a foundation for improved genetic diagnosis for people with IRDs.

%B Hum Mol Genet %8 2024 Mar 07 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/38453143?dopt=Abstract %R 10.1093/hmg/ddae028 %0 Journal Article %J Life Sci Alliance %D 2024 %T A comparative study of structural variant calling in WGS from Alzheimer's disease families. %A Malamon, John S %A Farrell, John J %A Xia, Li Charlie %A Dombroski, Beth A %A Das, Rueben G %A Way, Jessica %A Kuzma, Amanda B %A Valladares, Otto %A Leung, Yuk Yee %A Scanlon, Allison J %A Lopez, Irving Antonio Barrera %A Brehony, Jack %A Worley, Kim C %A Zhang, Nancy R %A Wang, Li-San %A Farrer, Lindsay A %A Schellenberg, Gerard D %A Lee, Wan-Ping %A Vardarajan, Badri N %K Alzheimer Disease %K Humans %K Whole Genome Sequencing %X

Detecting structural variants (SVs) in whole-genome sequencing poses significant challenges. We present a protocol for variant calling, merging, genotyping, sensitivity analysis, and laboratory validation for generating a high-quality SV call set in whole-genome sequencing from the Alzheimer's Disease Sequencing Project comprising 578 individuals from 111 families. Employing two complementary pipelines, Scalpel and Parliament, for SV/indel calling, we assessed sensitivity through sample replicates (N = 9) with in silico variant spike-ins. We developed a novel metric, D-score, to evaluate caller specificity for deletions. The accuracy of deletions was evaluated by Sanger sequencing. We generated a high-quality call set of 152,301 deletions of diverse sizes. Sanger sequencing validated 114 of 146 detected deletions (78.1%). Scalpel excelled in accuracy for deletions ≤100 bp, whereas Parliament was optimal for deletions >900 bp. Overall, 83.0% and 72.5% of calls by Scalpel and Parliament were validated, respectively, including all 11 deletions called by both Parliament and Scalpel between 101 and 900 bp. Our flexible protocol successfully generated a high-quality deletion call set and a truth set of Sanger sequencing-validated deletions with precise breakpoints spanning 1-17,000 bp.

%B Life Sci Alliance %V 7 %8 2024 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/38418088?dopt=Abstract %R 10.26508/lsa.202302181 %0 Journal Article %J bioRxiv %D 2024 %T Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms. %A Behera, Sairam %A Catreux, Severine %A Rossi, Massimiliano %A Truong, Sean %A Huang, Zhuoyi %A Ruehle, Michael %A Visvanath, Arun %A Parnaby, Gavin %A Roddey, Cooper %A Onuchic, Vitor %A Cameron, Daniel L %A English, Adam %A Mehtalia, Shyamal %A Han, James %A Mehio, Rami %A Fritz J Sedlazeck %X

Research and medical genomics require comprehensive and scalable solutions to drive the discovery of novel disease targets, evolutionary drivers, and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size (e.g., SNV/SV) or location (e.g., repeats). Here we present DRAGEN that utilizes novel methods based on multigenomes, hardware acceleration, and machine learning based variant detection to provide novel insights into individual genomes with ~30min computation time (from raw reads to variant detection). DRAGEN outperforms all other state-of-the-art methods in speed and accuracy across all variant types (SNV, indel, STR, SV, CNV) and further incorporates specialized methods to obtain key insights in medically relevant genes (e.g., HLA, SMN, GBA). We showcase DRAGEN across 3,202 genomes and demonstrate its scalability, accuracy, and innovations to further advance the integration of comprehensive genomics for research and medical applications.

%B bioRxiv %8 2024 Jan 06 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/38260545?dopt=Abstract %R 10.1101/2024.01.02.573821 %0 Journal Article %J bioRxiv %D 2024 %T Comprehensive single-cell atlas of the mouse retina. %A Li, Jin %A Choi, Jongsu %A Cheng, Xuesen %A Ma, Justin %A Pema, Shahil %A Sanes, Joshua R %A Mardon, Graeme %A Frankfort, Benjamin J %A Tran, Nicholas M %A Yumei Li %A Rui Chen %X

Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cellular heterogeneity at the single-cell resolution by classifying and characterizing cell types in multiple tissues and species. While several mouse retinal scRNA-seq reference datasets have been published, each dataset either has a relatively small number of cells or is focused on specific cell classes, and thus is suboptimal for assessing gene expression patterns across all retina types at the same time. To establish a unified and comprehensive reference for the mouse retina, we first generated the largest retinal scRNA-seq dataset to date, comprising approximately 190,000 single cells from C57BL/6J mouse whole retinas. This dataset was generated through the targeted enrichment of rare population cells via antibody-based magnetic cell sorting. By integrating this new dataset with public datasets, we conducted an integrated analysis to construct the Mouse Retina Cell Atlas (MRCA) for wild-type mice, which encompasses over 330,000 single cells. The MRCA characterizes 12 major classes and 138 cell types. It captured consensus cell type characterization from public datasets and identified additional new cell types. To facilitate the public use of the MRCA, we have deposited it in CELLxGENE, UCSC Cell Browser, and the Broad Single Cell Portal for visualization and gene expression exploration. The comprehensive MRCA serves as an easy-to-use, one-stop data resource for the mouse retina communities.

%B bioRxiv %8 2024 Jan 28 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/38328114?dopt=Abstract %R 10.1101/2024.01.24.577060 %0 Journal Article %J Brain %D 2023 %T Cation leak through the ATP1A3 pump causes spasticity and intellectual disability. %A Calame, Daniel G %A Moreno Vadillo, Cristina %A Berger, Seth %A Lotze, Timothy %A Shinawi, Marwan %A Poupak, Javaher %A Heller, Corina %A Cohen, Julie %A Person, Richard %A Telegrafi, Aida %A Phitsanuwong, Chalongchai %A Fiala, Kaylene %A Thiffault, Isabelle %A Del Viso, Florencia %A Zhou, Dihong %A Fleming, Emily A %A Pastinen, Tomi %A Fatemi, Ali %A Thomas, Sruthi %A Pascual, Samuel I %A Torres, Rosa J %A Prior, Carmen %A Gómez-González, Clara %A Biskup, Saskia %A Lupski, James R %A Maric, Dragan %A Holmgren, Miguel %A Regier, Debra %A Yano, Sho T %K Cations %K Cerebellar Ataxia %K Humans %K Intellectual Disability %K Muscle Spasticity %K Mutation %K Phenotype %K Sodium-Potassium-Exchanging ATPase %K Syndrome %X

ATP1A3 encodes the α3 subunit of the sodium-potassium ATPase, one of two isoforms responsible for powering electrochemical gradients in neurons. Heterozygous pathogenic ATP1A3 variants produce several distinct neurological syndromes, yet the molecular basis for phenotypic variability is unclear. We report a novel recurrent variant, ATP1A3(NM_152296.5):c.2324C>T; p.(Pro775Leu), in nine individuals associated with the primary clinical features of progressive or non-progressive spasticity and developmental delay/intellectual disability. No patients fulfil diagnostic criteria for ATP1A3-associated syndromes, including alternating hemiplegia of childhood, rapid-onset dystonia-parkinsonism or cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss (CAPOS), and none were suspected of having an ATP1A3-related disorder. Uniquely among known ATP1A3 variants, P775L causes leakage of sodium ions and protons into the cell, associated with impaired sodium binding/occlusion kinetics favouring states with fewer bound ions. These phenotypic and electrophysiologic studies demonstrate that ATP1A3:c.2324C>T; p.(Pro775Leu) results in mild ATP1A3-related phenotypes resembling complex hereditary spastic paraplegia or idiopathic spastic cerebral palsy. Cation leak provides a molecular explanation for this genotype-phenotype correlation, adding another mechanism to further explain phenotypic variability and highlighting the importance of biophysical properties beyond ion transport rate in ion transport diseases.

%B Brain %V 146 %P 3162-3171 %8 2023 Aug 01 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/37043503?dopt=Abstract %R 10.1093/brain/awad124 %0 Journal Article %J Dis Model Mech %D 2023 %T Ceramide compensation by ceramide synthases preserves retinal function and structure in a retinal dystrophy mouse model. %A Qian, Xinye %A Srinivasan, Tanmay %A He, Jessica %A Lu, Jiaxiong %A Jin, Yan %A Gu, Haiwei %A Rui Chen %K Animals %K Ceramides %K Mice %K Oxidoreductases %K Retina %K Retinal Dystrophies %X

Increasing evidence has supported the role of ceramide as a mediator of photoreceptor dysfunction or cell death in ceramide accumulation and deficiency contexts. TLCD3B, a non-canonical ceramide synthase, was previously identified in addition to the six canonical ceramide synthases (CerSs), and the Tlcd3b-/- mouse model exhibited both retinal dysfunction and degeneration. As previous canonical CerS-deficient mouse models failed to display retinal degeneration, the mechanisms of how TLCD3B interacts with CerSs have not been investigated. Additionally, as the ceramide profile of each CerS is distinct, it is unclear whether the overall level or the homeostasis of different ceramide species plays a critical role in photoreceptor degeneration. Interactions between TLCD3B with canonical CerSs expressed in the retina were examined by subretinally injecting recombinant adeno-associated virus 8 vectors containing the Cers2 (rAAV8-CerS2), Cers4 (rAAV8-CerS4) and Cers5 (rAAV8-CerS5) genes. Injection of all three rAAV8-CerS vectors restored retinal functions as indicated by improved electroretinogram responses, but only rAAV8-CerS5 successfully retained retinal morphology in Tlcd3b-/- mice. CerSs and TLCD3B played partially redundant roles. Additionally, rather than acting as an integral entity, different ceramide species had different impacts on retinal cells, suggesting that the maintenance of the overall ceramide profile is critical for retinal function.

%B Dis Model Mech %V 16 %8 2023 Jul 01 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/37466006?dopt=Abstract %R 10.1242/dmm.050168 %0 Journal Article %J Front Immunol %D 2023 %T Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. %A Mistretta, Brandon %A Rankothgedera, Sakuni %A Castillo, Micah %A Rao, Mitchell %A Holloway, Kimberly %A Bhardwaj, Anjana %A El Noafal, Maha %A Albarracin, Constance %A El-Zein, Randa %A Rezaei, Hengameh %A Su, Xiaoping %A Akbani, Rehan %A Shao, Xiaoshan M %A Czerniecki, Brian J %A Karchin, Rachel %A Bedrosian, Isabelle %A Gunaratne, Preethi H %K Animals %K Breast %K Breast Neoplasms %K Cancer Vaccines %K Female %K Genes, MHC Class I %K Humans %K Mammary Neoplasms, Animal %X

INTRODUCTION: We present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer.

METHOD: We mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot).

RESULTS: We uncovered 20 novel fusion transcripts from 75 breast tumors of 3 subtypes: TNBC, HER2+, and HR+. Of these, the NSFP1-LRRC37A2 fusion transcript was selected for further study. The 3833 bp chimeric RNA predicted by the consensus fusion junction sequence is consistent with a read-through transcription of the 5'-gene NSFP1-Pseudo gene NSFP1 (NSFtruncation at exon 12/13) followed by trans-splicing to connect withLRRC37A2 located immediately 3' through exon 1/2. A total of 15 different 8-mer neoantigen peptides discovered from the NSFP1 and LRRC37A2 truncations were predicted to bind to a total of 35 unique MHC class I alleles with a binding affinity of IC50<500nM.); 1 of which elicited a robust immune response.

CONCLUSION: Our data provides a framework to identify immunogenic neoantigen candidates from fusion transcripts and suggests a potential vaccine strategy to target the immunogenic neopeptides in patients with tumors carrying the NSFP1-LRRC37A2 fusion.

%B Front Immunol %V 14 %P 1188831 %8 2023 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/37744342?dopt=Abstract %R 10.3389/fimmu.2023.1188831 %0 Journal Article %J Pediatr Hematol Oncol %D 2023 %T Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study. %A Mangum, Ross %A Reuther, Jacquelyn %A Sen Baksi, Koel %A Gandhi, Ilavarasi %A Zabriskie, Ryan C %A Recinos, Alva %A Raesz-Martinez, Robin %A Lin, Frank Y %A Potter, Samara L %A Sher, Andrew C %A Kralik, Stephen F %A Mohila, Carrie A %A Chintagumpala, Murali M %A Donna M Muzny %A Jianhong Hu %A Richard A Gibbs %A Fisher, Kevin E %A Bernini, Juan Carlos %A Gill, Jonathan %A Griffin, Timothy C %A Tomlinson, Gail E %A Vallance, Kelly L %A Plon, Sharon E %A Roy, Angshumoy %A Parsons, D Williams %K Biomarkers, Tumor %K Brain Neoplasms %K Child %K Circulating Tumor DNA %K Feasibility Studies %K High-Throughput Nucleotide Sequencing %K Humans %K Mutation %X

The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time "liquid biopsy" for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.

%B Pediatr Hematol Oncol %V 40 %P 719-738 %8 2023 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/37366551?dopt=Abstract %R 10.1080/08880018.2023.2228837 %0 Journal Article %J Genet Med %D 2023 %T Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta. %A Caron, Véronique %A Chassaing, Nicolas %A Ragge, Nicola %A Boschann, Felix %A Ngu, Angelina My-Hoa %A Meloche, Elisabeth %A Chorfi, Sarah %A Lakhani, Saquib A %A Ji, Weizhen %A Steiner, Laurie %A Marcadier, Julien %A Jansen, Philip R %A van de Pol, Laura A %A van Hagen, Johanna M %A Russi, Alvaro Serrano %A Le Guyader, Gwenaël %A Nordenskjöld, Magnus %A Nordgren, Ann %A Anderlid, Britt-Marie %A Plaisancié, Julie %A Stoltenburg, Corinna %A Horn, Denise %A Drenckhahn, Anne %A Hamdan, Fadi F %A Lefebvre, Mathilde %A Attié-Bitach, Tania %A Forey, Peggy %A Smirnov, Vasily %A Ernould, Françoise %A Jacquemont, Marie-Line %A Grotto, Sarah %A Alcantud, Alberto %A Coret, Alicia %A Ferrer-Avargues, Rosario %A Srivastava, Siddharth %A Vincent-Delorme, Catherine %A Romoser, Shelby %A Safina, Nicole %A Saade, Dimah %A Lupski, James R %A Calame, Daniel G %A Geneviève, David %A Chatron, Nicolas %A Schluth-Bolard, Caroline %A Myers, Kenneth A %A Dobyns, William B %A Calvas, Patrick %A Salmon, Caroline %A Holt, Richard %A Elmslie, Frances %A Allaire, Marc %A Prigozhin, Daniil M %A Tremblay, André %A Michaud, Jacques L %K Humans %K Microphthalmos %K Receptors, Retinoic Acid %K Retinoids %X

PURPOSE: Dominant variants in the retinoic acid receptor beta (RARB) gene underlie a syndromic form of microphthalmia, known as MCOPS12, which is associated with other birth anomalies and global developmental delay with spasticity and/or dystonia. Here, we report 25 affected individuals with 17 novel pathogenic or likely pathogenic variants in RARB. This study aims to characterize the functional impact of these variants and describe the clinical spectrum of MCOPS12.

METHODS: We used in vitro transcriptional assays and in silico structural analysis to assess the functional relevance of RARB variants in affecting the normal response to retinoids.

RESULTS: We found that all RARB variants tested in our assays exhibited either a gain-of-function or a loss-of-function activity. Loss-of-function variants disrupted RARB function through a dominant-negative effect, possibly by disrupting ligand binding and/or coactivators' recruitment. By reviewing clinical data from 52 affected individuals, we found that disruption of RARB is associated with a more variable phenotype than initially suspected, with the absence in some individuals of cardinal features of MCOPS12, such as developmental eye anomaly or motor impairment.

CONCLUSION: Our study indicates that pathogenic variants in RARB are functionally heterogeneous and associated with extensive clinical heterogeneity.

%B Genet Med %V 25 %P 100856 %8 2023 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/37092537?dopt=Abstract %R 10.1016/j.gim.2023.100856 %0 Journal Article %J Brain %D 2023 %T The clinical and genetic spectrum of autosomal-recessive TOR1A-related disorders. %A Saffari, Afshin %A Lau, Tracy %A Tajsharghi, Homa %A Karimiani, Ehsan Ghayoor %A Kariminejad, Ariana %A Efthymiou, Stephanie %A Zifarelli, Giovanni %A Sultan, Tipu %A Toosi, Mehran Beiraghi %A Sedighzadeh, Sahar %A Siu, Victoria Mok %A Ortigoza-Escobar, Juan Darío %A AlShamsi, Aisha M %A Ibrahim, Shahnaz %A Al-Sannaa, Nouriya Abbas %A Al-Hertani, Walla %A Sandra, Whalen %A Tarnopolsky, Mark %A Alavi, Shahryar %A Li, Chumei %A Day-Salvatore, Debra-Lynn %A Martínez-González, Maria Jesús %A Levandoski, Kristin M %A Bedoukian, Emma %A Madan-Khetarpal, Suneeta %A Idleburg, Michaela J %A Menezes, Minal Juliet %A Siddharth, Aishwarya %A Platzer, Konrad %A Oppermann, Henry %A Smitka, Martin %A Collins, Felicity %A Lek, Monkol %A Shahrooei, Mohmmad %A Ghavideldarestani, Maryam %A Herman, Isabella %A Rendu, John %A Faure, Julien %A Baker, Janice %A Bhambhani, Vikas %A Calderwood, Laurel %A Akhondian, Javad %A Imannezhad, Shima %A Mirzadeh, Hanieh Sadat %A Hashemi, Narges %A Doosti, Mohammad %A Safi, Mojtaba %A Ahangari, Najmeh %A Torbati, Paria Najarzadeh %A Abedini, Soheila %A Salpietro, Vincenzo %A Gulec, Elif Yilmaz %A Eshaghian, Safieh %A Ghazavi, Mohammadreza %A Pascher, Michael T %A Vogel, Marina %A Abicht, Angela %A Moutton, Sebastien %A Bruel, Ange-Line %A Rieubland, Claudine %A Gallati, Sabina %A Strom, Tim M %A Lochmüller, Hanns %A Mohammadi, Mohammad Hasan %A Alvi, Javeria Raza %A Zackai, Elaine H %A Keena, Beth A %A Skraban, Cara M %A Berger, Seth I %A Andrew, Erin H %A Rahimian, Elham %A Morrow, Michelle M %A Wentzensen, Ingrid M %A Millan, Francisca %A Henderson, Lindsay B %A Dafsari, Hormos Salimi %A Jungbluth, Heinz %A Gomez-Ospina, Natalia %A McRae, Anne %A Peter, Merlene %A Veltra, Danai %A Marinakis, Nikolaos M %A Sofocleous, Christalena %A Ashrafzadeh, Farah %A Pehlivan, Davut %A Lemke, Johannes R %A Melki, Judith %A Benezit, Audrey %A Bauer, Peter %A Weis, Denisa %A James R Lupski %A Senderek, Jan %A Christodoulou, John %A Chung, Wendy K %A Goodchild, Rose %A Offiah, Amaka C %A Moreno-De-Luca, Andres %A Suri, Mohnish %A Ebrahimi-Fakhari, Darius %A Houlden, Henry %A Maroofian, Reza %K Cross-Sectional Studies %K Dystonia %K Dystonic Disorders %K Humans %K Male %K Molecular Chaperones %K Mutation %K Nervous System Malformations %K Phenotype %X

In the field of rare diseases, progress in molecular diagnostics led to the recognition that variants linked to autosomal-dominant neurodegenerative diseases of later onset can, in the context of biallelic inheritance, cause devastating neurodevelopmental disorders and infantile or childhood-onset neurodegeneration. TOR1A-associated arthrogryposis multiplex congenita 5 (AMC5) is a rare neurodevelopmental disorder arising from biallelic variants in TOR1A, a gene that in the heterozygous state is associated with torsion dystonia-1 (DYT1 or DYT-TOR1A), an early-onset dystonia with reduced penetrance. While 15 individuals with AMC5-TOR1A have been reported (less than 10 in detail), a systematic investigation of the full disease-associated spectrum has not been conducted. Here, we assess the clinical, radiological and molecular characteristics of 57 individuals from 40 families with biallelic variants in TOR1A. Median age at last follow-up was 3 years (0-24 years). Most individuals presented with severe congenital flexion contractures (95%) and variable developmental delay (79%). Motor symptoms were reported in 79% and included lower limb spasticity and pyramidal signs, as well as gait disturbances. Facial dysmorphism was an integral part of the phenotype, with key features being a broad/full nasal tip, narrowing of the forehead and full cheeks. Analysis of disease-associated manifestations delineated a phenotypic spectrum ranging from normal cognition and mild gait disturbance to congenital arthrogryposis, global developmental delay, intellectual disability, absent speech and inability to walk. In a subset, the presentation was consistent with foetal akinesia deformation sequence with severe intrauterine abnormalities. Survival was 71%, with higher mortality in males. Death occurred at a median age of 1.2 months (1 week-9 years), due to respiratory failure, cardiac arrest or sepsis. Analysis of brain MRI studies identified non-specific neuroimaging features, including a hypoplastic corpus callosum (72%), foci of signal abnormality in the subcortical and periventricular white matter (55%), diffuse white matter volume loss (45%), mega cisterna magna (36%) and arachnoid cysts (27%). The molecular spectrum included 22 distinct variants, defining a mutational hotspot in the C-terminal domain of the Torsin-1A protein. Genotype-phenotype analysis revealed an association of missense variants in the 3-helix bundle domain to an attenuated phenotype, while missense variants near the Walker A/B motif as well as biallelic truncating variants were linked to early death. In summary, this systematic cross-sectional analysis of a large cohort of individuals with biallelic TOR1A variants across a wide age-range delineates the clinical and genetic spectrum of TOR1A-related autosomal-recessive disease and highlights potential predictors for disease severity and survival.

%B Brain %V 146 %P 3273-3288 %8 2023 Aug 01 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/36757831?dopt=Abstract %R 10.1093/brain/awad039 %0 Journal Article %J Nature %D 2023 %T Clonal haematopoiesis and risk of chronic liver disease. %A Wong, Waihay J %A Emdin, Connor %A Bick, Alexander G %A Zekavat, Seyedeh M %A Niroula, Abhishek %A Pirruccello, James P %A Dichtel, Laura %A Griffin, Gabriel %A Uddin, Md Mesbah %A Gibson, Christopher J %A Kovalcik, Veronica %A Lin, Amy E %A McConkey, Marie E %A Vromman, Amelie %A Sellar, Rob S %A Kim, Peter G %A Agrawal, Mridul %A Weinstock, Joshua %A Long, Michelle T %A Yu, Bing %A Banerjee, Rajarshi %A Nicholls, Rowan C %A Dennis, Andrea %A Kelly, Matt %A Loh, Po-Ru %A McCarroll, Steve %A Eric Boerwinkle %A Vasan, Ramachandran S %A Jaiswal, Siddhartha %A Johnson, Andrew D %A Chung, Raymond T %A Corey, Kathleen %A Levy, Daniel %A Ballantyne, Christie %A Ebert, Benjamin L %A Natarajan, Pradeep %K Animals %K Clonal Hematopoiesis %K Disease Progression %K Disease Susceptibility %K Hepatitis %K Inflammation %K Liver Cirrhosis %K Mice %K Non-alcoholic Fatty Liver Disease %K Odds Ratio %X

Chronic liver disease is a major public health burden worldwide. Although different aetiologies and mechanisms of liver injury exist, progression of chronic liver disease follows a common pathway of liver inflammation, injury and fibrosis. Here we examined the association between clonal haematopoiesis of indeterminate potential (CHIP) and chronic liver disease in 214,563 individuals from 4 independent cohorts with whole-exome sequencing data (Framingham Heart Study, Atherosclerosis Risk in Communities Study, UK Biobank and Mass General Brigham Biobank). CHIP was associated with an increased risk of prevalent and incident chronic liver disease (odds ratio = 2.01, 95% confidence interval (95% CI) [1.46, 2.79]; P < 0.001). Individuals with CHIP were more likely to demonstrate liver inflammation and fibrosis detectable by magnetic resonance imaging compared to those without CHIP (odds ratio = 1.74, 95% CI [1.16, 2.60]; P = 0.007). To assess potential causality, Mendelian randomization analyses showed that genetic predisposition to CHIP was associated with a greater risk of chronic liver disease (odds ratio = 2.37, 95% CI [1.57, 3.6]; P < 0.001). In a dietary model of non-alcoholic steatohepatitis, mice transplanted with Tet2-deficient haematopoietic cells demonstrated more severe liver inflammation and fibrosis. These effects were mediated by the NLRP3 inflammasome and increased levels of expression of downstream inflammatory cytokines in Tet2-deficient macrophages. In summary, clonal haematopoiesis is associated with an elevated risk of liver inflammation and chronic liver disease progression through an aberrant inflammatory response.

%B Nature %V 616 %P 747-754 %8 2023 Apr %G eng %N 7958 %1 https://www.ncbi.nlm.nih.gov/pubmed/37046084?dopt=Abstract %R 10.1038/s41586-023-05857-4 %0 Journal Article %J Nature %D 2023 %T The complete sequence of a human Y chromosome. %A Rhie, Arang %A Nurk, Sergey %A Cechova, Monika %A Hoyt, Savannah J %A Taylor, Dylan J %A Altemose, Nicolas %A Hook, Paul W %A Koren, Sergey %A Rautiainen, Mikko %A Alexandrov, Ivan A %A Allen, Jamie %A Asri, Mobin %A Bzikadze, Andrey V %A Chen, Nae-Chyun %A Chin, Chen-Shan %A Diekhans, Mark %A Flicek, Paul %A Formenti, Giulio %A Fungtammasan, Arkarachai %A García Girón, Carlos %A Garrison, Erik %A Gershman, Ariel %A Gerton, Jennifer L %A Grady, Patrick G S %A Guarracino, Andrea %A Haggerty, Leanne %A Halabian, Reza %A Hansen, Nancy F %A Harris, Robert %A Hartley, Gabrielle A %A Harvey, William T %A Haukness, Marina %A Heinz, Jakob %A Hourlier, Thibaut %A Hubley, Robert M %A Hunt, Sarah E %A Hwang, Stephen %A Jain, Miten %A Kesharwani, Rupesh K %A Lewis, Alexandra P %A Li, Heng %A Logsdon, Glennis A %A Lucas, Julian K %A Makalowski, Wojciech %A Markovic, Christopher %A Martin, Fergal J %A Mc Cartney, Ann M %A McCoy, Rajiv C %A McDaniel, Jennifer %A McNulty, Brandy M %A Medvedev, Paul %A Mikheenko, Alla %A Munson, Katherine M %A Murphy, Terence D %A Olsen, Hugh E %A Olson, Nathan D %A Paulin, Luis F %A Porubsky, David %A Potapova, Tamara %A Ryabov, Fedor %A Salzberg, Steven L %A Sauria, Michael E G %A Fritz J Sedlazeck %A Shafin, Kishwar %A Shepelev, Valery A %A Shumate, Alaina %A Storer, Jessica M %A Surapaneni, Likhitha %A Taravella Oill, Angela M %A Thibaud-Nissen, Françoise %A Timp, Winston %A Tomaszkiewicz, Marta %A Vollger, Mitchell R %A Walenz, Brian P %A Watwood, Allison C %A Weissensteiner, Matthias H %A Wenger, Aaron M %A Wilson, Melissa A %A Zarate, Samantha %A Zhu, Yiming %A Zook, Justin M %A Eichler, Evan E %A O'Neill, Rachel J %A Schatz, Michael C %A Miga, Karen H %A Makova, Kateryna D %A Phillippy, Adam M %K Base Sequence %K Chromosomes, Human, Y %K DNA, Satellite %K Genetic Variation %K Genetics, Population %K Genomics %K Heterochromatin %K Humans %K Multigene Family %K Reference Standards %K Segmental Duplications, Genomic %K Sequence Analysis, DNA %K Tandem Repeat Sequences %K Telomere %X

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

%B Nature %V 621 %P 344-354 %8 2023 Sep %G eng %N 7978 %1 https://www.ncbi.nlm.nih.gov/pubmed/37612512?dopt=Abstract %R 10.1038/s41586-023-06457-y %0 Journal Article %J Mol Biol Evol %D 2023 %T Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. %A Jensen, Axel %A Swift, Frances %A de Vries, Dorien %A Beck, Robin M D %A Kuderna, Lukas F K %A Knauf, Sascha %A Chuma, Idrissa S %A Keyyu, Julius D %A Kitchener, Andrew C %A Farh, Kyle %A Jeffrey Rogers %A Marques-Bonet, Tomas %A Detwiler, Kate M %A Roos, Christian %A Guschanski, Katerina %K Animals %K Biological Evolution %K Gene Flow %K Genome %K Genomics %K Hybridization, Genetic %K Mammals %K Phylogeny %K Primates %X

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.

%B Mol Biol Evol %V 40 %8 2023 Dec 01 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/37987553?dopt=Abstract %R 10.1093/molbev/msad247 %0 Journal Article %J Am J Hum Genet %D 2022 %T C. Thomas Caskey, M.D. (1938-2022): A remembrance. %A Beaudet, Arthur L %A Richard A Gibbs %B Am J Hum Genet %V 109 %P 1185-1189 %8 2022 Jul 07 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/35803231?dopt=Abstract %R 10.1016/j.ajhg.2022.05.012 %0 Journal Article %J Genet Med %D 2022 %T Centers for Mendelian Genomics: A decade of facilitating gene discovery. %A Baxter, Samantha M %A Posey, Jennifer E %A Lake, Nicole J %A Sobreira, Nara %A Chong, Jessica X %A Buyske, Steven %A Blue, Elizabeth E %A Chadwick, Lisa H %A Coban-Akdemir, Zeynep H %A Doheny, Kimberly F %A Davis, Colleen P %A Lek, Monkol %A Wellington, Christopher %A Jhangiani, Shalini N %A Gerstein, Mark %A Richard A Gibbs %A Lifton, Richard P %A MacArthur, Daniel G %A Matise, Tara C %A James R Lupski %A Valle, David %A Bamshad, Michael J %A Hamosh, Ada %A Mane, Shrikant %A Nickerson, Deborah A %A Rehm, Heidi L %A O'Donnell-Luria, Anne %K Exome %K Exome Sequencing %K Genetic Association Studies %K Genomics %K Humans %K Phenotype %X

PURPOSE: Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration.

METHODS: Over the past 10 years, the National Institutes of Health-supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution.

RESULTS: We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher.

CONCLUSION: The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.

%B Genet Med %V 24 %P 784-797 %8 2022 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/35148959?dopt=Abstract %R 10.1016/j.gim.2021.12.005 %0 Journal Article %J Pediatr Blood Cancer %D 2022 %T Clinical and molecular features of pediatric cancer patients with Lynch syndrome. %A Scollon, Sarah %A Eldomery, Mohammad K %A Reuther, Jacquelyn %A Lin, Frank Y %A Potter, Samara L %A Desrosiers, Lauren %A McClain, Kenneth L %A Smith, Valeria %A Su, Jack Meng-Fen %A Venkatramani, Rajkumar %A Jianhong Hu %A Korchina, Viktoriya %A Zarrin-Khameh, Neda %A Richard A Gibbs %A Donna M Muzny %A Eng, Christine %A Roy, Angshumoy %A Parsons, D Williams %A Plon, Sharon E %K Brain Neoplasms %K Child %K Colorectal Neoplasms %K Colorectal Neoplasms, Hereditary Nonpolyposis %K DNA Mismatch Repair %K DNA-Binding Proteins %K Germ-Line Mutation %K Humans %K MutL Protein Homolog 1 %K MutS Homolog 2 Protein %K Neoplastic Syndromes, Hereditary %X

BACKGROUND: The association of childhood cancer with Lynch syndrome is not established compared with the significant pediatric cancer risk in recessive constitutional mismatch repair deficiency syndrome (CMMRD).

PROCEDURE: We describe the clinical features, germline analysis, and tumor genomic profiling of patients with Lynch syndrome among patients enrolled in pediatric cancer genomic studies.

RESULTS: There were six of 773 (0.8%) pediatric patients with solid tumors identified with Lynch syndrome, defined as a germline heterozygous pathogenic variant in one of the mismatch repair (MMR) genes (three with MSH6, two with MLH1, and one with MSH2). Tumor analysis demonstrated evidence for somatic second hits and/or increased tumor mutation burden in three of four patients with available tumor with potential implications for therapy and identification of at-risk family members. Only one patient met current guidelines for pediatric cancer genetics evaluation at the time of tumor diagnosis.

CONCLUSION: Approximately 1% of children with cancer have Lynch syndrome, which is missed with current referral guidelines, suggesting the importance of adding MMR genes to tumor and hereditary pediatric cancer panels. Tumor analysis may provide the first suggestion of an underlying cancer predisposition syndrome and is useful in distinguishing between Lynch syndrome and CMMRD.

%B Pediatr Blood Cancer %V 69 %P e29859 %8 2022 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/35713195?dopt=Abstract %R 10.1002/pbc.29859 %0 Journal Article %J J Med Primatol %D 2022 %T Clinical presentation, treatment, and genetic and histopathological analysis of juvenile cataracts and secondary glaucoma in a rhesus macaque (Macaca mulatta). %A Casanova, M Isabel %A Rui Chen %A Garzel, Laura M %A Olstad, Katherine J %A Kim, Soohyun %A R. Alan Harris %A Yumei Li %A Raveendran, Muthuswamy %A Liang, Qingnan %A Wang, Jun %A Yiu, Glenn %A Stout, John Timothy %A Roberts, Jeffrey A %A Jeffrey Rogers %A Moshiri, Ala %A Thomasy, Sara M %K Animals %K Cataract %K Glaucoma %K Intraocular Pressure %K Macaca mulatta %X

This report describes the clinical and histological findings, genetic study, and treatment in a 1.3-year-old rhesus macaque with bilateral cataracts and unilateral secondary glaucoma. Intravitreal injection of gentamicin decreased the intraocular pressure from 56 to <2 mm Hg. A putative genetic cause of the cataracts was not identified.

%B J Med Primatol %V 51 %P 119-123 %8 2022 Apr %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/34897697?dopt=Abstract %R 10.1111/jmp.12560 %0 Journal Article %J Mass Spectrom Rev %D 2022 %T Clinical proteomics towards multiomics in cancer. %A Creighton, Chad J %X

Recent technological advancements in mass spectrometry (MS)-based proteomics technologies have accelerated its application to study greater and greater numbers of human tumor specimens. Over the last several years, the Clinical Proteomic Tumor Analysis Consortium, the International Cancer Proteogenome Consortium, and others have generated MS-based proteomic profiling data combined with corresponding multiomics data on thousands of human tumors to date. Proteomic data sets in the public domain can be re-examined by other researchers with different questions in mind from what the original studies explored. In this review, we examine the increasing role of proteomics in studying cancer, along with the potential for previous studies and their associated data sets to contribute to improving the diagnosis and treatment of cancer in the clinical setting. We also explore publicly available proteomics and multi-omics data from cancer cell line models to show how such data may aid in identifying therapeutic strategies for cancer subsets.

%B Mass Spectrom Rev %P e21827 %8 2022 Dec 10 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/36495097?dopt=Abstract %R 10.1002/mas.21827 %0 Journal Article %J Nat Commun %D 2022 %T Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease. %A Uddin, M D Mesbah %A Nguyen, Ngoc Quynh H %A Yu, Bing %A Brody, Jennifer A %A Pampana, Akhil %A Nakao, Tetsushi %A Fornage, Myriam %A Bressler, Jan %A Sotoodehnia, Nona %A Weinstock, Joshua S %A Honigberg, Michael C %A Nachun, Daniel %A Bhattacharya, Romit %A Griffin, Gabriel K %A Chander, Varuna %A Richard A Gibbs %A Rotter, Jerome I %A Liu, Chunyu %A Baccarelli, Andrea A %A Chasman, Daniel I %A Whitsel, Eric A %A Kiel, Douglas P %A Murabito, Joanne M %A Eric Boerwinkle %A Ebert, Benjamin L %A Jaiswal, Siddhartha %A Floyd, James S %A Bick, Alexander G %A Ballantyne, Christie M %A Psaty, Bruce M %A Natarajan, Pradeep %A Conneely, Karen N %K Clonal Hematopoiesis %K Coronary Artery Disease %K DNA Methylation %K Hematopoiesis %K Hematopoietic Stem Cells %K Humans %X

Age-related changes to the genome-wide DNA methylation (DNAm) pattern observed in blood are well-documented. Clonal hematopoiesis of indeterminate potential (CHIP), characterized by the age-related acquisition and expansion of leukemogenic mutations in hematopoietic stem cells (HSCs), is associated with blood cancer and coronary artery disease (CAD). Epigenetic regulators DNMT3A and TET2 are the two most frequently mutated CHIP genes. Here, we present results from an epigenome-wide association study for CHIP in 582 Cardiovascular Health Study (CHS) participants, with replication in 2655 Atherosclerosis Risk in Communities (ARIC) Study participants. We show that DNMT3A and TET2 CHIP have distinct and directionally opposing genome-wide DNAm association patterns consistent with their regulatory roles, albeit both promoting self-renewal of HSCs. Mendelian randomization analyses indicate that a subset of DNAm alterations associated with these two leading CHIP genes may promote the risk for CAD.

%B Nat Commun %V 13 %P 5350 %8 2022 Sep 12 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/36097025?dopt=Abstract %R 10.1038/s41467-022-33093-3 %0 Journal Article %J PLoS Genet %D 2022 %T Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer. %A Ozirmak Lermi, Nejla %A Gray, Stanton B %A Bowen, Charles M %A Reyes-Uribe, Laura %A Dray, Beth K %A Deng, Nan %A R. Alan Harris %A Raveendran, Muthuswamy %A Benavides, Fernando %A Hodo, Carolyn L %A Taggart, Melissa W %A Colbert Maresso, Karen %A Sinha, Krishna M %A Jeffrey Rogers %A Vilar, Eduardo %K Animals %K Colonic Neoplasms %K Colorectal Neoplasms %K Colorectal Neoplasms, Hereditary Nonpolyposis %K DNA Methylation %K DNA Mismatch Repair %K Genomics %K Humans %K Macaca mulatta %K Mice %K Microsatellite Instability %K MutL Protein Homolog 1 %X

Colorectal cancer (CRC) remains the third most common cancer in the US with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1 (c.1029C %B PLoS Genet %V 18 %P e1010163 %8 2022 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/35446842?dopt=Abstract %R 10.1371/journal.pgen.1010163 %0 Journal Article %J Science %D 2022 %T A complete reference genome improves analysis of human genetic variation. %A Aganezov, Sergey %A Yan, Stephanie M %A Soto, Daniela C %A Kirsche, Melanie %A Zarate, Samantha %A Avdeyev, Pavel %A Taylor, Dylan J %A Shafin, Kishwar %A Shumate, Alaina %A Xiao, Chunlin %A Wagner, Justin %A McDaniel, Jennifer %A Olson, Nathan D %A Sauria, Michael E G %A Vollger, Mitchell R %A Rhie, Arang %A Meredith, Melissa %A Martin, Skylar %A Lee, Joyce %A Koren, Sergey %A Rosenfeld, Jeffrey A %A Paten, Benedict %A Layer, Ryan %A Chin, Chen-Shan %A Fritz J Sedlazeck %A Hansen, Nancy F %A Miller, Danny E %A Phillippy, Adam M %A Miga, Karen H %A McCoy, Rajiv C %A Dennis, Megan Y %A Zook, Justin M %A Schatz, Michael C %K Genetic Variation %K Genome, Human %K Genomics %K Humans %K Reference Standards %K Sequence Analysis, DNA %X

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.

%B Science %V 376 %P eabl3533 %8 2022 Apr %G eng %N 6588 %1 https://www.ncbi.nlm.nih.gov/pubmed/35357935?dopt=Abstract %R 10.1126/science.abl3533 %0 Journal Article %J Science %D 2022 %T The complete sequence of a human genome. %A Nurk, Sergey %A Koren, Sergey %A Rhie, Arang %A Rautiainen, Mikko %A Bzikadze, Andrey V %A Mikheenko, Alla %A Vollger, Mitchell R %A Altemose, Nicolas %A Uralsky, Lev %A Gershman, Ariel %A Aganezov, Sergey %A Hoyt, Savannah J %A Diekhans, Mark %A Logsdon, Glennis A %A Alonge, Michael %A Antonarakis, Stylianos E %A Borchers, Matthew %A Bouffard, Gerard G %A Brooks, Shelise Y %A Caldas, Gina V %A Chen, Nae-Chyun %A Cheng, Haoyu %A Chin, Chen-Shan %A Chow, William %A de Lima, Leonardo G %A Dishuck, Philip C %A Durbin, Richard %A Dvorkina, Tatiana %A Fiddes, Ian T %A Formenti, Giulio %A Fulton, Robert S %A Fungtammasan, Arkarachai %A Garrison, Erik %A Grady, Patrick G S %A Graves-Lindsay, Tina A %A Hall, Ira M %A Hansen, Nancy F %A Hartley, Gabrielle A %A Haukness, Marina %A Howe, Kerstin %A Hunkapiller, Michael W %A Jain, Chirag %A Jain, Miten %A Jarvis, Erich D %A Kerpedjiev, Peter %A Kirsche, Melanie %A Kolmogorov, Mikhail %A Korlach, Jonas %A Kremitzki, Milinn %A Li, Heng %A Maduro, Valerie V %A Marschall, Tobias %A McCartney, Ann M %A McDaniel, Jennifer %A Miller, Danny E %A Mullikin, James C %A Myers, Eugene W %A Olson, Nathan D %A Paten, Benedict %A Peluso, Paul %A Pevzner, Pavel A %A Porubsky, David %A Potapova, Tamara %A Rogaev, Evgeny I %A Rosenfeld, Jeffrey A %A Salzberg, Steven L %A Schneider, Valerie A %A Fritz J Sedlazeck %A Shafin, Kishwar %A Shew, Colin J %A Shumate, Alaina %A Sims, Ying %A Smit, Arian F A %A Soto, Daniela C %A Sović, Ivan %A Storer, Jessica M %A Streets, Aaron %A Sullivan, Beth A %A Thibaud-Nissen, Françoise %A Torrance, James %A Wagner, Justin %A Walenz, Brian P %A Wenger, Aaron %A Wood, Jonathan M D %A Xiao, Chunlin %A Yan, Stephanie M %A Young, Alice C %A Zarate, Samantha %A Surti, Urvashi %A McCoy, Rajiv C %A Dennis, Megan Y %A Alexandrov, Ivan A %A Gerton, Jennifer L %A O'Neill, Rachel J %A Timp, Winston %A Zook, Justin M %A Schatz, Michael C %A Eichler, Evan E %A Miga, Karen H %A Phillippy, Adam M %K Cell Line %K Chromosomes, Artificial, Bacterial %K Chromosomes, Human %K Genome, Human %K Human Genome Project %K Humans %K Reference Values %K Sequence Analysis, DNA %X

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

%B Science %V 376 %P 44-53 %8 2022 Apr %G eng %N 6588 %1 https://www.ncbi.nlm.nih.gov/pubmed/35357919?dopt=Abstract %R 10.1126/science.abj6987 %0 Journal Article %J Commun Biol %D 2022 %T Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson's disease-associated GBA gene. %A Toffoli, Marco %A Chen, Xiao %A Fritz J Sedlazeck %A Lee, Chiao-Yin %A Mullin, Stephen %A Higgins, Abigail %A Koletsi, Sofia %A Garcia-Segura, Monica Emili %A Sammler, Esther %A Scholz, Sonja W %A Schapira, Anthony H V %A Eberle, Michael A %A Proukakis, Christos %K Alleles %K Glucosylceramidase %K Heterozygote %K Humans %K Lewy Body Disease %K Parkinson Disease %X

GBA variants carriers are at increased risk of Parkinson's disease (PD) and Lewy body dementia (LBD). The presence of pseudogene GBAP1 predisposes to structural variants, complicating genetic analysis. We present two methods to resolve recombinant alleles and other variants in GBA: Gauchian, a tool for short-read, whole-genome sequencing data analysis, and Oxford Nanopore sequencing after PCR enrichment. Both methods were concordant for 42 samples carrying a range of recombinants and GBAP1-related mutations, and Gauchian outperformed the GATK Best Practices pipeline. Applying Gauchian to sequencing of over 10,000 individuals shows that copy number variants (CNVs) spanning GBAP1 are relatively common in Africans. CNV frequencies in PD and LBD are similar to controls. Gains may coexist with other mutations in patients, and a modifying effect cannot be excluded. Gauchian detects more GBA variants in LBD than PD, especially severe ones. These findings highlight the importance of accurate GBA analysis in these patients.

%B Commun Biol %V 5 %P 670 %8 2022 Jul 06 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/35794204?dopt=Abstract %R 10.1038/s42003-022-03610-7 %0 Journal Article %J Gigascience %D 2022 %T Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. %A R. Alan Harris %A Raveendran, Muthuswamy %A Lyfoung, Dustin T %A Fritz J Sedlazeck %A Mahmoud, Medhat %A Prall, Trent M %A Karl, Julie A %A Harshavardhan Doddapaneni %A Meng, Qingchang %A Yi Han %A Donna M Muzny %A Wiseman, Roger W %A O'Connor, David H %A Jeffrey Rogers %K Animals %K Chromosomes, Mammalian %K Genome %K High-Throughput Nucleotide Sequencing %K Mesocricetus %K Whole Genome Sequencing %X

BACKGROUND: The Syrian hamster (Mesocricetus auratus) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was generated in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and greater continuity.

FINDINGS: Here, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gb, similar to the 2.50-Gb length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity, with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein-coding genes and 10,459 noncoding genes are annotated in BCM_Maur_2.0 compared to 20,495 protein-coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where ∼17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0, in which the number of unresolved bases is reduced to 3.00%.

CONCLUSIONS: Access to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.

%B Gigascience %V 11 %8 2022 May 28 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/35640223?dopt=Abstract %R 10.1093/gigascience/giac039 %0 Journal Article %J Transl Psychiatry %D 2022 %T Correction: Association of low-frequency and rare coding variants with information processing speed. %A Bressler, Jan %A Davies, Gail %A Smith, Albert V %A Saba, Yasaman %A Bis, Joshua C %A Jian, Xueqiu %A Hayward, Caroline %A Yanek, Lisa %A Smith, Jennifer A %A Mirza, Saira S %A Wang, Ruiqi %A Adams, Hieab H H %A Becker, Diane %A Eric Boerwinkle %A Campbell, Archie %A Cox, Simon R %A Eiriksdottir, Gudny %A Fawns-Ritchie, Chloe %A Gottesman, Rebecca F %A Grove, Megan L %A Guo, Xiuqing %A Hofer, Edith %A Kardia, Sharon L R %A Knol, Maria J %A Koini, Marisa %A Lopez, Oscar L %A Marioni, Riccardo E %A Nyquist, Paul %A Pattie, Alison %A Polasek, Ozren %A Porteous, David J %A Rudan, Igor %A Satizabal, Claudia L %A Schmidt, Helena %A Schmidt, Reinhold %A Sidney, Stephen %A Simino, Jeannette %A Smith, Blair H %A Turner, Stephen T %A van der Lee, Sven J %A Ware, Erin B %A Whitmer, Rachel A %A Yaffe, Kristine %A Yang, Qiong %A Zhao, Wei %A Gudnason, Vilmundur %A Launer, Lenore J %A Fitzpatrick, Annette L %A Psaty, Bruce M %A Fornage, Myriam %A Arfan Ikram, M %A van Duijn, Cornelia M %A Seshadri, Sudha %A Mosley, Thomas H %A Deary, Ian J %B Transl Psychiatry %V 12 %P 88 %8 2022 Mar 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/35232957?dopt=Abstract %R 10.1038/s41398-022-01852-x %0 Journal Article %J HGG Adv %D 2022 %T CRISPR/Cas9-induced gene conversion between paralogs. %A Yanovsky-Dagan, Shira %A Frumkin, Ayala %A James R Lupski %A Harel, Tamar %X

Paralogs and pseudogenes are abundant within the human genome, and can mediate non-allelic homologous recombination (NAHR) or gene conversion events. The locus contains three paralogs situated in tandem, and is therefore prone to NAHR-mediated deletions and duplications associated with severe neurological phenotypes. To study this locus further, we aimed to generate biallelic loss-of-function variants in by CRISPR/Cas9 genome editing. Unexpectedly, two of the generated clones underwent gene conversion, as evidenced by replacement of the targeted sequence of by a donor sequence from its paralog We highlight the complexity of CRISPR/Cas9 design, end-product formation, and recombination repair mechanisms for CRISPR/Cas9 delivery as a nucleic acid molecular therapy when targeting genes that have paralogs or pseudogenes, and advocate meticulous evaluation of resultant clones in model organisms. In addition, we suggest that endogenous gene conversion may be used to repair missense variants in genes with paralogs or pseudogenes.

%B HGG Adv %V 3 %P 100092 %8 2022 Apr 14 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/35199044?dopt=Abstract %R 10.1016/j.xhgg.2022.100092 %0 Journal Article %J Nat Biotechnol %D 2022 %T Curated variation benchmarks for challenging medically relevant autosomal genes. %A Wagner, Justin %A Olson, Nathan D %A Harris, Lindsay %A McDaniel, Jennifer %A Cheng, Haoyu %A Fungtammasan, Arkarachai %A Hwang, Yih-Chii %A Gupta, Richa %A Wenger, Aaron M %A Rowell, William J %A Khan, Ziad M %A Farek, Jesse %A Zhu, Yiming %A Pisupati, Aishwarya %A Mahmoud, Medhat %A Xiao, Chunlin %A Yoo, Byunggil %A Sahraeian, Sayed Mohammad Ebrahim %A Miller, Danny E %A Jáspez, David %A Lorenzo-Salazar, José M %A Muñoz-Barrera, Adrián %A Rubio-Rodríguez, Luis A %A Flores, Carlos %A Narzisi, Giuseppe %A Evani, Uday Shanker %A Clarke, Wayne E %A Lee, Joyce %A Mason, Christopher E %A Lincoln, Stephen E %A Miga, Karen H %A Ebbert, Mark T W %A Shumate, Alaina %A Li, Heng %A Chin, Chen-Shan %A Zook, Justin M %A Fritz J Sedlazeck %K Genome, Human %K Haplotypes %K Humans %K Sequence Analysis, DNA %X

The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically relevant genes due to their repetitiveness or polymorphic complexity. Here, we characterize 273 of these 395 challenging autosomal genes using a haplotype-resolved whole-genome assembly. This curated benchmark reports over 17,000 single-nucleotide variations, 3,600 insertions and deletions and 200 structural variations each for human genome reference GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically relevant genes, including CBS, CRYAA and KCNE1. When masking these false duplications, variant recall can improve from 8% to 100%. Forming benchmarks from a haplotype-resolved whole-genome assembly may become a prototype for future benchmarks covering the whole genome.

%B Nat Biotechnol %V 40 %P 672-680 %8 2022 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/35132260?dopt=Abstract %R 10.1038/s41587-021-01158-1 %0 Journal Article %J Hum Mol Genet %D 2022 %T Cwc27, associated with retinal degeneration, functions as a splicing factor in vivo. %A Bertrand, Renae Elaine %A Wang, Jun %A Yumei Li %A Cheng, Xuesen %A Wang, Keqing %A Stoilov, Peter %A Rui Chen %K Alternative Splicing %K Animals %K Introns %K Mice %K Peptidylprolyl Isomerase %K Retinal Degeneration %K RNA Splice Sites %K RNA Splicing %K RNA Splicing Factors %K Spliceosomes %X

Previous in vitro studies indicate that CWC27 functions as a splicing factor in the Bact spliceosome complex, interacting with CWC22 to form a landing platform for eIF4A3, a core component of the exon junction complex. However, the function of CWC27 as a splicing factor has not been validated in any in vivo systems. CWC27 variants have been shown to cause autosomal recessive retinal degeneration, in both syndromic and non-syndromic forms. The Cwc27K338fs/K338fs mouse model was shown to have significant retinal dysfunction and degeneration by 6 months of age. In this report, we have taken advantage of the Cwc27K338fs/K338fs mouse model to show that Cwc27 is involved in splicing in vivo in the context of the retina. Bulk RNA and single cell RNA-sequencing of the mouse retina showed that there were gene expression and splicing pattern changes, including alternative splice site usage and intron retention. Positive staining for CHOP suggests that ER stress may be activated in response to the splicing pattern changes and is a likely contributor to the disease mechanism. Our results provide the first evidence that CWC27 functions as a splicing factor in an in vivo context. The splicing defects and gene expression changes observed in the Cwc27K338fs/K338fs mouse retina provide insight to the potential disease mechanisms, paving the way for targeted therapeutic development.

%B Hum Mol Genet %V 31 %P 1278-1292 %8 2022 Apr 22 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/34726245?dopt=Abstract %R 10.1093/hmg/ddab319 %0 Journal Article %J J Mol Diagn %D 2022 %T CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project. %A Gaedigk, Andrea %A Boone, Erin C %A Steven E Scherer %A Lee, Seung-Been %A Numanagić, Ibrahim %A Sahinalp, Cenk %A Smith, Joshua D %A McGee, Sean %A Radhakrishnan, Aparna %A Xiang Qin %A Wang, Wendy Y %A Farrow, Emily G %A Gonzaludo, Nina %A Halpern, Aaron L %A Nickerson, Deborah A %A Miller, Neil A %A Pratt, Victoria M %A Kalman, Lisa V %K Alleles %K Cytochrome P-450 CYP2C19 %K Cytochrome P-450 CYP2C8 %K Cytochrome P-450 CYP2C9 %K Genetic Testing %K Genotype %K Haplotypes %K High-Throughput Nucleotide Sequencing %K Humans %X

Pharmacogenetic tests typically target selected sequence variants to identify haplotypes that are often defined by star (∗) allele nomenclature. Due to their design, these targeted genotyping assays are unable to detect novel variants that may change the function of the gene product and thereby affect phenotype prediction and patient care. In the current study, 137 DNA samples that were previously characterized by the Genetic Testing Reference Material (GeT-RM) program using a variety of targeted genotyping methods were recharacterized using targeted and whole genome sequencing analysis. Sequence data were analyzed using three genotype calling tools to identify star allele diplotypes for CYP2C8, CYP2C9, and CYP2C19. The genotype calls from next-generation sequencing (NGS) correlated well to those previously reported, except when novel alleles were present in a sample. Six novel alleles and 38 novel suballeles were identified in the three genes due to identification of variants not covered by targeted genotyping assays. In addition, several ambiguous genotype calls from a previous study were resolved using the NGS and/or long-read NGS data. Diplotype calls were mostly consistent between the calling algorithms, although several discrepancies were noted. This study highlights the utility of NGS for pharmacogenetic testing and demonstrates that there are many novel alleles that are yet to be discovered, even in highly characterized genes such as CYP2C9 and CYP2C19.

%B J Mol Diagn %V 24 %P 337-350 %8 2022 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/35134542?dopt=Abstract %R 10.1016/j.jmoldx.2021.12.011 %0 Journal Article %J Genet Med %D 2021 %T Ceramide synthase TLCD3B is a novel gene associated with human recessive retinal dystrophy. %A Bertrand, Renae Elaine %A Wang, Jun %A Xiong, Kaitlyn H %A Thangavel, Chinthana %A Qian, Xinye %A Ba-Abbad, Rola %A Liang, Qingnan %A Simões, Renata T %A Sampaio, Shirley A M %A Carss, Keren J %A Lucy Raymond, F %A Robson, Anthony G %A Webster, Andrew R %A Arno, Gavin %A Porto, Fernanda Belga Ottoni %A Rui Chen %K Animals %K Electroretinography %K Humans %K Mice %K Oxidoreductases %K Retina %K Retinal Cone Photoreceptor Cells %K Retinal Degeneration %K Retinal Dystrophies %X

PURPOSE: Previous studies suggest that ceramide is a proapoptotic lipid as high levels of ceramides can lead to apoptosis of neuronal cells, including photoreceptors. However, no pathogenic variant in ceramide synthases has been identified in human patients and knockout of various ceramide synthases in mice has not led to photoreceptor degeneration.

METHODS: Exome sequencing was used to identify candidate disease genes in patients with vision loss as confirmed by standard evaluation methods, including electroretinography (ERG) and optical coherence tomography. The vision loss phenotype in mice was evaluated by ERG and histological analyses.

RESULTS: Here we have identified four patients with cone-rod dystrophy or maculopathy from three families carrying pathogenic variants in TLCD3B. Consistent with the phenotype observed in patients, the Tlcd3b mice exhibited a significant reduction of the cone photoreceptor light responses, thinning of the outer nuclear layer, and loss of cone photoreceptors across the retina.

CONCLUSION: Our results provide a link between loss-of-function variants in a ceramide synthase gene and human retinal dystrophy. Establishment of the Tlcd3b knockout murine model, an in vivo photoreceptor cell degeneration model due to loss of a ceramide synthase, will provide a unique opportunity in probing the role of ceramide in survival and function of photoreceptor cells.

%B Genet Med %V 23 %P 488-497 %8 2021 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/33077892?dopt=Abstract %R 10.1038/s41436-020-01003-x %0 Journal Article %J Front Genet %D 2021 %T Chromoanagenesis Event Underlies a Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome. %A Grochowski, Christopher M %A Krepischi, Ana C V %A Eisfeldt, Jesper %A Du, Haowei %A Bertola, Debora R %A Oliveira, Danyllo %A Costa, Silvia S %A James R Lupski %A Lindstrand, Anna %A Carvalho, Claudia M B %X

Chromoanagenesis is a descriptive term that encompasses classes of catastrophic mutagenic processes that generate localized and complex chromosome rearrangements in both somatic and germline genomes. Herein, we describe a 5-year-old female presenting with a constellation of clinical features consistent with a clinical diagnosis of Coffin-Siris syndrome 1 (CSS1). Initial G-banded karyotyping detected a 90-Mb pericentric and a 47-Mb paracentric inversion on a single chromosome. Subsequent analysis of short-read whole-genome sequencing data and genomic optical mapping revealed additional inversions, all clustered on chromosome 6, one of them disrupting for which haploinsufficiency leads to the CSS1 disease trait (MIM:135900). The aggregate structural variant data show that the resolved, the resolved derivative chromosome architecture presents four inversions, one pericentric and three paracentric, involving six breakpoint junctions in what appears to be a shuffling of genomic material on this chromosome. Each junction was resolved to nucleotide-level resolution with mutational signatures suggestive of non-homologous end joining. The disruption of the gene is shown to occur between the fourth and fifth exon of the canonical transcript with subsequent qPCR studies confirming a decrease in expression in the patient versus healthy controls. Deciphering the underlying genomic architecture of chromosomal rearrangements and complex structural variants may require multiple technologies and can be critical to elucidating the molecular etiology of a patient's clinical phenotype or resolving unsolved Mendelian disease cases.

%B Front Genet %V 12 %P 708348 %8 2021 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/34512724?dopt=Abstract %R 10.3389/fgene.2021.708348 %0 Journal Article %J Nat Commun %D 2021 %T Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices. %A Natarajan, Pradeep %A Pampana, Akhil %A Graham, Sarah E %A Ruotsalainen, Sanni E %A Perry, James A %A de Vries, Paul S %A Broome, Jai G %A Pirruccello, James P %A Honigberg, Michael C %A Aragam, Krishna %A Wolford, Brooke %A Brody, Jennifer A %A Antonacci-Fulton, Lucinda %A Arden, Moscati %A Aslibekyan, Stella %A Assimes, Themistocles L %A Ballantyne, Christie M %A Bielak, Lawrence F %A Bis, Joshua C %A Cade, Brian E %A Do, Ron %A Harshavardhan Doddapaneni %A Emery, Leslie S %A Hung, Yi-Jen %A Irvin, Marguerite R %A Khan, Alyna T %A Lange, Leslie %A Lee, Jiwon %A Lemaitre, Rozenn N %A Martin, Lisa W %A Ginger A Metcalf %A Montasser, May E %A Moon, Jee-Young %A Donna M Muzny %A O'Connell, Jeffrey R %A Palmer, Nicholette D %A Peralta, Juan M %A Peyser, Patricia A %A Stilp, Adrienne M %A Tsai, Michael %A Wang, Fei Fei %A Weeks, Daniel E %A Yanek, Lisa R %A Wilson, James G %A Abecasis, Goncalo %A Arnett, Donna K %A Becker, Lewis C %A Blangero, John %A Eric Boerwinkle %A Bowden, Donald W %A Chang, Yi-Cheng %A Chen, Yii-Der I %A Choi, Won Jung %A Correa, Adolfo %A Curran, Joanne E %A Daly, Mark J %A Dutcher, Susan K %A Ellinor, Patrick T %A Fornage, Myriam %A Freedman, Barry I %A Gabriel, Stacey %A Germer, Soren %A Richard A Gibbs %A He, Jiang %A Hveem, Kristian %A Jarvik, Gail P %A Kaplan, Robert C %A Kardia, Sharon L R %A Kenny, Eimear %A Kim, Ryan W %A Kooperberg, Charles %A Laurie, Cathy C %A Lee, Seonwook %A Lloyd-Jones, Don M %A Loos, Ruth J F %A Lubitz, Steven A %A Mathias, Rasika A %A Martinez, Karine A Viaud %A McGarvey, Stephen T %A Mitchell, Braxton D %A Nickerson, Deborah A %A North, Kari E %A Palotie, Aarno %A Park, Cheol Joo %A Psaty, Bruce M %A Rao, D C %A Redline, Susan %A Reiner, Alexander P %A Seo, Daekwan %A Seo, Jeong-Sun %A Smith, Albert V %A Tracy, Russell P %A Vasan, Ramachandran S %A Kathiresan, Sekar %A Cupples, L Adrienne %A Rotter, Jerome I %A Morrison, Alanna C %A Rich, Stephen S %A Ripatti, Samuli %A Willer, Cristen %A Peloso, Gina M %K Cardiometabolic Risk Factors %K Chromosomes, Human, X %K Eye Proteins %K Female %K Gene Expression Regulation %K Genetic Association Studies %K Genetic Loci %K Genetic Predisposition to Disease %K Genotype %K Humans %K Lipids %K Male %K Middle Aged %K Nerve Tissue Proteins %K Phenomics %K Polymorphism, Single Nucleotide %K Subcutaneous Tissue %K Whole Genome Sequencing %X

Autosomal genetic analyses of blood lipids have yielded key insights for coronary heart disease (CHD). However, X chromosome genetic variation is understudied for blood lipids in large sample sizes. We now analyze genetic and blood lipid data in a high-coverage whole X chromosome sequencing study of 65,322 multi-ancestry participants and perform replication among 456,893 European participants. Common alleles on chromosome Xq23 are strongly associated with reduced total cholesterol, LDL cholesterol, and triglycerides (min P = 8.5 × 10), with similar effects for males and females. Chromosome Xq23 lipid-lowering alleles are associated with reduced odds for CHD among 42,545 cases and 591,247 controls (P = 1.7 × 10), and reduced odds for diabetes mellitus type 2 among 54,095 cases and 573,885 controls (P = 1.4 × 10). Although we observe an association with increased BMI, waist-to-hip ratio adjusted for BMI is reduced, bioimpedance analyses indicate increased gluteofemoral fat, and abdominal MRI analyses indicate reduced visceral adiposity. Co-localization analyses strongly correlate increased CHRDL1 gene expression, particularly in adipose tissue, with reduced concentrations of blood lipids.

%B Nat Commun %V 12 %P 2182 %8 2021 Apr 12 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33846329?dopt=Abstract %R 10.1038/s41467-021-22339-1 %0 Journal Article %J Nat Biotechnol %D 2021 %T Chromosome-scale, haplotype-resolved assembly of human genomes. %A Garg, Shilpa %A Fungtammasan, Arkarachai %A Carroll, Andrew %A Chou, Mike %A Schmitt, Anthony %A Zhou, Xiang %A Mac, Stephen %A Peluso, Paul %A Hatas, Emily %A Ghurye, Jay %A Maguire, Jared %A Mahmoud, Medhat %A Cheng, Haoyu %A Heller, David %A Zook, Justin M %A Moemke, Tobias %A Marschall, Tobias %A Fritz J Sedlazeck %A Aach, John %A Chin, Chen-Shan %A Church, George M %A Li, Heng %K Algorithms %K Chromosomes, Human %K Genome, Human %K Haplotypes %K Heterozygote %K Humans %K Polymorphism, Single Nucleotide %X

Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which limits their application. We present a method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day. Applied to four public human genomes, PGP1, HG002, NA12878 and HG00733, DipAsm produced haplotype-resolved assemblies with minimum contig length needed to cover 50% of the known genome (NG50) up to 25 Mb and phased ~99.5% of heterozygous sites at 98-99% accuracy, outperforming other approaches in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies for the discovery of structural variants (SVs), including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as the human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) regions. DipAsm will facilitate high-quality precision medicine and studies of individual haplotype variation and population diversity.

%B Nat Biotechnol %V 39 %P 309-312 %8 2021 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/33288905?dopt=Abstract %R 10.1038/s41587-020-0711-0 %0 Journal Article %J Am J Med Genet A %D 2021 %T Clan genomics: From OMIM phenotypic traits to genes and biology. %A James R Lupski %K Computational Biology %K Databases, Genetic %K Genetic Diseases, Inborn %K Genetics, Medical %K Genomics %K Humans %K Phenotype %X

Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.

%B Am J Med Genet A %V 185 %P 3294-3313 %8 2021 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/34405553?dopt=Abstract %R 10.1002/ajmg.a.62434 %0 Journal Article %J Am J Med Genet A %D 2021 %T Clinical characterization of individuals with the distal 1q21.1 microdeletion. %A Edwards, Stacey D %A Schulze, Katharina V %A Rosenfeld, Jill A %A Westerfield, Lauren E %A Gerard, Amanda %A Bo Yuan %A Grigorenko, Elena L %A Posey, Jennifer E %A Bi, Weimin %A Liu, Pengfei %K Abnormalities, Multiple %K Adolescent %K Adult %K Child %K Child, Preschool %K Chromosome Deletion %K Chromosomes, Human, Pair 1 %K Developmental Disabilities %K DNA Copy Number Variations %K Failure to Thrive %K Female %K Genetic Counseling %K Genetic Testing %K Heart Defects, Congenital %K Humans %K Infant %K Intellectual Disability %K Male %K Megalencephaly %K Microcephaly %K Pedigree %K Seizures %K Young Adult %X

Distal 1q21.1 microdeletions have shown highly variable clinical expressivity and incomplete penetrance, with affected individuals manifesting a broad spectrum of nonspecific features. The goals of this study were to better describe the phenotypic spectrum of patients with distal 1q21.1 microdeletions and to compare the clinical features among affected individuals. We performed a retrospective chart review of 47 individuals with distal 1q21.1 microdeletions tested at a large clinical genetic testing laboratory, with most patients being clinically evaluated in the same children's hospital. Health information such as growth charts, results of imaging studies, developmental history, and progress notes were collected. Statistical analysis was performed using Fisher's exact test to compare clinical features among study subjects. Common features in our cohort include microcephaly (51.2%), seizures (29.8%), developmental delay (74.5%), failure to thrive (FTT) (68.1%), dysmorphic features (63.8%), and a variety of congenital anomalies such as cardiac abnormalities (23.4%) and genitourinary abnormalities (19.1%). Compared to prior literature, we found that seizures, brain anomalies, and FTT were more prevalent among our study cohort. Females were more likely than males to have microcephaly (p = 0.0199) and cardiac abnormalities (p = 0.0018). Based on existing genome-wide clinical testing results, at least a quarter of the cohort had additional genetic findings that may impact the phenotype of the individual. Our study represents the largest cohort of distal 1q21.1 microdeletion carriers available in the literature thus far, and it further illustrates the wide spectrum of clinical manifestations among symptomatic individuals. These results may allow for improved genetic counseling and management of affected individuals. Future studies may help to elucidate the underlying molecular mechanisms impacting the phenotypic variability observed with this microdeletion.

%B Am J Med Genet A %V 185 %P 1388-1398 %8 2021 05 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/33576134?dopt=Abstract %R 10.1002/ajmg.a.62104 %0 Journal Article %J Hum Mutat %D 2021 %T Clinical, neuroimaging, and molecular spectrum of TECPR2-associated hereditary sensory and autonomic neuropathy with intellectual disability. %A Neuser, Sonja %A Brechmann, Barbara %A Heimer, Gali %A Brösse, Ines %A Schubert, Susanna %A O'Grady, Lauren %A Zech, Michael %A Srivastava, Siddharth %A Sweetser, David A %A Dincer, Yasemin %A Mall, Volker %A Winkelmann, Juliane %A Behrends, Christian %A Darras, Basil T %A Graham, Robert J %A Jayakar, Parul %A Byrne, Barry %A Bar-Aluma, Bat El %A Haberman, Yael %A Szeinberg, Amir %A Aldhalaan, Hesham M %A Hashem, Mais %A Al Tenaiji, Amal %A Ismayl, Omar %A Al Nuaimi, Asma E %A Maher, Karima %A Ibrahim, Shahnaz %A Khan, Fatima %A Houlden, Henry %A Ramakumaran, Vijayalakshmi S %A Pagnamenta, Alistair T %A Posey, Jennifer E %A James R Lupski %A Tan, Wen-Hann %A ElGhazali, Gehad %A Herman, Isabella %A Muñoz, Tatiana %A Repetto, Gabriela M %A Seitz, Angelika %A Krumbiegel, Mandy %A Poli, Maria Cecilia %A Kini, Usha %A Efthymiou, Stephanie %A Meiler, Jens %A Maroofian, Reza %A Alkuraya, Fowzan S %A Abou Jamra, Rami %A Popp, Bernt %A Ben-Zeev, Bruria %A Ebrahimi-Fakhari, Darius %K Adolescent %K Carrier Proteins %K Child %K Child, Preschool %K Cohort Studies %K Cross-Sectional Studies %K Family %K Female %K Hereditary Sensory and Autonomic Neuropathies %K Humans %K Infant %K Intellectual Disability %K Magnetic Resonance Imaging %K Male %K Models, Molecular %K Mutation, Missense %K Nerve Tissue Proteins %K Neuroimaging %K Pedigree %K Phenotype %K Protein Conformation %X

Bi-allelic TECPR2 variants have been associated with a complex syndrome with features of both a neurodevelopmental and neurodegenerative disorder. Here, we provide a comprehensive clinical description and variant interpretation framework for this genetic locus. Through international collaboration, we identified 17 individuals from 15 families with bi-allelic TECPR2-variants. We systemically reviewed clinical and molecular data from this cohort and 11 cases previously reported. Phenotypes were standardized using Human Phenotype Ontology terms. A cross-sectional analysis revealed global developmental delay/intellectual disability, muscular hypotonia, ataxia, hyporeflexia, respiratory infections, and central/nocturnal hypopnea as core manifestations. A review of brain magnetic resonance imaging scans demonstrated a thin corpus callosum in 52%. We evaluated 17 distinct variants. Missense variants in TECPR2 are predominantly located in the N- and C-terminal regions containing β-propeller repeats. Despite constituting nearly half of disease-associated TECPR2 variants, classifying missense variants as (likely) pathogenic according to ACMG criteria remains challenging. We estimate a pathogenic variant carrier frequency of 1/1221 in the general and 1/155 in the Jewish Ashkenazi populations. Based on clinical, neuroimaging, and genetic data, we provide recommendations for variant reporting, clinical assessment, and surveillance/treatment of individuals with TECPR2-associated disorder. This sets the stage for future prospective natural history studies.

%B Hum Mutat %V 42 %P 762-776 %8 2021 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/33847017?dopt=Abstract %R 10.1002/humu.24206 %0 Journal Article %J Am J Med Genet A %D 2021 %T Clinical presentation and evolution of Xia-Gibbs syndrome due to p.Gly375ArgfsTer3 variant in a patient from DR Congo (Central Africa). %A Mubungu, Gerrye %A Makay, Prince %A Boujemla, Bouchra %A Yanda, Stephane %A Posey, Jennifer E %A James R Lupski %A Bours, Vincent %A Lukusa, Prosper %A Devriendt, Koenraad %A Lumaka, Aimé %K Abnormalities, Multiple %K Agenesis of Corpus Callosum %K Attention Deficit Disorder with Hyperactivity %K Child %K Democratic Republic of the Congo %K Developmental Disabilities %K DNA-Binding Proteins %K Exome Sequencing %K Face %K Frameshift Mutation %K Humans %K Intellectual Disability %K Language Development Disorders %K Male %K Mitral Valve Insufficiency %K Palate %K Syndrome %K Talipes Cavus %X

Xia-Gibbs syndrome (XGS) is a very rare genetic condition. The clinical spectrum is very broad and variable. The phenotype and evolution in a Congolese boy with XGS have been reported. At 6 years he had speech delay, drooling, marked hyperactivity, attention deficit, aggressive behavior, and intellectual disability. Dysmorphological evaluation revealed strabismus, mild unilateral ptosis, uplifted ear lobes, flat philtrum, thin upper lip vermillion, high arched palate, and flat feet. Patient-only whole exome sequencing identified a known pathogenic frameshift variant in the AHDC1 gene [NM_001029882.3(AHDC1):c.1122dupC;(p.Gly375ArgfsTer3)]. The clinical follow-up revealed the deterioration of his fine motor skills and significant cerebellar phenotype including tremor, pes cavus, and gait instability at the age of 12 years. This patient was compared with three previously reported patients with the same variant but did not identify a consistent pattern in the evolution of symptoms with age.

%B Am J Med Genet A %V 185 %P 990-994 %8 2021 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/33372375?dopt=Abstract %R 10.1002/ajmg.a.62049 %0 Journal Article %J Nat Commun %D 2021 %T Common variants in Alzheimer's disease and risk stratification by polygenic risk scores. %A de Rojas, Itziar %A Moreno-Grau, Sonia %A Tesi, Niccolo %A Grenier-Boley, Benjamin %A Andrade, Victor %A Jansen, Iris E %A Pedersen, Nancy L %A Stringa, Najada %A Zettergren, Anna %A Hernández, Isabel %A Montrreal, Laura %A Antúnez, Carmen %A Antonell, Anna %A Tankard, Rick M %A Bis, Joshua C %A Sims, Rebecca %A Bellenguez, Céline %A Quintela, Inés %A González-Perez, Antonio %A Calero, Miguel %A Franco-Macías, Emilio %A Macías, Juan %A Blesa, Rafael %A Cervera-Carles, Laura %A Menéndez-González, Manuel %A Frank-García, Ana %A Royo, Jose Luís %A Moreno, Fermin %A Huerto Vilas, Raquel %A Baquero, Miquel %A Diez-Fairen, Monica %A Lage, Carmen %A García-Madrona, Sebastián %A García-González, Pablo %A Alarcón-Martín, Emilio %A Valero, Sergi %A Sotolongo-Grau, Oscar %A Ullgren, Abbe %A Naj, Adam C %A Lemstra, Afina W %A Benaque, Alba %A Pérez-Cordón, Alba %A Benussi, Alberto %A Rábano, Alberto %A Padovani, Alessandro %A Squassina, Alessio %A de Mendonça, Alexandre %A Arias Pastor, Alfonso %A Kok, Almar A L %A Meggy, Alun %A Pastor, Ana Belén %A Espinosa, Ana %A Corma-Gómez, Anaïs %A Martín Montes, Angel %A Sanabria, Ángela %A DeStefano, Anita L %A Schneider, Anja %A Haapasalo, Annakaisa %A Kinhult Ståhlbom, Anne %A Tybjærg-Hansen, Anne %A Hartmann, Annette M %A Spottke, Annika %A Corbatón-Anchuelo, Arturo %A Rongve, Arvid %A Borroni, Barbara %A Arosio, Beatrice %A Nacmias, Benedetta %A Nordestgaard, Børge G %A Kunkle, Brian W %A Charbonnier, Camille %A Abdelnour, Carla %A Masullo, Carlo %A Martínez Rodríguez, Carmen %A Muñoz-Fernandez, Carmen %A Dufouil, Carole %A Graff, Caroline %A Ferreira, Catarina B %A Chillotti, Caterina %A Reynolds, Chandra A %A Fenoglio, Chiara %A Van Broeckhoven, Christine %A Clark, Christopher %A Pisanu, Claudia %A Satizabal, Claudia L %A Holmes, Clive %A Buiza-Rueda, Dolores %A Aarsland, Dag %A Rujescu, Dan %A Alcolea, Daniel %A Galimberti, Daniela %A Wallon, David %A Seripa, Davide %A Grünblatt, Edna %A Dardiotis, Efthimios %A Düzel, Emrah %A Scarpini, Elio %A Conti, Elisa %A Rubino, Elisa %A Gelpi, Ellen %A Rodriguez-Rodriguez, Eloy %A Duron, Emmanuelle %A Eric Boerwinkle %A Ferri, Evelyn %A Tagliavini, Fabrizio %A Küçükali, Fahri %A Pasquier, Florence %A Sanchez-Garcia, Florentino %A Mangialasche, Francesca %A Jessen, Frank %A Nicolas, Gaël %A Selbæk, Geir %A Ortega, Gemma %A Chêne, Geneviève %A Hadjigeorgiou, Georgios %A Rossi, Giacomina %A Spalletta, Gianfranco %A Giaccone, Giorgio %A Grande, Giulia %A Binetti, Giuliano %A Papenberg, Goran %A Hampel, Harald %A Bailly, Henri %A Zetterberg, Henrik %A Soininen, Hilkka %A Karlsson, Ida K %A Alvarez, Ignacio %A Appollonio, Ildebrando %A Giegling, Ina %A Skoog, Ingmar %A Saltvedt, Ingvild %A Rainero, Innocenzo %A Rosas Allende, Irene %A Hort, Jakub %A Diehl-Schmid, Janine %A Van Dongen, Jasper %A Vidal, Jean-Sebastien %A Lehtisalo, Jenni %A Wiltfang, Jens %A Thomassen, Jesper Qvist %A Kornhuber, Johannes %A Haines, Jonathan L %A Vogelgsang, Jonathan %A Pineda, Juan A %A Fortea, Juan %A Popp, Julius %A Deckert, Jürgen %A Buerger, Katharina %A Morgan, Kevin %A Fließbach, Klaus %A Sleegers, Kristel %A Molina-Porcel, Laura %A Kilander, Lena %A Weinhold, Leonie %A Farrer, Lindsay A %A Wang, Li-San %A Kleineidam, Luca %A Farotti, Lucia %A Parnetti, Lucilla %A Tremolizzo, Lucio %A Hausner, Lucrezia %A Benussi, Luisa %A Froelich, Lutz %A Ikram, M Arfan %A Deniz-Naranjo, M Candida %A Tsolaki, Magda %A Rosende-Roca, Maitée %A Löwenmark, Malin %A Hulsman, Marc %A Spallazzi, Marco %A Pericak-Vance, Margaret A %A Esiri, Margaret %A Bernal Sánchez-Arjona, María %A Dalmasso, Maria Carolina %A Martínez-Larrad, María Teresa %A Arcaro, Marina %A Nöthen, Markus M %A Fernández-Fuertes, Marta %A Dichgans, Martin %A Ingelsson, Martin %A Herrmann, Martin J %A Scherer, Martin %A Vyhnalek, Martin %A Kosmidis, Mary H %A Yannakoulia, Mary %A Schmid, Matthias %A Ewers, Michael %A Heneka, Michael T %A Wagner, Michael %A Scamosci, Michela %A Kivipelto, Miia %A Hiltunen, Mikko %A Zulaica, Miren %A Alegret, Montserrat %A Fornage, Myriam %A Roberto, Natalia %A van Schoor, Natasja M %A Seidu, Nazib M %A Banaj, Nerisa %A Armstrong, Nicola J %A Scarmeas, Nikolaos %A Scherbaum, Norbert %A Goldhardt, Oliver %A Hanon, Oliver %A Peters, Oliver %A Skrobot, Olivia Anna %A Quenez, Olivier %A Lerch, Ondrej %A Bossù, Paola %A Caffarra, Paolo %A Dionigi Rossi, Paolo %A Sakka, Paraskevi %A Mecocci, Patrizia %A Hoffmann, Per %A Holmans, Peter A %A Fischer, Peter %A Riederer, Peter %A Yang, Qiong %A Marshall, Rachel %A Kalaria, Rajesh N %A Mayeux, Richard %A Vandenberghe, Rik %A Cecchetti, Roberta %A Ghidoni, Roberta %A Frikke-Schmidt, Ruth %A Sorbi, Sandro %A Hägg, Sara %A Engelborghs, Sebastiaan %A Helisalmi, Seppo %A Botne Sando, Sigrid %A Kern, Silke %A Archetti, Silvana %A Boschi, Silvia %A Fostinelli, Silvia %A Gil, Silvia %A Mendoza, Silvia %A Mead, Simon %A Ciccone, Simona %A Djurovic, Srdjan %A Heilmann-Heimbach, Stefanie %A Riedel-Heller, Steffi %A Kuulasmaa, Teemu %A Del Ser, Teodoro %A Lebouvier, Thibaud %A Polak, Thomas %A Ngandu, Tiia %A Grimmer, Timo %A Bessi, Valentina %A Escott-Price, Valentina %A Giedraitis, Vilmantas %A Deramecourt, Vincent %A Maier, Wolfgang %A Jian, Xueqiu %A Pijnenburg, Yolande A L %A Kehoe, Patrick Gavin %A Garcia-Ribas, Guillermo %A Sánchez-Juan, Pascual %A Pastor, Pau %A Pérez-Tur, Jordi %A Piñol-Ripoll, Gerard %A Lopez de Munain, Adolfo %A García-Alberca, Jose María %A Bullido, María J %A Alvarez, Victoria %A Lleo, Alberto %A Real, Luis M %A Mir, Pablo %A Medina, Miguel %A Scheltens, Philip %A Holstege, Henne %A Marquié, Marta %A Sáez, María Eugenia %A Carracedo, Ángel %A Amouyel, Philippe %A Schellenberg, Gerard D %A Williams, Julie %A Seshadri, Sudha %A van Duijn, Cornelia M %A Mather, Karen A %A Sánchez-Valle, Raquel %A Serrano-Ríos, Manuel %A Orellana, Adelina %A Tarraga, Lluis %A Blennow, Kaj %A Huisman, Martijn %A Andreassen, Ole A %A Posthuma, Danielle %A Clarimon, Jordi %A Boada, Mercè %A van der Flier, Wiesje M %A Ramirez, Alfredo %A Lambert, Jean-Charles %A van der Lee, Sven J %A Ruiz, Agustin %K Age of Onset %K Aged %K Aged, 80 and over %K Alzheimer Disease %K Amyloid beta-Protein Precursor %K Apolipoproteins E %K Case-Control Studies %K Cohort Studies %K Datasets as Topic %K Female %K Follow-Up Studies %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Heterozygote %K Humans %K Male %K Middle Aged %K Multifactorial Inheritance %K Polymorphism, Single Nucleotide %K Risk Assessment %K Risk Factors %X

Genetic discoveries of Alzheimer's disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery n = 409,435 and validation size n = 58,190). Here, we add six variants associated with Alzheimer's disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer's disease patients in APOE ɛ4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer's disease.

%B Nat Commun %V 12 %P 3417 %8 2021 Jun 07 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/34099642?dopt=Abstract %R 10.1038/s41467-021-22491-8 %0 Journal Article %J Sci Adv %D 2021 %T Comparative genomic analysis of sifakas () reveals selection for folivory and high heterozygosity despite endangered status. %A Guevara, Elaine E %A Webster, Timothy H %A Lawler, Richard R %A Bradley, Brenda J %A Greene, Lydia K %A Ranaivonasy, Jeannin %A Ratsirarson, Joelisoa %A R. Alan Harris %A Liu, Yue %A Murali, Shwetha %A Raveendran, Muthuswamy %A Hughes, Daniel S T %A Donna M Muzny %A Yoder, Anne D %A Kim C Worley %A Jeffrey Rogers %X

Sifakas (genus ) are critically endangered, large-bodied diurnal lemurs that eat leaf-based diets and show corresponding anatomical and microbial adaptations to folivory. We report on the genome assembly of Coquerel's sifaka () and the resequenced genomes of Verreaux's (), the golden-crowned (), and the diademed () sifakas. We find high heterozygosity in all sifakas compared with other primates and endangered mammals. Demographic reconstructions nevertheless suggest declines in effective population size beginning before human arrival on Madagascar. Comparative genomic analyses indicate pervasive accelerated evolution in the ancestral sifaka lineage affecting genes in several complementary pathways relevant to folivory, including nutrient absorption and xenobiotic and fatty acid metabolism. Sifakas show convergent evolution at the level of the pathway, gene family, gene, and amino acid substitution with other folivores. Although sifakas have relatively generalized diets, the physiological challenges of habitual folivory likely led to strong selection.

%B Sci Adv %V 7 %8 2021 Apr %G eng %N 17 %1 https://www.ncbi.nlm.nih.gov/pubmed/33893095?dopt=Abstract %R 10.1126/sciadv.abd2274 %0 Journal Article %J J Clin Immunol %D 2021 %T Complicated Diagnosis and Treatment of HA20 due to Contiguous Gene Deletions involving 6q23.3. %A Wu, Chung Wah %A Sasa, Ghadir %A Salih, Amanda %A Nicholas, Sarah %A Vogel, Tiphanie P %A Cahill, Gina %A Kuehn, Hye Sun %A Rosenzweig, Sergio D %A Zhou, Qing %A Chinn, Ivan K %A Bo Yuan %K Adolescent %K Antibodies, Monoclonal, Humanized %K Chromosomes, Human, Pair 6 %K Female %K Gene Deletion %K Haploinsufficiency %K Hereditary Autoinflammatory Diseases %K Humans %K Tumor Necrosis Factor alpha-Induced Protein 3 %B J Clin Immunol %V 41 %P 1420-1423 %8 2021 08 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/34032947?dopt=Abstract %R 10.1007/s10875-021-01048-w %0 Journal Article %J BMC Bioinformatics %D 2021 %T A consensus-based ensemble approach to improve transcriptome assembly. %A Voshall, Adam %A Behera, Sairam %A Li, Xiangjun %A Yu, Xiao-Hong %A Kapil, Kushagra %A Deogun, Jitender S %A Shanklin, John %A Cahoon, Edgar B %A Moriyama, Etsuko N %K Consensus %K Genome %K Transcriptome %X

BACKGROUND: Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes.

RESULTS: In this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble.

CONCLUSIONS: Without using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from: http://bioinfolab.unl.edu/emlab/consemble/ .

%B BMC Bioinformatics %V 22 %P 513 %8 2021 Oct 21 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/34674629?dopt=Abstract %R 10.1186/s12859-021-04434-8 %0 Journal Article %J Mol Genet Genomic Med %D 2021 %T Contribution of uniparental disomy in a clinical trio exome cohort of 2675 patients. %A Wang, Lei %A Liu, Pengfei %A Bi, Weimin %A Sim, Teresa %A Wang, Xia %A Walkiewicz, Magdalene %A Leduc, Magalie Sophie %A Meng, Linyan %A Xia, Fan %A Christine M Eng %A Yang, Yaping %A Bo Yuan %A Dai, Hongzheng %K Chromosome Disorders %K Humans %K Pedigree %K Uniparental Disomy %K Whole Exome Sequencing %X

BACKGROUND: Uniparental disomy (UPD) is the inheritance of two homologous chromosomes from the same parent. UPD may result in clinical phenotypes when occurring on chromosomes with specific imprinting pattern, when leading to homozygosity of a deleterious recessive allele inherited from one carrier parent, or when associated with a mosaic aneuploidy. Due to the importance of UPD in genetic disease etiology, UPD analysis has started to be implemented in the context of exome sequencing (ES) or genome sequencing.

METHODS: We developed an in-house algorithm TRIPS (Trio Parentage/UPD Studies) to identify UPD events in trio ES cases. This method identifies regions with uniparental inheritance by utilizing the trio genotyping data obtained from the concurrent SNP array to delineate the parental origin of the SNPs in the proband.

RESULTS: We identified 16 UPD events from 2675 ES trios. Among those, four events led to imprinting disorders, seven unmasked a pathogenic/likely pathogenic variant in a recessive disease gene, and two were consistent with a mosaic genome wide paternal UPD pattern. Twelve of these UPD events directly contributed to the molecular diagnosis of the patients.

CONCLUSION: Our study demonstrated the contribution of UPD to the molecular diagnosis in one clinical ES cohort, thus UPD analysis should be incorporated into routine clinical ES interpretation.

%B Mol Genet Genomic Med %V 9 %P e1792 %8 2021 11 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/34587367?dopt=Abstract %R 10.1002/mgg3.1792 %0 Journal Article %J Am J Hum Genet %D 2021 %T COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay. %A Marom, Ronit %A Burrage, Lindsay C %A Venditti, Rossella %A Clément, Aurélie %A Blanco-Sánchez, Bernardo %A Jain, Mahim %A Scott, Daryl A %A Rosenfeld, Jill A %A Sutton, V Reid %A Shinawi, Marwan %A Mirzaa, Ghayda %A DeVile, Catherine %A Roberts, Rowenna %A Calder, Alistair D %A Allgrove, Jeremy %A Grafe, Ingo %A Lanza, Denise G %A Li, Xiaohui %A Joeng, Kyu Sang %A Lee, Yi-Chien %A Song, I-Wen %A Sliepka, Joseph M %A Batkovskyte, Dominyka %A Washington, Megan %A Dawson, Brian C %A Jin, Zixue %A Jiang, Ming-Ming %A Chen, Shan %A Chen, Yuqing %A Tran, Alyssa A %A Emrick, Lisa T %A David R Murdock %A Hanchard, Neil A %A Zapata, Gladys E %A Mehta, Nitesh R %A Weis, Mary Ann %A Scott, Abbey A %A Tremp, Brenna A %A Phillips, Jennifer B %A Wegner, Jeremy %A Taylor-Miller, Tashunka %A Richard A Gibbs %A Donna M Muzny %A Jhangiani, Shalini N %A Hicks, John %A Stottmann, Rolf W %A Dickinson, Mary E %A Seavitt, John R %A Heaney, Jason D %A Eyre, David R %A Westerfield, Monte %A De Matteis, Maria Antonietta %A Lee, Brendan %K Animals %K Ascorbic Acid %K Bone and Bones %K Brain %K Child %K Child, Preschool %K Coat Protein Complex I %K Coatomer Protein %K Collagen Type I %K Developmental Disabilities %K Embryo, Nonmammalian %K Endoplasmic Reticulum %K Female %K Fibroblasts %K Gene Expression Regulation, Developmental %K Golgi Apparatus %K Haploinsufficiency %K Humans %K Intellectual Disability %K Male %K Mice %K Osteoporosis %K RNA, Small Interfering %K Severity of Illness Index %K Zebrafish %X

Coatomer complexes function in the sorting and trafficking of proteins between subcellular organelles. Pathogenic variants in coatomer subunits or associated factors have been reported in multi-systemic disorders, i.e., coatopathies, that can affect the skeletal and central nervous systems. We have identified loss-of-function variants in COPB2, a component of the coatomer complex I (COPI), in individuals presenting with osteoporosis, fractures, and developmental delay of variable severity. Electron microscopy of COPB2-deficient subjects' fibroblasts showed dilated endoplasmic reticulum (ER) with granular material, prominent rough ER, and vacuoles, consistent with an intracellular trafficking defect. We studied the effect of COPB2 deficiency on collagen trafficking because of the critical role of collagen secretion in bone biology. COPB2 siRNA-treated fibroblasts showed delayed collagen secretion with retention of type I collagen in the ER and Golgi and altered distribution of Golgi markers. copb2-null zebrafish embryos showed retention of type II collagen, disorganization of the ER and Golgi, and early larval lethality. Copb2 mice exhibited low bone mass, and consistent with the findings in human cells and zebrafish, studies in Copb2 mouse fibroblasts suggest ER stress and a Golgi defect. Interestingly, ascorbic acid treatment partially rescued the zebrafish developmental phenotype and the cellular phenotype in Copb2 mouse fibroblasts. This work identifies a form of coatopathy due to COPB2 haploinsufficiency, explores a potential therapeutic approach for this disorder, and highlights the role of the COPI complex as a regulator of skeletal homeostasis.

%B Am J Hum Genet %V 108 %P 1710-1724 %8 2021 Sep 02 %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/34450031?dopt=Abstract %R 10.1016/j.ajhg.2021.08.002 %0 Journal Article %J BMC Ecol Evol %D 2021 %T Correction to: Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. %A Petersen, Malte %A Armisén, David %A Richard A Gibbs %A Hering, Lars %A Khila, Abderrahman %A Mayer, Georg %A Stephen Richards %A Niehuis, Oliver %A Misof, Bernhard %B BMC Ecol Evol %V 21 %P 146 %8 2021 Jul 16 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/34271865?dopt=Abstract %R 10.1186/s12862-021-01778-w %0 Journal Article %J Int J Biol Sci %D 2021 %T COVID-19 disease and malignant cancers: The impact for the gene expression in susceptibility to SARS-CoV-2. %A Li, Dabing %A Liu, Xiaoyan %A Zhang, Lianmei %A He, Jiayue %A Chen, Xianmao %A Liu, Shuguang %A Fu, Jiewen %A Fu, Shangyi %A Chen, Hanchun %A Fu, Junjiang %A Cheng, Jingliang %K Antineoplastic Agents %K Cell Line, Tumor %K COVID-19 %K Deoxyadenosines %K Disease Susceptibility %K Endoplasmic Reticulum Chaperone BiP %K Furin %K Humans %K Neoplasms %K Protein Isoforms %K Serine Endopeptidases %X

Furin is a proprotein convertase that activates different kinds of regulatory proteins, including SARS-CoV-2 spike protein which contains an additional furin-specific cleavage site. It is essential in predicting cancer patients' susceptibility to SARS-CoV-2 and the disease outcomes due to varying furin expressions in tumor tissues. In this study, we analyzed furin's expression, methylation, mutation rate, functional enrichment, survival rate and COVID-19 outcomes in normal and cancer tissues using online databases, and our IHC. As a result, furin presented with biased expression profiles in normal tissues, showing 12.25-fold higher than ACE2 in the lungs. The furin expression in tumors were significantly increased in ESCA and TGCT, and decreased in DLBC and THYM, indicating furin may play critical mechanistic functions in COVID-19 viral entry into cells in these cancer patients. Line with furin over/downexpression, furin promoter hypo-/hyper-methylation may be the regulatory cause of disease and lead to pathogenesis of ESCA and THYM. Furthermore, presence of FURIN-201 isoform with functional domains (P_proprotein, Peptidase_S8 and S8_pro-domain) is highest in all cancer types in comparison to other isoforms, demonstrating its use in tumorigenesis and SARS-Cov-2 entry into tumor tissues. Furin mutation frequency was highest in UCES, and its mutation might elevate ACE2 expression in LUAD and UCEC, reduce ACE2 expression in COAD, elevate HSPA5 expression in PAAD, and elevate TMPRSS2 expression in BRCA. These results showed that furin mutations mostly increased expression of ACE2, HSPA5, and TMPRSS2 in certain cancers, indicating furin mutations might facilitate COVID-19 cell entry in cancer patients. In addition, high expression of furin was significantly inversely correlated with long overall survival (OS) in LGG and correlated with long OS in COAD and KIRC, indicating that it could be used as a favorable prognostic marker for cancer patients' survival. GO and KEGG demonstrated that furin was mostly enriched in genes for metabolic and biosynthetic processes, retinal dehydrogenase activity, tRNA methyltransferase activity, and genes involving COVID-19, further supporting its role in COVID-19 and cancer metabolism. Moreover, Cordycepin (CD) inhibited furin expression in a dosage dependent manner. Altogether, furin's high expression might not only implies increased susceptibility to SARS-CoV-2 and higher severity of COVID-19 symptoms in cancer patients, but also it highlights the need for cancer treatment and therapy during the COVID-19 pandemic. CD might have a potential to develop an anti-SARS-CoV-2 drug through inhibiting furin expression.

%B Int J Biol Sci %V 17 %P 3954-3967 %8 2021 %G eng %N 14 %1 https://www.ncbi.nlm.nih.gov/pubmed/34671211?dopt=Abstract %R 10.7150/ijbs.63072 %0 Journal Article %J Genome Biol %D 2021 %T Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. %A Gong, Binsheng %A Li, Dan %A Kusko, Rebecca %A Novoradovskaya, Natalia %A Zhang, Yifan %A Wang, Shangzi %A Pabón-Peña, Carlos %A Zhang, Zhihong %A Lai, Kevin %A Cai, Wanshi %A LoCoco, Jennifer S %A Lader, Eric %A Richmond, Todd A %A Mittal, Vinay K %A Liu, Liang-Chun %A Johann, Donald J %A Willey, James C %A Bushel, Pierre R %A Yu, Ying %A Xu, Chang %A Chen, Guangchun %A Burgess, Daniel %A Cawley, Simon %A Giorda, Kristina %A Haseley, Nathan %A Qiu, Fujun %A Wilkins, Katherine %A Arib, Hanane %A Attwooll, Claire %A Babson, Kevin %A Bao, Longlong %A Bao, Wenjun %A Lucas, Anne Bergstrom %A Best, Hunter %A Bhandari, Ambica %A Bisgin, Halil %A Blackburn, James %A Blomquist, Thomas M %A Boardman, Lisa %A Burgher, Blake %A Butler, Daniel J %A Chang, Chia-Jung %A Chaubey, Alka %A Chen, Tao %A Chierici, Marco %A Chin, Christopher R %A Close, Devin %A Conroy, Jeffrey %A Cooley Coleman, Jessica %A Craig, Daniel J %A Crawford, Erin %A Del Pozo, Angela %A Deveson, Ira W %A Duncan, Daniel %A Eterovic, Agda Karina %A Fan, Xiaohui %A Foox, Jonathan %A Furlanello, Cesare %A Ghosal, Abhisek %A Glenn, Sean %A Guan, Meijian %A Haag, Christine %A Hang, Xinyi %A Happe, Scott %A Hennigan, Brittany %A Hipp, Jennifer %A Hong, Huixiao %A Horvath, Kyle %A Jianhong Hu %A Hung, Li-Yuan %A Jarosz, Mirna %A Kerkhof, Jennifer %A Kipp, Benjamin %A Kreil, David Philip %A Łabaj, Paweł %A Lapunzina, Pablo %A Li, Peng %A Li, Quan-Zhen %A Li, Weihua %A Li, Zhiguang %A Liang, Yu %A Liu, Shaoqing %A Liu, Zhichao %A Ma, Charles %A Marella, Narasimha %A Martín-Arenas, Rubén %A Megherbi, Dalila B %A Meng, Qingchang %A Mieczkowski, Piotr A %A Morrison, Tom %A Donna M Muzny %A Ning, Baitang %A Parsons, Barbara L %A Paweletz, Cloud P %A Pirooznia, Mehdi %A Qu, Wubin %A Raymond, Amelia %A Rindler, Paul %A Ringler, Rebecca %A Sadikovic, Bekim %A Scherer, Andreas %A Schulze, Egbert %A Sebra, Robert %A Shaknovich, Rita %A Shi, Qiang %A Shi, Tieliu %A Silla-Castro, Juan Carlos %A Smith, Melissa %A López, Mario Solís %A Song, Ping %A Stetson, Daniel %A Strahl, Maya %A Stuart, Alan %A Supplee, Julianna %A Szankasi, Philippe %A Tan, Haowen %A Tang, Lin-Ya %A Tao, Yonghui %A Thakkar, Shraddha %A Thierry-Mieg, Danielle %A Thierry-Mieg, Jean %A Thodima, Venkat J %A Thomas, David %A Tichý, Boris %A Tom, Nikola %A Garcia, Elena Vallespin %A Verma, Suman %A Kimberly Walker %A Wang, Charles %A Wang, Junwen %A Wang, Yexun %A Wen, Zhining %A Wirta, Valtteri %A Wu, Leihong %A Xiao, Chunlin %A Xiao, Wenzhong %A Xu, Shibei %A Yang, Mary %A Ying, Jianming %A Yip, Shun H %A Zhang, Guangliang %A Zhang, Sa %A Zhao, Meiru %A Zheng, Yuanting %A Zhou, Xiaoyan %A Mason, Christopher E %A Mercer, Timothy %A Tong, Weida %A Shi, Leming %A Jones, Wendell %A Xu, Joshua %K Biomarkers, Tumor %K DNA Copy Number Variations %K Genetic Testing %K Genomics %K Humans %K Molecular Diagnostic Techniques %K Mutation %K Neoplasms %K Oncogenes %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Sensitivity and Specificity %X

BACKGROUND: Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.

RESULTS: All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.

CONCLUSION: This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.

%B Genome Biol %V 22 %P 109 %8 2021 Apr 16 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33863344?dopt=Abstract %R 10.1186/s13059-021-02315-0 %0 Journal Article %J Expert Rev Mol Diagn %D 2020 %T Clinical genomics and contextualizing genome variation in the diagnostic laboratory. %A James R Lupski %A Liu, Pengfei %A Stankiewicz, Pawel %A Carvalho, Claudia M B %A Posey, Jennifer E %K Clinical Laboratory Techniques %K Computational Biology %K DNA Copy Number Variations %K Gene Dosage %K Genetic Association Studies %K Genetic Predisposition to Disease %K Genetic Testing %K Genetic Variation %K Genome, Human %K Genomics %K Humans %K Molecular Sequence Annotation %K Mutation %K Phenotype %K Rare Diseases %X

INTRODUCTION: The human genome contains the instructions for the development and biological homeostasis of the human organism and the genetic transmission of traits. Genome variation in human populations is the basis of evolution; individual or personal genomes vary tremendously, making each of us truly unique.

AREAS COVERED: Assaying this individual variation using genomic technologies has many applications in clinical medicine, from elucidating the biology of disease to designing strategies to ameliorate perturbations from homeostasis. Detecting pathogenic rare variation in a genome may provide a molecular diagnosis that can be informative for patient management and family healthcare.

EXPERT OPINION: Despite the increasing clinical use of unbiased genomic testing, including chromosome microarray analysis (CMA) with array comparative genomic hybridization (aCGH) or SNP arrays, clinical exome sequencing (cES), and whole-genome sequencing (WGS), to survey genome-wide for molecular aberrations, clinical acumen paired with an understanding of the limitations of each testing type will be needed to achieve molecular diagnoses. Potential opportunities for improving case solved rates, functionally annotating the majority of genes in the human genome, and further understanding genetic contributions to disease will empower clinical genomics and the precision medicine initiative.

%B Expert Rev Mol Diagn %V 20 %P 995-1002 %8 2020 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/32954863?dopt=Abstract %R 10.1080/14737159.2020.1826312 %0 Journal Article %J J Clin Invest %D 2020 %T A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi transfer. %A Bajaj, Lakshya %A Sharma, Jaiprakash %A di Ronza, Alberto %A Zhang, Pengcheng %A Eblimit, Aiden %A Pal, Rituraj %A Roman, Dany %A Collette, John R %A Booth, Clarissa %A Chang, Kevin T %A Sifers, Richard N %A Jung, Sung Y %A Weimer, Jill M %A Rui Chen %A Schekman, Randy W %A Sardiello, Marco %K Animals %K Endoplasmic Reticulum %K Golgi Apparatus %K Lysosomes %K Membrane Proteins %K Mice %K Mice, Knockout %K Multiprotein Complexes %K Neuronal Ceroid-Lipofuscinoses %K Protein Transport %X

Lysosomal enzymes are synthesized in the endoplasmic reticulum (ER) and transferred to the Golgi complex by interaction with the Batten disease protein CLN8 (ceroid lipofuscinosis, neuronal, 8). Here we investigated the relationship of this pathway with CLN6, an ER-associated protein of unknown function that is defective in a different Batten disease subtype. Experiments focused on protein interaction and trafficking identified CLN6 as an obligate component of a CLN6-CLN8 complex (herein referred to as EGRESS: ER-to-Golgi relaying of enzymes of the lysosomal system), which recruits lysosomal enzymes at the ER to promote their Golgi transfer. Mutagenesis experiments showed that the second luminal loop of CLN6 is required for the interaction of CLN6 with the enzymes but dispensable for interaction with CLN8. In vitro and in vivo studies showed that CLN6 deficiency results in inefficient ER export of lysosomal enzymes and diminished levels of the enzymes at the lysosome. Mice lacking both CLN6 and CLN8 did not display aggravated pathology compared with the single deficiencies, indicating that the EGRESS complex works as a functional unit. These results identify CLN6 and the EGRESS complex as key players in lysosome biogenesis and shed light on the molecular etiology of Batten disease caused by defects in CLN6.

%B J Clin Invest %V 130 %P 4118-4132 %8 2020 Aug 03 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/32597833?dopt=Abstract %R 10.1172/JCI130955 %0 Journal Article %J Genet Med %D 2020 %T CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. %A Bo Yuan %A Wang, Lei %A Liu, Pengfei %A Shaw, Chad %A Dai, Hongzheng %A Cooper, Lance %A Zhu, Wenmiao %A Anderson, Stephanie A %A Meng, Linyan %A Wang, Xia %A Wang, Yue %A Xia, Fan %A Xiao, Rui %A Braxton, Alicia %A Peacock, Sandra %A Schmitt, Eric %A Ward, Patricia A %A Vetrini, Francesco %A He, Weimin %A Chiang, Theodore %A Donna M Muzny %A Richard A Gibbs %A Beaudet, Arthur L %A Breman, Amy M %A Smith, Janice %A Cheung, Sau Wai %A Bacino, Carlos A %A Eng, Christine M %A Yang, Yaping %A James R Lupski %A Bi, Weimin %K Child %K DNA Copy Number Variations %K Exome Sequencing %K Exons %K Humans %K INDEL Mutation %K Retrospective Studies %X

PURPOSE: Improved resolution of molecular diagnostic technologies enabled detection of smaller sized exonic level copy-number variants (CNVs). The contribution of CNVs to autosomal recessive (AR) conditions may be better recognized using a large clinical cohort.

METHODS: We retrospectively investigated the CNVs' contribution to AR conditions in cases subjected to chromosomal microarray analysis (CMA, N = ~70,000) and/or clinical exome sequencing (ES, N = ~12,000) at Baylor Genetics; most had pediatric onset neurodevelopmental disorders.

RESULTS: CNVs contributed to biallelic variations in 87 cases, including 81 singletons and three affected sibling pairs. Seventy cases had CNVs affecting both alleles, and 17 had a CNV and a single-nucleotide variant (SNV)/indel in trans. In total, 94.3% of AR-CNVs affected one gene; among these 41.4% were single-exon and 35.0% were multiexon partial-gene events. Sixty-nine percent of homozygous AR-CNVs were embedded in homozygous genomic intervals. Five cases had large deletions unmasking an SNV/indel on the intact allele for a recessive condition, resulting in multiple molecular diagnoses.

CONCLUSIONS: AR-CNVs are often smaller in size, transmitted through generations, and underrecognized due to limitations in clinical CNV detection methods. Our findings from a large clinical cohort emphasized integrated CNV and SNV/indel analyses for precise clinical and molecular diagnosis especially in the context of genomic disorders.

%B Genet Med %V 22 %P 1633-1641 %8 2020 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/32576985?dopt=Abstract %R 10.1038/s41436-020-0864-8 %0 Journal Article %J Int J Epidemiol %D 2020 %T Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol). %A Bielinski, Suzette J %A St Sauver, Jennifer L %A Olson, Janet E %A Larson, Nicholas B %A Black, John L %A Steven E Scherer %A Bernard, Matthew E %A Eric Boerwinkle %A Borah, Bijan J %A Caraballo, Pedro J %A Curry, Timothy B %A Harshavardhan Doddapaneni %A Formea, Christine M %A Freimuth, Robert R %A Richard A Gibbs %A Giri, Jyothsna %A Hathcock, Matthew A %A Jianhong Hu %A Jacobson, Debra J %A Jones, Leila A %A Sara E Kalla %A Koep, Tyler H %A Korchina, Viktoriya %A Kovar, Christie L %A Lee, Sandra %A Liu, Hongfang %A Matey, Eric T %A McGree, Michaela E %A McAllister, Tammy M %A Moyer, Ann M %A Donna M Muzny %A Nicholson, Wayne T %A Oyen, Lance J %A Xiang Qin %A Raj, Ritika %A Roger, Véronique L %A Rohrer Vitek, Carolyn R %A Ross, Jason L %A Sharp, Richard R %A Takahashi, Paul Y %A Eric Venner %A Kimberly Walker %A Wang, Liwei %A Wang, Qiaoyan %A Wright, Jessica A %A Wu, Tsung-Jung %A Wang, Liewei %A Weinshilboum, Richard M %K Clinical Protocols %K Cohort Studies %K Female %K Genomics %K Humans %K Male %K Pharmacogenetics %K Precision Medicine %B Int J Epidemiol %V 49 %P 23-24k %8 2020 Feb 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31378813?dopt=Abstract %R 10.1093/ije/dyz123 %0 Journal Article %J Hum Mol Genet %D 2020 %T Combination of whole exome sequencing and animal modeling identifies TMPRSS9 as a candidate gene for autism spectrum disorder. %A Chen, Chun-An %A Pal, Rituraj %A Yin, Jiani %A Tao, Huifang %A Amawi, Abdallah %A Aniko Sabo %A Bainbridge, Matthew N %A Richard A Gibbs %A Zoghbi, Huda Y %A Schaaf, Christian P %K Adolescent %K Adult %K Animals %K Anxiety Disorders %K Autism Spectrum Disorder %K Child %K Child, Preschool %K Codon, Nonsense %K Exome Sequencing %K Female %K Humans %K Male %K Membrane Proteins %K Memory Disorders %K Mice %K Mice, Knockout %K Motor Activity %K Phenotype %K Serine Endopeptidases %X

Autism spectrum disorders are associated with some degree of developmental regression in up to 30% of all cases. Rarely, however, is the regression so extreme that a developmentally advanced young child would lose almost all ability to communicate and interact with her surroundings. We applied trio whole exome sequencing to a young woman who experienced extreme developmental regression starting at 2.5 years of age and identified compound heterozygous nonsense mutations in TMPRSS9, which encodes for polyserase-1, a transmembrane serine protease of poorly understood physiological function. Using semiquantitative polymerase chain reaction, we showed that Tmprss9 is expressed in various mouse tissues, including the brain. To study the consequences of TMPRSS9 loss of function on the mammalian brain, we generated a knockout mouse model. Through a battery of behavioral assays, we found that Tmprss9-/- mice showed decreased social interest and social recognition. We observed a borderline recognition memory deficit by novel object recognition in aged Tmprss9-/- female mice, but not in aged Tmprss9-/- male mice or younger adult Tmprss9-/- mice in both sexes. This study provides evidence to suggest that loss of function variants in TMPRSS9 are related to an autism spectrum disorder. However, the identification of more individuals with similar phenotypes and TMPRSS9 loss of function variants is required to establish a robust gene-disease relationship.

%B Hum Mol Genet %V 29 %P 459-470 %8 2020 Feb 01 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/31943016?dopt=Abstract %R 10.1093/hmg/ddz305 %0 Journal Article %J Mol Genet Genomic Med %D 2020 %T Community-based recruitment and exome sequencing indicates high diagnostic yield in adults with intellectual disability. %A Aniko Sabo %A David R Murdock %A Dugan, Shannon %A Meng, Qingchang %A Marie-Claude Gingras %A Jianhong Hu %A Donna M Muzny %A Richard A Gibbs %K Adult %K Exome Sequencing %K Female %K Genetic Testing %K Humans %K Independent Living %K Intellectual Disability %K Male %K Mediator Complex %K Membrane Proteins %K Nuclear Proteins %K Patient Selection %K Sensitivity and Specificity %K Tumor Suppressor Proteins %X

BACKGROUND: Establishing a genetic diagnosis for individuals with intellectual disability (ID) benefits patients and their families as it may inform the prognosis, lead to appropriate therapy, and facilitate access to medical and supportive services. Exome sequencing has been successfully applied in a diagnostic setting, but most clinical exome referrals are pediatric patients, with many adults with ID lacking a comprehensive genetic evaluation.

METHODS: Our unique recruitment strategy involved partnering with service and education providers for individuals with ID. We performed exome sequencing and analysis, and clinical variant interpretation for each recruited family.

RESULTS: All five families enrolled in the study opted-in for the return of genetic results. In three out of five families exome sequencing analysis identified pathogenic or likely pathogenic variants in KANSL1, TUSC3, and MED13L genes. Families discussed the results and any potential medical follow-up in an appointment with a board certified clinical geneticist.

CONCLUSION: Our study suggests high yield of exome sequencing as a diagnostic tool in adult patients with ID who have not undergone comprehensive sequencing-based genetic testing. Research studies including an option of return of results through a genetic clinic could help minimize the disparity in exome diagnostic testing between pediatric and adult patients with ID.

%B Mol Genet Genomic Med %V 8 %P e1439 %8 2020 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/32767738?dopt=Abstract %R 10.1002/mgg3.1439 %0 Journal Article %J mSphere %D 2020 %T Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing. %A Byrd, Doratha A %A Sinha, Rashmi %A Hoffman, Kristi L %A Chen, Jun %A Hua, Xing %A Shi, Jianxin %A Chia, Nicholas %A Petrosino, Joseph %A Vogtmann, Emily %K Adult %K DNA, Bacterial %K Ethanol %K Feces %K Female %K Freezing %K Gastrointestinal Microbiome %K Healthy Volunteers %K Humans %K Male %K Metagenome %K Metagenomics %K Middle Aged %K Preservation, Biological %K RNA, Ribosomal, 16S %K Specimen Handling %K Temperature %K Whole Genome Sequencing %X

Few previous studies have assessed stability and "gold-standard" concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies. A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.

%B mSphere %V 5 %8 2020 Feb 26 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/32250964?dopt=Abstract %R 10.1128/mSphere.00827-19 %0 Journal Article %J Genome Res %D 2020 %T Complex mosaic structural variations in human fetal brains. %A Sekar, Shobana %A Tomasini, Livia %A Proukakis, Christos %A Bae, Taejeong %A Manlove, Logan %A Jang, Yeongjun %A Scuderi, Soraya %A Zhou, Bo %A Kalyva, Maria %A Amiri, Anahita %A Mariani, Jessica %A Fritz J Sedlazeck %A Urban, Alexander E %A Vaccarino, Flora M %A Abyzov, Alexej %K Brain %K Clonal Evolution %K DNA, Circular %K Female %K Genomic Structural Variation %K Genotyping Techniques %K Gestational Age %K Humans %K Mosaicism %K Neurogenesis %K Pregnancy %K Sequence Analysis, DNA %X

Somatic mosaicism, manifesting as single nucleotide variants (SNVs), mobile element insertions, and structural changes in the DNA, is a common phenomenon in human brain cells, with potential functional consequences. Using a clonal approach, we previously detected 200-400 mosaic SNVs per cell in three human fetal brains (15-21 wk postconception). However, structural variation in the human fetal brain has not yet been investigated. Here, we discover and validate four mosaic structural variants (SVs) in the same brains and resolve their precise breakpoints. The SVs were of kilobase scale and complex, consisting of deletion(s) and rearranged genomic fragments, which sometimes originated from different chromosomes. Sequences at the breakpoints of these rearrangements had microhomologies, suggesting their origin from replication errors. One SV was found in two clones, and we timed its origin to ∼14 wk postconception. No large scale mosaic copy number variants (CNVs) were detectable in normal fetal human brains, suggesting that previously reported megabase-scale CNVs in neurons arise at later stages of development. By reanalysis of public single nuclei data from adult brain neurons, we detected an extrachromosomal circular DNA event. Our study reveals the existence of mosaic SVs in the developing human brain, likely arising from cell proliferation during mid-neurogenesis. Although relatively rare compared to SNVs and present in ∼10% of neurons, SVs in developing human brain affect a comparable number of bases in the genome (∼6200 vs. ∼4000 bp), implying that they may have similar functional consequences.

%B Genome Res %V 30 %P 1695-1704 %8 2020 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/33122304?dopt=Abstract %R 10.1101/gr.262667.120 %0 Journal Article %J Genome Res %D 2020 %T Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. %A Aganezov, Sergey %A Goodwin, Sara %A Sherman, Rachel M %A Fritz J Sedlazeck %A Arun, Gayatri %A Bhatia, Sonam %A Lee, Isac %A Kirsche, Melanie %A Wappel, Robert %A Kramer, Melissa %A Kostroff, Karen %A Spector, David L %A Timp, Winston %A McCombie, W Richard %A Schatz, Michael C %K Breast Neoplasms %K Cell Line, Tumor %K DNA Copy Number Variations %K DNA Methylation %K DNA, Neoplasm %K Female %K Genomic Structural Variation %K Humans %K Nanopores %K Organoids %K RNA-Seq %K Whole Genome Sequencing %X

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. We performed whole-genome sequencing of the SKBR3 breast cancer cell line and patient-derived tumor and normal organoids from two breast cancer patients using Illumina/10x Genomics, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT) sequencing. We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble of methods. Our findings show that long-read sequencing allows for substantially more accurate and sensitive SV detection, with between 90% and 95% of variants supported by each long-read technology also supported by the other. We also report high accuracy for long reads even at relatively low coverage (25×-30×). Furthermore, we integrated SV and CNV data into a unifying karyotype-graph structure to present a more accurate representation of the mutated cancer genomes. We find hundreds of variants within known cancer-related genes detectable only through long-read sequencing. These findings highlight the need for long-read sequencing of cancer genomes for the precise analysis of their genetic instability.

%B Genome Res %V 30 %P 1258-1273 %8 2020 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/32887686?dopt=Abstract %R 10.1101/gr.260497.119 %0 Journal Article %J Am J Med Genet A %D 2020 %T Congenital diaphragmatic hernia as a prominent feature of a SPECC1L-related syndrome. %A Wild, K Taylor %A Gordon, Tia %A Bhoj, Elizabeth J %A Du, Haowei %A Jhangiani, Shalini N %A Posey, Jennifer E %A James R Lupski %A Scott, Daryl A %A Zackai, Elaine H %K Abnormalities, Multiple %K Child, Preschool %K Female %K Gestational Age %K Hernias, Diaphragmatic, Congenital %K Humans %K Infant %K Infant, Newborn %K Male %K Mutation, Missense %K Phosphoproteins %K Syndrome %X

Congenital diaphragmatic hernias (CDH) confer substantial morbidity and mortality. Genetic defects, including chromosomal anomalies, copy number variants, and sequence variants are identified in ~30% of patients with CDH. A genetic etiology is not yet found in 70% of patients, however there is a growing number of genetic syndromes and single gene disorders associated with CDH. While there have been two reported individuals with X-linked Opitz G/BBB syndrome with MID1 mutations who have CDH as an associated feature, CDH appears to be a much more prominent feature of a SPECC1L-related autosomal dominant Opitz G/BBB syndrome. Features unique to autosomal dominant Opitz G/BBB syndrome include branchial fistulae, omphalocele, and a bicornuate uterus. Here we present one new individual and five previously reported individuals with CDH found to have SPECC1L mutations. These cases provide strong evidence that SPECC1L is a bona fide CDH gene. We conclude that a SPECC1L-related Opitz G/BBB syndrome should be considered in any patient with CDH who has additional features of hypertelorism, a prominent forehead, a broad nasal bridge, anteverted nares, cleft lip/palate, branchial fistulae, omphalocele, and/or bicornuate uterus.

%B Am J Med Genet A %V 182 %P 2919-2925 %8 2020 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/32954677?dopt=Abstract %R 10.1002/ajmg.a.61878 %0 Journal Article %J PLoS Genet %D 2020 %T Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). %A Brasó-Vives, Marina %A Povolotskaya, Inna S %A Hartasánchez, Diego A %A Farré, Xavier %A Fernandez-Callejo, Marcos %A Raveendran, Muthuswamy %A R. Alan Harris %A Rosene, Douglas L %A Lorente-Galdos, Belen %A Navarro, Arcadi %A Marques-Bonet, Tomas %A Jeffrey Rogers %A Juan, David %K Animals %K Chromosome Mapping %K DNA Copy Number Variations %K Female %K Gene Duplication %K Genetics, Population %K Genome %K High-Throughput Nucleotide Sequencing %K Humans %K Macaca mulatta %K Male %K Open Reading Frames %K Phylogeny %K Sequence Analysis, DNA %K Species Specificity %X

The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources of genomic diversity within and between species and a widely recognized cause of inter-individual differences in disease risk. However, copy number differences among rhesus macaques and between the human and macaque genomes, as well as the relevance of this diversity to research involving this nonhuman primate, remain understudied. Here we present a high-resolution map of sequence copy number for the rhesus macaque genome constructed from a dataset of 198 individuals. Our results show that about one-eighth of the rhesus macaque reference genome is composed of recently duplicated regions, either copy number variable regions or fixed duplications. Comparison with human genomic copy number maps based on previously published data shows that, despite overall similarities in the genome-wide distribution of these regions, there are specific differences at the chromosome level. Some of these create differences in the copy number profile between human disease genes and their rhesus macaque orthologs. Our results highlight the importance of addressing the number of copies of target genes in the design of experiments and cautions against human-centered assumptions in research conducted with model organisms. Overall, we present a genome-wide copy number map from a large sample of rhesus macaque individuals representing an important novel contribution concerning the evolution of copy number in primate genomes.

%B PLoS Genet %V 16 %P e1008742 %8 2020 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/32392208?dopt=Abstract %R 10.1371/journal.pgen.1008742 %0 Journal Article %J BMC Biol %D 2020 %T Correction to: Genome-enabled insights into the biology of thrips as crop pests. %A Rotenberg, Dorith %A Baumann, Aaron A %A Ben-Mahmoud, Sulley %A Christiaens, Olivier %A Dermauw, Wannes %A Ioannidis, Panagiotis %A Jacobs, Chris G C %A Vargas Jentzsch, Iris M %A Oliver, Jonathan E %A Poelchau, Monica F %A Rajarapu, Swapna Priya %A Schneweis, Derek J %A Snoeck, Simon %A Taning, Clauvis N T %A Wei, Dong %A Widana Gamage, Shirani M K %A Hughes, Daniel S T %A Murali, Shwetha C %A Bailey, Samuel T %A Bejerman, Nicolas E %A Holmes, Christopher J %A Jennings, Emily C %A Rosendale, Andrew J %A Rosselot, Andrew %A Hervey, Kaylee %A Schneweis, Brandi A %A Cheng, Sammy %A Childers, Christopher %A Simão, Felipe A %A Dietzgen, Ralf G %A Chao, Hsu %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dugan, Shannon %A Yi Han %A Lee, Sandra L %A Donna M Muzny %A Qu, Jiaxin %A Kim C Worley %A Benoit, Joshua B %A Friedrich, Markus %A Jones, Jeffery W %A Panfilio, Kristen A %A Park, Yoonseong %A Robertson, Hugh M %A Smagghe, Guy %A Ullman, Diane E %A Van der Zee, Maurijn %A Van Leeuwen, Thomas %A Veenstra, Jan A %A Waterhouse, Robert M %A Weirauch, Matthew T %A Werren, John H %A Whitfield, Anna E %A Zdobnov, Evgeny M %A Richard A Gibbs %A Stephen Richards %X

An amendment to this paper has been published and can be accessed via the original article.

%B BMC Biol %V 18 %P 169 %8 2020 Nov 16 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33198778?dopt=Abstract %R 10.1186/s12915-020-00915-z %0 Journal Article %J Mol Psychiatry %D 2020 %T Correction: Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. %A Bis, Joshua C %A Jian, Xueqiu %A Kunkle, Brian W %A Chen, Yuning %A Hamilton-Nelson, Kara L %A Bush, William S %A Salerno, William J %A Lancour, Daniel %A Ma, Yiyi %A Renton, Alan E %A Marcora, Edoardo %A Farrell, John J %A Zhao, Yi %A Qu, Liming %A Ahmad, Shahzad %A Amin, Najaf %A Amouyel, Philippe %A Beecham, Gary W %A Below, Jennifer E %A Campion, Dominique %A Cantwell, Laura %A Charbonnier, Camille %A Chung, Jaeyoon %A Crane, Paul K %A Cruchaga, Carlos %A Cupples, L Adrienne %A Dartigues, Jean-François %A Debette, Stephanie %A Deleuze, Jean-François %A Fulton, Lucinda %A Gabriel, Stacey B %A Genin, Emmanuelle %A Richard A Gibbs %A Goate, Alison %A Grenier-Boley, Benjamin %A Gupta, Namrata %A Haines, Jonathan L %A Havulinna, Aki S %A Helisalmi, Seppo %A Hiltunen, Mikko %A Howrigan, Daniel P %A Ikram, M Arfan %A Kaprio, Jaakko %A Konrad, Jan %A Kuzma, Amanda %A Lander, Eric S %A Lathrop, Mark %A Lehtimäki, Terho %A Lin, Honghuang %A Mattila, Kari %A Mayeux, Richard %A Donna M Muzny %A Nasser, Waleed %A Neale, Benjamin %A Nho, Kwangsik %A Nicolas, Gaël %A Patel, Devanshi %A Pericak-Vance, Margaret A %A Perola, Markus %A Psaty, Bruce M %A Quenez, Olivier %A Rajabli, Farid %A Redon, Richard %A Reitz, Christiane %A Remes, Anne M %A Salomaa, Veikko %A Sarnowski, Chloe %A Schmidt, Helena %A Schmidt, Michael %A Schmidt, Reinhold %A Soininen, Hilkka %A Thornton, Timothy A %A Tosto, Giuseppe %A Tzourio, Christophe %A van der Lee, Sven J %A van Duijn, Cornelia M %A Valladares, Otto %A Vardarajan, Badri %A Wang, Li-San %A Wang, Weixin %A Wijsman, Ellen %A Wilson, Richard K %A Witten, Daniela %A Kim C Worley %A Zhang, Xiaoling %A Bellenguez, Céline %A Lambert, Jean-Charles %A Kurki, Mitja I %A Palotie, Aarno %A Daly, Mark %A Eric Boerwinkle %A Lunetta, Kathryn L %A DeStefano, Anita L %A Dupuis, Josée %A Martin, Eden R %A Schellenberg, Gerard D %A Seshadri, Sudha %A Naj, Adam C %A Fornage, Myriam %A Farrer, Lindsay A %X

A correction to this paper has been published and can be accessed via a link at the top of the paper.

%B Mol Psychiatry %V 25 %P 1901-1903 %8 2020 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/31636380?dopt=Abstract %R 10.1038/s41380-019-0529-7 %0 Journal Article %J eNeurologicalSci %D 2020 %T Corrigendum to 'Association of sickle cell trait with measures of cognitive function and dementia in African Americans' Vol. 16 (2019), 100,201. %A Chen, Nemin %A Caruso, Christina %A Alonso, Alvaro %A Derebail, Vimal K %A Kshirsagar, Abhijit V %A Sharrett, A Richey %A Key, Nigel S %A Gottesman, Rebecca F %A Grove, Megan L %A Bressler, Jan %A Eric Boerwinkle %A Windham, B Gwen %A Mosley, Thomas H %A Hyacinth, Hyacinth I %X

[This corrects the article DOI: 10.1016/j.ensci.2019.100201.].

%B eNeurologicalSci %V 21 %P 100281 %8 2020 Dec %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/33313427?dopt=Abstract %R 10.1016/j.ensci.2020.100281 %0 Journal Article %J Circulation %D 2020 %T Critical Role of Cytosolic DNA and Its Sensing Adaptor STING in Aortic Degeneration, Dissection, and Rupture. %A Luo, Wei %A Wang, Yidan %A Zhang, Lin %A Ren, Pingping %A Zhang, Chen %A Li, Yanming %A Azares, Alon R %A Zhang, Michelle %A Guo, Jiao %A Ghaghada, Ketan B %A Starosolski, Zbigniew A %A Rajapakshe, Kimal %A Coarfa, Cristian %A Yumei Li %A Rui Chen %A Fujiwara, Keigi %A Abe, Jun-Ichi %A Coselli, Joseph S %A Milewicz, Dianna M %A LeMaire, Scott A %A Shen, Ying H %K Animals %K Aortic Dissection %K Aortic Rupture %K Cytosol %K DNA %K Female %K Male %K Membrane Proteins %K Mice %K Mice, Knockout %K Signal Transduction %X

BACKGROUND: Sporadic aortic aneurysm and dissection (AAD), caused by progressive aortic smooth muscle cell (SMC) loss and extracellular matrix degradation, is a highly lethal condition. Identifying mechanisms that drive aortic degeneration is a crucial step in developing an effective pharmacologic treatment to prevent disease progression. Recent evidence has indicated that cytosolic DNA and abnormal activation of the cytosolic DNA sensing adaptor STING (stimulator of interferon genes) play a critical role in vascular inflammation and destruction. Here, we examined the involvement of this mechanism in aortic degeneration and sporadic AAD formation.

METHODS: The presence of cytosolic DNA in aortic cells and activation of the STING pathway were examined in aortic tissues from patients with sporadic ascending thoracic AAD. The role of STING in AAD development was evaluated in -deficient () mice in a sporadic AAD model induced by challenging mice with a combination of a high-fat diet and angiotensin II. We also examined the direct effects of STING on SMC death and macrophage activation in vitro.

RESULTS: In human sporadic AAD tissues, we observed the presence of cytosolic DNA in SMCs and macrophages and significant activation of the STING pathway. In the sporadic AAD model, mice showed significant reductions in challenge-induced aortic enlargement, dissection, and rupture in both the thoracic and abdominal aortic regions. Single-cell transcriptome analysis revealed that aortic challenge in wild-type mice induced the DNA damage response, the inflammatory response, dedifferentiation and cell death in SMCs, and matrix metalloproteinase expression in macrophages. These changes were attenuated in challenged mice. Mechanistically, nuclear and mitochondrial DNA damage in SMCs and the subsequent leak of DNA to the cytosol activated STING signaling, which induced cell death through apoptosis and necroptosis. In addition, DNA from damaged SMCs was engulfed by macrophages in which it activated STING and its target interferon regulatory factor 3, which directly induced matrix metalloproteinase-9 expression. We also found that pharmacologically inhibiting STING activation partially prevented AAD development.

CONCLUSIONS: Our findings indicate that the presence of cytosolic DNA and subsequent activation of cytosolic DNA sensing adaptor STING signaling represent a key mechanism in aortic degeneration and that targeting STING may prevent sporadic AAD development.

%B Circulation %V 141 %P 42-66 %8 2020 Jan 07 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31887080?dopt=Abstract %R 10.1161/CIRCULATIONAHA.119.041460 %0 Journal Article %J Annu Rev Genomics Hum Genet %D 2020 %T Cultivating DNA Sequencing Technology After the Human Genome Project. %A Schloss, Jeffery A %A Richard A Gibbs %A Makhijani, Vinod B %A Marziali, Andre %K Genome, Human %K High-Throughput Nucleotide Sequencing %K Human Genome Project %K Humans %K Sequence Analysis, DNA %X

When the Human Genome Project was completed in 2003, automated Sanger DNA sequencing with fluorescent dye labels was the dominant technology. Several nascent alternative methods based on older ideas that had not been fully developed were the focus of technical researchers and companies. Funding agencies recognized the dynamic nature of technology development and that, beyond the Human Genome Project, there were growing opportunities to deploy DNA sequencing in biological research. Consequently, the National Human Genome Research Institute of the National Institutes of Health created a program-widely known as the Advanced Sequencing Technology Program-that stimulated all stages of development of new DNA sequencing methods, from innovation to advanced manufacturing and production testing, with the goal of reducing the cost of sequencing a human genome first to $100,000 and then to $1,000. The events of this period provide a powerful example of how judicious funding of academic and commercial partners can rapidly advance core technology developments that lead to profound advances across the scientific landscape.

%B Annu Rev Genomics Hum Genet %V 21 %P 117-138 %8 2020 Aug 31 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/32283947?dopt=Abstract %R 10.1146/annurev-genom-111919-082433 %0 Journal Article %J Hum Mutat %D 2020 %T Cytogenetically visible inversions are formed by multiple molecular mechanisms. %A Pettersson, Maria %A Grochowski, Christopher M %A Wincent, Josephine %A Eisfeldt, Jesper %A Breman, Amy M %A Cheung, Sau W %A Krepischi, Ana C V %A Rosenberg, Carla %A James R Lupski %A Ottosson, Jesper %A Lovmar, Lovisa %A Gacic, Jelena %A Lundberg, Elisabeth S %A Nilsson, Daniel %A Carvalho, Claudia M B %A Lindstrand, Anna %K Chromosome Inversion %K Comparative Genomic Hybridization %K DNA End-Joining Repair %K DNA Repair %K Female %K Gene Frequency %K Haplotypes %K Heterozygote %K Homologous Recombination %K Humans %K Karyotyping %K Male %K Pedigree %K Whole Genome Sequencing %X

Cytogenetically detected inversions are generally assumed to be copy number and phenotypically neutral events. While nonallelic homologous recombination is thought to play a major role, recent data suggest the involvement of other molecular mechanisms in inversion formation. Using a combination of short-read whole-genome sequencing (WGS), 10X Genomics Chromium WGS, droplet digital polymerase chain reaction and array comparative genomic hybridization we investigated the genomic structure of 18 large unique cytogenetically detected chromosomal inversions and achieved nucleotide resolution of at least one chromosomal inversion junction for 13/18 (72%). Surprisingly, we observed that seemingly copy number neutral inversions can be accompanied by a copy-number gain of up to 350 kb and local genomic complexities (3/18, 17%). In the resolved inversions, the mutational signatures are consistent with nonhomologous end-joining (8/13, 62%) or microhomology-mediated break-induced replication (5/13, 38%). Our study indicates that short-read 30x coverage WGS can detect a substantial fraction of chromosomal inversions. Moreover, replication-based mechanisms are responsible for approximately 38% of those events leading to a significant proportion of inversions that are actually accompanied by additional copy-number variation potentially contributing to the overall phenotypic presentation of those patients.

%B Hum Mutat %V 41 %P 1979-1998 %8 2020 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/32906200?dopt=Abstract %R 10.1002/humu.24106 %0 Journal Article %J BMC Ophthalmol %D 2019 %T A case report of two siblings with Alstrom syndrome without hearing loss associated with two new ALMS1 variants. %A Shurygina, Maria F %A Parker, Maria A %A Schlechter, Catie L %A Rui Chen %A Yumei Li %A Weleber, Richard G %A Yang, Paul %A Pennesi, Mark E %K Adult %K Alstrom Syndrome %K Cell Cycle Proteins %K Humans %K Male %K Mutation %K Retinal Degeneration %K Siblings %K Young Adult %X

BACKGROUND: Alström syndrome (AS) is a rare monogenic disorder characterized by progressive multi-organ pathology including retinal degeneration, hearing impairment and type 2 diabetes. Here we present clinical features in two siblings diagnosed with Alström syndrome associated with two novel changes in ALMS1.

CASE PRESENTATION: Two siblings originally diagnosed as having achromatopsia presented with mild light sensitivity, nonspecific otitis media, and mild developmental delay during the first decade of life with a relatively stable ocular appearance during second decade, late onset of nystagmus and dyschromatopsia (after 20 years) and preserved vision during the third decade of life. One sibling had late onset hearing loss and both siblings had symmetric high myopia, normal stature, and ptosis. Clinical findings revealed structural and functional tests consistent with a cone-rod dystrophy. Novel variants c.9894dupC (p.S3298 fs) and c.10769delC (p.T3590 fs) in ALMS1 gene were found.

CONCLUSIONS: Two North American siblings who presented with a mild clinical phenotype of Alström syndrome were found to have novel mutations in ALMS1. These two frame-shift mutations segregated with the disease phenotype lending evidence to their pathogenicity.

%B BMC Ophthalmol %V 19 %P 246 %8 2019 Dec 07 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31810438?dopt=Abstract %R 10.1186/s12886-019-1259-y %0 Journal Article %J Genet Med %D 2019 %T Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. %A Bo Yuan %A Neira, Juanita %A Pehlivan, Davut %A Santiago-Sim, Teresa %A Song, Xiaofei %A Rosenfeld, Jill %A Posey, Jennifer E %A Patel, Vipulkumar %A Jin, Weihong %A Adam, Margaret P %A Baple, Emma L %A Dean, John %A Fong, Chin-To %A Hickey, Scott E %A Hudgins, Louanne %A Leon, Eyby %A Madan-Khetarpal, Suneeta %A Rawlins, Lettie %A Rustad, Cecilie F %A Stray-Pedersen, Asbjørg %A Tveten, Kristian %A Wenger, Olivia %A Diaz, Jullianne %A Jenkins, Laura %A Martin, Laura %A McGuire, Marianne %A Pietryga, Marguerite %A Ramsdell, Linda %A Slattery, Leah %A Abid, Farida %A Bertuch, Alison A %A Grange, Dorothy %A Immken, Ladonna %A Schaaf, Christian P %A Van Esch, Hilde %A Bi, Weimin %A Cheung, Sau Wai %A Breman, Amy M %A Smith, Janice L %A Shaw, Chad %A Crosby, Andrew H %A Christine M Eng %A Yang, Yaping %A James R Lupski %A Xiao, Rui %A Liu, Pengfei %K Adolescent %K Alleles %K Antigens, Nuclear %K Biological Variation, Population %K Carrier Proteins %K Cell Cycle Proteins %K Child %K Child, Preschool %K Chromosomal Proteins, Non-Histone %K Cohort Studies %K De Lange Syndrome %K Exome %K Female %K Gene Frequency %K Genetic Heterogeneity %K Humans %K INDEL Mutation %K Male %K Mutation %K Nuclear Proteins %K Phenotype %K Polymorphism, Single Nucleotide %K Proto-Oncogene Proteins %K Retrospective Studies %K Whole Exome Sequencing %X

PURPOSE: Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective.

METHODS: We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization.

RESULTS: Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS.

CONCLUSION: CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.

%B Genet Med %V 21 %P 663-675 %8 2019 03 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/30158690?dopt=Abstract %R 10.1038/s41436-018-0085-6 %0 Journal Article %J Sci Adv %D 2019 %T The comparative genomics and complex population history of baboons. %A Jeffrey Rogers %A Raveendran, Muthuswamy %A R. Alan Harris %A Mailund, Thomas %A Leppälä, Kalle %A Athanasiadis, Georgios %A Schierup, Mikkel Heide %A Cheng, Jade %A Munch, Kasper %A Walker, Jerilyn A %A Konkel, Miriam K %A Jordan, Vallmer %A Steely, Cody J %A Beckstrom, Thomas O %A Bergey, Christina %A Burrell, Andrew %A Schrempf, Dominik %A Noll, Angela %A Kothe, Maximillian %A Kopp, Gisela H %A Liu, Yue %A Murali, Shwetha %A Billis, Konstantinos %A Martin, Fergal J %A Muffato, Matthieu %A Cox, Laura %A Else, James %A Disotell, Todd %A Donna M Muzny %A Phillips-Conroy, Jane %A Aken, Bronwen %A Eichler, Evan E %A Marques-Bonet, Tomas %A Kosiol, Carolin %A Batzer, Mark A %A Hahn, Matthew W %A Tung, Jenny %A Zinner, Dietmar %A Roos, Christian %A Jolly, Clifford J %A Richard A Gibbs %A Kim C Worley %K Animals %K Base Sequence %K Biological Evolution %K Female %K Gene Flow %K Genomics %K Haplotypes %K Humans %K Hybridization, Genetic %K Male %K Papio %K Phylogeny %K Polymorphism, Genetic %K Whole Genome Sequencing %X

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus ) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon () and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

%B Sci Adv %V 5 %P eaau6947 %8 2019 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30854422?dopt=Abstract %R 10.1126/sciadv.aau6947 %0 Journal Article %J Am J Hum Genet %D 2019 %T Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. %A Karolak, Justyna A %A Vincent, Marie %A Deutsch, Gail %A Gambin, Tomasz %A Cogné, Benjamin %A Pichon, Olivier %A Vetrini, Francesco %A Mefford, Heather C %A Dines, Jennifer N %A Golden-Grant, Katie %A Dipple, Katrina %A Freed, Amanda S %A Leppig, Kathleen A %A Dishop, Megan %A Mowat, David %A Bennetts, Bruce %A Gifford, Andrew J %A Weber, Martin A %A Lee, Anna F %A Boerkoel, Cornelius F %A Bartell, Tina M %A Ward-Melver, Catherine %A Besnard, Thomas %A Petit, Florence %A Bache, Iben %A Tümer, Zeynep %A Denis-Musquer, Marie %A Joubert, Madeleine %A Martinovic, Jelena %A Bénéteau, Claire %A Molin, Arnaud %A Carles, Dominique %A André, Gwenaelle %A Bieth, Eric %A Chassaing, Nicolas %A Devisme, Louise %A Chalabreysse, Lara %A Pasquier, Laurent %A Secq, Véronique %A Don, Massimiliano %A Orsaria, Maria %A Missirian, Chantal %A Mortreux, Jérémie %A Sanlaville, Damien %A Pons, Linda %A Küry, Sébastien %A Bézieau, Stéphane %A Liet, Jean-Michel %A Joram, Nicolas %A Bihouée, Tiphaine %A Scott, Daryl A %A Brown, Chester W %A Scaglia, Fernando %A Tsai, Anne Chun-Hui %A Grange, Dorothy K %A Phillips, John A %A Pfotenhauer, Jean P %A Jhangiani, Shalini N %A Gonzaga-Jauregui, Claudia G %A Chung, Wendy K %A Schauer, Galen M %A Lipson, Mark H %A Mercer, Catherine L %A van Haeringen, Arie %A Liu, Qian %A Popek, Edwina %A Coban Akdemir, Zeynep H %A James R Lupski %A Szafranski, Przemyslaw %A Isidor, Bertrand %A Le Caignec, Cedric %A Stankiewicz, Paweł %K DNA Copy Number Variations %K Female %K Fibroblast Growth Factor 10 %K Gene Expression Regulation %K Gestational Age %K Humans %K Infant, Newborn %K Infant, Newborn, Diseases %K Lung %K Lung Diseases %K Male %K Maternal Inheritance %K Organogenesis %K Paternal Inheritance %K Pedigree %K Polymorphism, Single Nucleotide %K Receptor, Fibroblast Growth Factor, Type 2 %K Signal Transduction %K T-Box Domain Proteins %X

Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping ∼2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmonary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung.

%B Am J Hum Genet %V 104 %P 213-228 %8 2019 Feb 07 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/30639323?dopt=Abstract %R 10.1016/j.ajhg.2018.12.010 %0 Journal Article %J Am J Epidemiol %D 2019 %T The Consortium of Metabolomics Studies (COMETS): Metabolomics in 47 Prospective Cohort Studies. %A Yu, Bing %A Zanetti, Krista A %A Temprosa, Marinella %A Albanes, Demetrius %A Appel, Nathan %A Barrera, Clara Barrios %A Ben-Shlomo, Yoav %A Eric Boerwinkle %A Casas, Juan P %A Clish, Clary %A Dale, Caroline %A Dehghan, Abbas %A Derkach, Andriy %A Eliassen, A Heather %A Elliott, Paul %A Fahy, Eoin %A Gieger, Christian %A Gunter, Marc J %A Harada, Sei %A Harris, Tamara %A Herr, Deron R %A Herrington, David %A Hirschhorn, Joel N %A Hoover, Elise %A Hsing, Ann W %A Johansson, Mattias %A Kelly, Rachel S %A Khoo, Chin Meng %A Kivimaki, Mika %A Kristal, Bruce S %A Langenberg, Claudia %A Lasky-Su, Jessica %A Lawlor, Deborah A %A Lotta, Luca A %A Mangino, Massimo %A Le Marchand, Loïc %A Mathé, Ewy %A Matthews, Charles E %A Menni, Cristina %A Mucci, Lorelei A %A Murphy, Rachel %A Oresic, Matej %A Orwoll, Eric %A Ose, Jennifer %A Pereira, Alexandre C %A Playdon, Mary C %A Poston, Lucilla %A Price, Jackie %A Qi, Qibin %A Rexrode, Kathryn %A Risch, Adam %A Sampson, Joshua %A Seow, Wei Jie %A Sesso, Howard D %A Shah, Svati H %A Shu, Xiao-Ou %A Smith, Gordon C S %A Sovio, Ulla %A Stevens, Victoria L %A Stolzenberg-Solomon, Rachael %A Takebayashi, Toru %A Tillin, Therese %A Travis, Ruth %A Tzoulaki, Ioanna %A Ulrich, Cornelia M %A Vasan, Ramachandran S %A Verma, Mukesh %A Wang, Ying %A Wareham, Nick J %A Wong, Andrew %A Younes, Naji %A Zhao, Hua %A Zheng, Wei %A Moore, Steven C %K Adolescent %K Adult %K Aged %K Aged, 80 and over %K Biomarkers %K Body Mass Index %K Child %K Epidemiologic Methods %K Epidemiology %K Female %K Global Health %K Health Behavior %K Hematologic Tests %K Humans %K Longitudinal Studies %K Male %K Metabolomics %K Middle Aged %K Prospective Studies %K Socioeconomic Factors %K Young Adult %X

The Consortium of Metabolomics Studies (COMETS) was established in 2014 to facilitate large-scale collaborative research on the human metabolome and its relationship with disease etiology, diagnosis, and prognosis. COMETS comprises 47 cohorts from Asia, Europe, North America, and South America that together include more than 136,000 participants with blood metabolomics data on samples collected from 1985 to 2017. Metabolomics data were provided by 17 different platforms, with the most frequently used labs being Metabolon, Inc. (14 cohorts), the Broad Institute (15 cohorts), and Nightingale Health (11 cohorts). Participants have been followed for a median of 23 years for health outcomes including death, cancer, cardiovascular disease, diabetes, and others; many of the studies are ongoing. Available exposure-related data include common clinical measurements and behavioral factors, as well as genome-wide genotype data. Two feasibility studies were conducted to evaluate the comparability of metabolomics platforms used by COMETS cohorts. The first study showed that the overlap between any 2 different laboratories ranged from 6 to 121 metabolites at 5 leading laboratories. The second study showed that the median Spearman correlation comparing 111 overlapping metabolites captured by Metabolon and the Broad Institute was 0.79 (interquartile range, 0.56-0.89).

%B Am J Epidemiol %V 188 %P 991-1012 %8 2019 Jun 01 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/31155658?dopt=Abstract %R 10.1093/aje/kwz028 %0 Journal Article %J Genome Med %D 2019 %T Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. %A Dharmadhikari, Avinash V %A Ghosh, Rajarshi %A Bo Yuan %A Liu, Pengfei %A Dai, Hongzheng %A Al Masri, Sami %A Scull, Jennifer %A Posey, Jennifer E %A Jiang, Allen H %A He, Weimin %A Vetrini, Francesco %A Braxton, Alicia A %A Ward, Patricia %A Chiang, Theodore %A Qu, Chunjing %A Gu, Shen %A Shaw, Chad A %A Smith, Janice L %A Lalani, Seema %A Stankiewicz, Pawel %A Cheung, Sau-Wai %A Bacino, Carlos A %A Patel, Ankita %A Breman, Amy M %A Wang, Xia %A Meng, Linyan %A Xiao, Rui %A Xia, Fan %A Donna M Muzny %A Richard A Gibbs %A Beaudet, Arthur L %A Eng, Christine M %A James R Lupski %A Yang, Yaping %A Bi, Weimin %K Chromosome Aberrations %K DNA Copy Number Variations %K Exome Sequencing %K Female %K Genetic Testing %K Homozygote %K Humans %K Limit of Detection %K Male %K Microarray Analysis %X

BACKGROUND: Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES.

METHODS: In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array.

RESULTS: The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities.

CONCLUSIONS: Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations.

%B Genome Med %V 11 %P 30 %8 2019 May 17 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31101064?dopt=Abstract %R 10.1186/s13073-019-0639-5 %0 Journal Article %J Genome Med %D 2019 %T Correction to: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. %A Vetrini, Francesco %A McKee, Shane %A Rosenfeld, Jill A %A Suri, Mohnish %A Lewis, Andrea M %A Nugent, Kimberly Margaret %A Roeder, Elizabeth %A Littlejohn, Rebecca O %A Holder, Sue %A Zhu, Wenmiao %A Alaimo, Joseph T %A Graham, Brett %A Harris, Jill M %A Gibson, James B %A Pastore, Matthew %A McBride, Kim L %A Komara, Makanko %A Al-Gazali, Lihadh %A Al Shamsi, Aisha %A Fanning, Elizabeth A %A Wierenga, Klaas J %A Scott, Daryl A %A Ben-Neriah, Ziva %A Meiner, Vardiella %A Cassuto, Hanoch %A Elpeleg, Orly %A Lloyd Holder, J %A Burrage, Lindsay C %A Seaver, Laurie H %A Van Maldergem, Lionel %A Mahida, Sonal %A Soul, Janet S %A Marlatt, Margaret %A Matyakhina, Ludmila %A Vogt, Julie %A Gold, June-Anne %A Park, Soo-Mi %A Varghese, Vinod %A Lampe, Anne K %A Kumar, Ajith %A Lees, Melissa %A Holder-Espinasse, Muriel %A McConnell, Vivienne %A Bernhard, Birgitta %A Blair, Ed %A Harrison, Victoria %A Donna M Muzny %A Richard A Gibbs %A Sarah H Elsea %A Posey, Jennifer E %A Bi, Weimin %A Lalani, Seema %A Xia, Fan %A Yang, Yaping %A Eng, Christine M %A James R Lupski %A Liu, Pengfei %X

It was highlighted that the original article [1] contained a typographical error in the Results section. Subject 17 was incorrectly cited as Subject 1. This Correction article shows the revised statement. The original article has been updated.

%B Genome Med %V 11 %P 16 %8 2019 Mar 25 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30909959?dopt=Abstract %R 10.1186/s13073-019-0630-1 %0 Journal Article %J J Clin Invest %D 2018 %T CD163+ macrophages promote angiogenesis and vascular permeability accompanied by inflammation in atherosclerosis. %A Guo, Liang %A Akahori, Hirokuni %A Harari, Emanuel %A Smith, Samantha L %A Polavarapu, Rohini %A Karmali, Vinit %A Otsuka, Fumiyuki %A Gannon, Rachel L %A Braumann, Ryan E %A Dickinson, Megan H %A Gupta, Anuj %A Jenkins, Audrey L %A Lipinski, Michael J %A Kim, Johoon %A Chhour, Peter %A de Vries, Paul S %A Jinnouchi, Hiroyuki %A Kutys, Robert %A Mori, Hiroyoshi %A Kutyna, Matthew D %A Torii, Sho %A Sakamoto, Atsushi %A Choi, Cheol Ung %A Cheng, Qi %A Grove, Megan L %A Sawan, Mariem A %A Zhang, Yin %A Cao, Yihai %A Kolodgie, Frank D %A Cormode, David P %A Arking, Dan E %A Boerwinkle, Eric %A Morrison, Alanna C %A Erdmann, Jeanette %A Sotoodehnia, Nona %A Virmani, Renu %A Finn, Aloke V %K Adult %K Animals %K Antigens, CD %K Antigens, Differentiation, Myelomonocytic %K Atherosclerosis %K Coronary Disease %K Coronary Vessels %K Disease Progression %K Female %K Hemoglobins %K Humans %K Inflammation %K Macrophages %K Male %K Mice %K Mice, Inbred C57BL %K Middle Aged %K Myocardial Infarction %K Neovascularization, Pathologic %K Oxidative Stress %K Permeability %K Phenotype %K Polymorphism, Single Nucleotide %K Receptors, Cell Surface %K Signal Transduction %X

Intake of hemoglobin by the hemoglobin-haptoglobin receptor CD163 leads to a distinct alternative non-foam cell antiinflammatory macrophage phenotype that was previously considered atheroprotective. Here, we reveal an unexpected but important pathogenic role for these macrophages in atherosclerosis. Using human atherosclerotic samples, cultured cells, and a mouse model of advanced atherosclerosis, we investigated the role of intraplaque hemorrhage on macrophage function with respect to angiogenesis, vascular permeability, inflammation, and plaque progression. In human atherosclerotic lesions, CD163+ macrophages were associated with plaque progression, microvascularity, and a high level of HIF1α and VEGF-A expression. We observed irregular vascular endothelial cadherin in intraplaque microvessels surrounded by CD163+ macrophages. Within these cells, activation of HIF1α via inhibition of prolyl hydroxylases promoted VEGF-mediated increases in intraplaque angiogenesis, vascular permeability, and inflammatory cell recruitment. CD163+ macrophages increased intraplaque endothelial VCAM expression and plaque inflammation. Subjects with homozygous minor alleles of the SNP rs7136716 had elevated microvessel density, increased expression of CD163 in ruptured coronary plaques, and a higher risk of myocardial infarction and coronary heart disease in population cohorts. Thus, our findings highlight a nonlipid-driven mechanism by which alternative macrophages promote plaque angiogenesis, leakiness, inflammation, and progression via the CD163/HIF1α/VEGF-A pathway.

%B J Clin Invest %V 128 %P 1106-1124 %8 2018 Mar 01 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/29457790?dopt=Abstract %R 10.1172/JCI93025 %0 Journal Article %J Diagn Microbiol Infect Dis %D 2018 %T Challenges of Francisella classification exemplified by an atypical clinical isolate. %A Matz, L M %A Kamdar, K Y %A Holder, M E %A Metcalf, G A %A Weissenberger, G M %A Meng, Q %A Vee, V %A Han, Y %A Muzny, D M %A Gibbs, R A %A Johnson, C L %A Revell, P A %A Petrosino, J F %K Child %K DNA, Bacterial %K Francisella %K Genes, Bacterial %K Genetic Variation %K Genome, Bacterial %K Genotype %K Humans %K Lymph Nodes %K Male %K Oxidoreductases %K Sequence Analysis, DNA %K Tularemia %K Virulence Factors %K Whole Genome Sequencing %X

The accumulation of sequenced Francisella strains has made it increasingly apparent that the 16S rRNA gene alone is not enough to stratify the Francisella genus into precise and clinically useful classifications. Continued whole-genome sequencing of isolates will provide a larger base of knowledge for targeted approaches with broad applicability. Additionally, examination of genomic information on a case-by-case basis will help resolve outstanding questions regarding strain stratification. We report the complete genome sequence of a clinical isolate, designated here as F. novicida-like strain TCH2015, acquired from the lymph node of a 6-year-old male. Two features were atypical for F. novicida: exhibition of functional oxidase activity and additional gene content, including proposed virulence determinants. These differences, which could potentially impact virulence and clinical diagnosis, emphasize the need for more comprehensive methods to profile Francisella isolates. This study highlights the value of whole-genome sequencing, which will lead to a more robust database of environmental and clinical genomes and inform strategies to improve detection and classification of Francisella strains.

%B Diagn Microbiol Infect Dis %V 90 %P 241-247 %8 2018 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/29329757?dopt=Abstract %R 10.1016/j.diagmicrobio.2017.11.023 %0 Journal Article %J J Immunother Cancer %D 2018 %T Change in Neutrophil-to-lymphocyte ratio (NLR) in response to immune checkpoint blockade for metastatic renal cell carcinoma. %A Lalani, Aly-Khan A %A Xie, Wanling %A Martini, Dylan J %A Steinharter, John A %A Norton, Craig K %A Krajewski, Katherine M %A Duquette, Audrey %A Bossé, Dominick %A Bellmunt, Joaquim %A Van Allen, Eliezer M %A McGregor, Bradley A %A Creighton, Chad J %A Harshman, Lauren C %A Choueiri, Toni K %K Adult %K Aged %K Aged, 80 and over %K Antineoplastic Agents, Immunological %K B7-H1 Antigen %K Carcinoma, Renal Cell %K Female %K Humans %K Kidney Neoplasms %K Lymphocytes %K Male %K Middle Aged %K Neutrophils %K Programmed Cell Death 1 Receptor %K Survival Analysis %K Treatment Outcome %K Young Adult %X

BACKGROUND: An elevated Neutrophil-to-lymphocyte ratio (NLR) is associated with worse outcomes in several malignancies. However, its role with contemporary immune checkpoint blockade (ICB) is unknown. We investigated the utility of NLR in metastatic renal cell carcinoma (mRCC) patients treated with PD-1/PD-L1 ICB.

METHODS: We examined NLR at baseline and 6 (±2) weeks later in 142 patients treated between 2009 and 2017 at Dana-Farber Cancer Institute (Boston, USA). Landmark analysis at 6 weeks was conducted to explore the prognostic value of relative NLR change on overall survival (OS), progression-free survival (PFS), and objective response rate (ORR). Cox and logistic regression models allowed for adjustment of line of therapy, number of IMDC risk factors, histology and baseline NLR.

RESULTS: Median follow up was 16.6 months (range: 0.7-67.8). Median duration on therapy was 5.1 months (<1-61.4). IMDC risk groups were: 18% favorable, 60% intermediate, 23% poor-risk. Forty-four percent were on first-line ICB and 56% on 2nd line or more. Median NLR was 3.9 (1.3-42.4) at baseline and 4.1 (1.1-96.4) at week 6. Patients with a higher baseline NLR showed a trend toward lower ORR, shorter PFS, and shorter OS. Higher NLR at 6 weeks was a significantly stronger predictor of all three outcomes than baseline NLR. Relative NLR change by ≥25% from baseline to 6 weeks after ICB therapy was associated with reduced ORR and an independent prognostic factor for PFS (p < 0.001) and OS (p = 0.004), whereas a decrease in NLR by ≥25% was associated with improved outcomes.

CONCLUSIONS: Early decline and NLR at 6 weeks are associated with significantly improved outcomes in mRCC patients treated with ICB. The prognostic value of the readily-available NLR warrants larger, prospective validation.

%B J Immunother Cancer %V 6 %P 5 %8 2018 Jan 22 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29353553?dopt=Abstract %R 10.1186/s40425-018-0315-0 %0 Journal Article %J mSystems %D 2018 %T Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes. %A Tsukayama, Pablo %A Boolchandani, Manish %A Patel, Sanket %A Pehrsson, Erica C %A Gibson, Molly K %A Chiou, Kenneth L %A Jolly, Clifford J %A Jeffrey Rogers %A Phillips-Conroy, Jane E %A Dantas, Gautam %X

Environmental microbes have harbored the capacity for antibiotic production for millions of years, spanning the evolution of humans and other vertebrates. However, the industrial-scale use of antibiotics in clinical and agricultural practice over the past century has led to a substantial increase in exposure of these agents to human and environmental microbiota. This perturbation is predicted to alter the ecology of microbial communities and to promote the evolution and transfer of antibiotic resistance (AR) genes. We studied wild and captive baboon populations to understand the effects of exposure to humans and human activities (e.g., antibiotic therapy) on the composition of the primate fecal microbiota and the antibiotic-resistant genes that it collectively harbors (the "resistome"). Using a culture-independent metagenomic approach, we identified functional antibiotic resistance genes in the gut microbiota of wild and captive baboon groups and saw marked variation in microbiota architecture and resistomes across habitats and lifeways. Our results support the view that antibiotic resistance is an ancient feature of gut microbial communities and that sharing habitats with humans may have important effects on the structure and function of the primate microbiota. Antibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the effect of human exposure and to understand how the primate microbiota may have been altered during the antibiotic era. We used culture-independent and bioinformatics methods to identify functional resistance genes in the guts of wild and captive baboons and show that exposure to humans is associated with changes in microbiota composition and resistome expansion compared to wild baboon groups. Our results suggest that captivity and lifestyle changes associated with human contact can lead to marked changes in the ecology of primate gut communities.

%B mSystems %V 3 %8 2018 May-Jun %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/29963641?dopt=Abstract %R 10.1128/mSystems.00016-18 %0 Journal Article %J Genet Med %D 2018 %T Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. %A Sanghvi, Rashesh V %A Buhay, Christian J %A Powell, Bradford C %A Tsai, Ellen A %A Dorschner, Michael O %A Hong, Celine S %A Lebo, Matthew S %A Sasson, Ariella %A Hanna, David S %A McGee, Sean %A Bowling, Kevin M %A Cooper, Gregory M %A Gray, David E %A Lonigro, Robert J %A Dunford, Andrew %A Brennan, Christine A %A Cibulskis, Carrie %A Walker, Kimberly %A Carneiro, Mauricio O %A Sailsbery, Joshua %A Hindorff, Lucia A %A Robinson, Dan R %A Santani, Avni %A Sarmady, Mahdi %A Rehm, Heidi L %A Biesecker, Leslie G %A Nickerson, Deborah A %A Hutter, Carolyn M %A Garraway, Levi %A Muzny, Donna M %A Wagle, Nikhil %K Base Sequence %K Chromosome Mapping %K Exome %K Exome Sequencing %K Genome, Human %K High-Throughput Nucleotide Sequencing %K Humans %K Sequence Analysis, DNA %K Software %K Whole Genome Sequencing %X

PURPOSE: As massively parallel sequencing is increasingly being used for clinical decision making, it has become critical to understand parameters that affect sequencing quality and to establish methods for measuring and reporting clinical sequencing standards. In this report, we propose a definition for reduced coverage regions and describe a set of standards for variant calling in clinical sequencing applications.

METHODS: To enable sequencing centers to assess the regions of poor sequencing quality in their own data, we optimized and used a tool (ExCID) to identify reduced coverage loci within genes or regions of particular interest. We used this framework to examine sequencing data from 500 patients generated in 10 projects at sequencing centers in the National Human Genome Research Institute/National Cancer Institute Clinical Sequencing Exploratory Research Consortium.

RESULTS: This approach identified reduced coverage regions in clinically relevant genes, including known clinically relevant loci that were uniquely missed at individual centers, in multiple centers, and in all centers.

CONCLUSION: This report provides a process road map for clinical sequencing centers looking to perform similar analyses on their data.

%B Genet Med %V 20 %P 855-866 %8 2018 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/29144510?dopt=Abstract %R 10.1038/gim.2017.192 %0 Journal Article %J Expert Rev Anticancer Ther %D 2018 %T The clinical applications of The Cancer Genome Atlas project for bladder cancer. %A Creighton, Chad J %K Gene Expression Regulation, Neoplastic %K Genome, Human %K Genomics %K Humans %K Precision Medicine %K Urinary Bladder Neoplasms %X

Knowledge of the molecular subtypes of bladder cancer enables powerful generalizations involving the distinctive biology and pathways driving different disease subsets. Areas covered: In this review, we summarize the findings of a number of published studies exploring the molecular landscape of bladder cancer by analysis of genomic data from The Cancer Genome Atlas (TCGA). TCGA project has provided a comprehensive data resource of 412 muscle-invasive bladder cancers as characterized by multiple molecular analytical platforms. These data have been and will continue to be utilized in numerous subsequent studies aimed at better understanding the molecular basis of bladder cancer. The catalog of DNA-level alterations can greatly inform personalized and precision medicine approaches. Molecular subtypes of bladder cancer include distinct 'basal/squamous' and 'luminal' subtypes, cancers with papillary histology, disease subsets with prominent leukocyte infiltration and immune checkpoint marker expression, and a 'neuronal' subtype lacking small cell or neuroendocrine histology. The gene-level alterations and subtypes as revealed by TCGA data are relevant from the standpoint of both basic biology and clinical trial studies. Expert commentary: Multiple studies analyzing TCGA muscle-invasive bladder cancer cases point to the existence of five major expression-based molecular subtypes of the disease, with these subtypes having therapeutic implications.

%B Expert Rev Anticancer Ther %V 18 %P 973-980 %8 2018 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/30081681?dopt=Abstract %R 10.1080/14737140.2018.1508999 %0 Journal Article %J Genome Med %D 2018 %T Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. %A Normand, Elizabeth A %A Braxton, Alicia %A Nassef, Salma %A Ward, Patricia A %A Vetrini, Francesco %A He, Weimin %A Patel, Vipulkumar %A Qu, Chunjing %A Westerfield, Lauren E %A Stover, Samantha %A Dharmadhikari, Avinash V %A Donna M Muzny %A Richard A Gibbs %A Dai, Hongzheng %A Meng, Linyan %A Wang, Xia %A Xiao, Rui %A Liu, Pengfei %A Bi, Weimin %A Xia, Fan %A Walkiewicz, Magdalena %A Van den Veyver, Ignatia B %A Eng, Christine M %A Yang, Yaping %K Exome Sequencing %K Family %K Fetus %K Genetic Diseases, Inborn %K Humans %K Inheritance Patterns %K Phenotype %K Ultrasonography, Prenatal %X

BACKGROUND: Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting.

METHODS: We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive "fetal exomes" performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher's exact test.

RESULTS: Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families.

CONCLUSION: Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis.

%B Genome Med %V 10 %P 74 %8 2018 Sep 28 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30266093?dopt=Abstract %R 10.1186/s13073-018-0582-x %0 Journal Article %J Hum Genet %D 2018 %T The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease. %A Liu, Jiaqi %A Zhou, Yangzhong %A Liu, Sen %A Song, Xiaofei %A Yang, Xin-Zhuang %A Fan, Yanhui %A Chen, Weisheng %A Akdemir, Zeynep Coban %A Yan, Zihui %A Zuo, Yuzhi %A Du, Renqian %A Liu, Zhenlei %A Bo Yuan %A Zhao, Sen %A Liu, Gang %A Chen, Yixin %A Zhao, Yanxue %A Lin, Mao %A Zhu, Qiankun %A Niu, Yuchen %A Liu, Pengfei %A Ikegawa, Shiro %A Song, You-Qiang %A Posey, Jennifer E %A Qiu, Guixing %A Zhang, Feng %A Wu, Zhihong %A James R Lupski %A Wu, Nan %K Adolescent %K Congenital Abnormalities %K DNA Copy Number Variations %K Female %K Genetic Predisposition to Disease %K Genome, Human %K Genome-Wide Association Study %K Genomics %K Genotype %K Haplotypes %K Humans %K Phenotype %K Polymorphism, Single Nucleotide %K Scoliosis %X

With the recent advance in genome-wide association studies (GWAS), disease-associated single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) have been extensively reported. Accordingly, the issue of incorrect identification of recombination events that can induce the distortion of multi-allelic or hemizygous variants has received more attention. However, the potential distorted calculation bias or significance of a detected association in a GWAS due to the coexistence of CNVs and SNPs in the same genomic region may remain under-recognized. Here we performed the association study within a congenital scoliosis (CS) cohort whose genetic etiology was recently elucidated as a compound inheritance model, including mostly one rare variant deletion CNV null allele and one common variant non-coding hypomorphic haplotype of the TBX6 gene. We demonstrated that the existence of a deletion in TBX6 led to an overestimation of the contribution of the SNPs on the hypomorphic allele. Furthermore, we generalized a model to explain the calculation bias, or distorted significance calculation for an association study, that can be 'induced' by CNVs at a locus. Meanwhile, overlapping between the disease-associated SNPs from published GWAS and common CNVs (overlap 10%) and pathogenic/likely pathogenic CNVs (overlap 99.69%) was significantly higher than the random distribution (p < 1 × 10 and p = 0.034, respectively), indicating that such co-existence of CNV and SNV alleles might generally influence data interpretation and potential outcomes of a GWAS. We also verified and assessed the influence of colocalizing CNVs to the detection sensitivity of disease-associated SNP variant alleles in another adolescent idiopathic scoliosis (AIS) genome-wide association study. We proposed that detecting co-existent CNVs when evaluating the association signals between SNPs and disease traits could improve genetic model analyses and better integrate GWAS with robust Mendelian principles.

%B Hum Genet %V 137 %P 553-567 %8 2018 Jul %G eng %N 6-7 %1 https://www.ncbi.nlm.nih.gov/pubmed/30019117?dopt=Abstract %R 10.1007/s00439-018-1910-3 %0 Journal Article %J Circ Genom Precis Med %D 2018 %T Common Coding Variants in Are Associated With the Nav1.8 Late Current and Cardiac Conduction. %A Macri, Vincenzo %A Brody, Jennifer A %A Arking, Dan E %A Hucker, William J %A Yin, Xiaoyan %A Lin, Honghuang %A Mills, Robert W %A Sinner, Moritz F %A Lubitz, Steven A %A Liu, Ching-Ti %A Morrison, Alanna C %A Alonso, Alvaro %A Li, Ning %A Fedorov, Vadim V %A Janssen, Paul M %A Bis, Joshua C %A Heckbert, Susan R %A Dolmatova, Elena V %A Lumley, Thomas %A Sitlani, Colleen M %A Cupples, L Adrienne %A Pulit, Sara L %A Newton-Cheh, Christopher %A Barnard, John %A Smith, Jonathan D %A Van Wagoner, David R %A Chung, Mina K %A Vlahakes, Gus J %A O'Donnell, Christopher J %A Rotter, Jerome I %A Margulies, Kenneth B %A Morley, Michael P %A Cappola, Thomas P %A Benjamin, Emelia J %A Muzny, Donna %A Gibbs, Richard A %A Jackson, Rebecca D %A Magnani, Jared W %A Herndon, Caroline N %A Rich, Stephen S %A Psaty, Bruce M %A Milan, David J %A Boerwinkle, Eric %A Mohler, Peter J %A Sotoodehnia, Nona %A Ellinor, Patrick T %K Biophysical Phenomena %K Electrocardiography %K Genetic Association Studies %K Haplotypes %K Heart Conduction System %K Humans %K Ion Channel Gating %K Mutation, Missense %K NAV1.8 Voltage-Gated Sodium Channel %K Polymorphism, Single Nucleotide %K Quantitative Trait Loci %X

BACKGROUND: Genetic variants at the / locus are strongly associated with electrocardiographic PR and QRS intervals. While is the canonical cardiac sodium channel gene, the role of in cardiac conduction is less well characterized.

METHODS: We sequenced the locus in 3699 European-ancestry individuals to identify variants associated with cardiac conduction, and replicated our findings in 21,000 individuals of European ancestry. We examined association with expression in human atrial tissue. We explored the biophysical effect of variation on channel function using cellular electrophysiology.

RESULTS: We identified 2 intronic single nucleotide polymorphisms in high linkage disequilibrium (  =0.86) with each other to be the strongest signals for PR (rs10428132, β=-4.74, =1.52×10) and QRS intervals (rs6599251, QRS β=-0.73; =1.2×10), respectively. Although these variants were not associated with or expression in human atrial tissue (n=490), they were in high linkage disequilibrium (  ≥0.72) with a common missense variant, rs6795970 (V1073A). In total, we identified 7 missense variants, 4 of which (I962V, P1045T, V1073A, and L1092P) were associated with cardiac conduction. These 4 missense variants cluster in the cytoplasmic linker of the second and third domains of the SCN10A protein and together form 6 common haplotypes. Using cellular electrophysiology, we found that haplotypes associated with shorter PR intervals had a significantly larger percentage of late current compared with wild-type (I962V+V1073A+L1092P, 20.2±3.3%, =0.03, and I962V+V1073A, 22.4±0.8%, =0.0004 versus wild-type 11.7±1.6%), and the haplotype associated with the longest PR interval had a significantly smaller late current percentage (P1045T, 6.4±1.2%, =0.03).

CONCLUSIONS: Our findings suggest an association between genetic variation in , the late sodium current, and alterations in cardiac conduction.

%B Circ Genom Precis Med %V 11 %P e001663 %8 2018 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/29752399?dopt=Abstract %R 10.1161/CIRCGEN.116.001663 %0 Journal Article %J BMC Biol %D 2018 %T Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum. %A Lindsey, Amelia R I %A Kelkar, Yogeshwar D %A Wu, Xin %A Sun, Dan %A Martinson, Ellen O %A Yan, Zhichao %A Rugman-Jones, Paul F %A Hughes, Daniel S T %A Murali, Shwetha C %A Qu, Jiaxin %A Dugan, Shannon %A Lee, Sandra L %A Chao, Hsu %A Dinh, Huyen %A Han, Yi %A Doddapaneni, Harsha Vardhan %A Worley, Kim C %A Muzny, Donna M %A Ye, Gongyin %A Gibbs, Richard A %A Richards, Stephen %A Yi, Soojin V %A Stouthamer, Richard %A Werren, John H %K Animals %K Evolution, Molecular %K Genomics %K Moths %K Pest Control, Biological %K Phylogeny %K Wasps %K Whole Genome Sequencing %X

BACKGROUND: Trichogrammatids are minute parasitoid wasps that develop within other insect eggs. They are less than half a millimeter long, smaller than some protozoans. The Trichogrammatidae are one of the earliest branching families of Chalcidoidea: a diverse superfamily of approximately half a million species of parasitoid wasps, proposed to have evolved from a miniaturized ancestor. Trichogramma are frequently used in agriculture, released as biological control agents against major moth and butterfly pests. Additionally, Trichogramma are well known for their symbiotic bacteria that induce asexual reproduction in infected females. Knowledge of the genome sequence of Trichogramma is a major step towards further understanding its biology and potential applications in pest control.

RESULTS: We report the 195-Mb genome sequence of Trichogramma pretiosum and uncover signatures of miniaturization and adaptation in Trichogramma and related parasitoids. Comparative analyses reveal relatively rapid evolution of proteins involved in ribosome biogenesis and function, transcriptional regulation, and ploidy regulation. Chalcids also show loss or especially rapid evolution of 285 gene clusters conserved in other Hymenoptera, including many that are involved in signal transduction and embryonic development. Comparisons between sexual and asexual lineages of Trichogramma pretiosum reveal that there is no strong evidence for genome degradation (e.g., gene loss) in the asexual lineage, although it does contain a lower repeat content than the sexual lineage. Trichogramma shows particularly rapid genome evolution compared to other hymenopterans. We speculate these changes reflect adaptations to miniaturization, and to life as a specialized egg parasitoid.

CONCLUSIONS: The genomes of Trichogramma and related parasitoids are a valuable resource for future studies of these diverse and economically important insects, including explorations of parasitoid biology, symbiosis, asexuality, biological control, and the evolution of miniaturization. Understanding the molecular determinants of parasitism can also inform mass rearing of Trichogramma and other parasitoids for biological control.

%B BMC Biol %V 16 %P 54 %8 2018 May 18 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29776407?dopt=Abstract %R 10.1186/s12915-018-0520-9 %0 Journal Article %J Am J Primatol %D 2018 %T Comparison of vitamin D metabolites in wild and captive baboons. %A Ziegler, Toni E %A Kapoor, Amita %A Binkley, Neil C %A Rice, Karen S %A Jeffrey Rogers %A Jolly, Clifford J %A Phillips-Conroy, Jane E %K Africa South of the Sahara %K Aging %K Animal Distribution %K Animals %K Animals, Wild %K Animals, Zoo %K Dietary Supplements %K Male %K Papio %K Skin Pigmentation %K Species Specificity %K Vitamin D %K Vitamin D Deficiency %X

Vitamin D adequacy is essential for multiple physiologic processes. With limited exposure to sunlight for vitamin D synthesis, captive primates are supplemented with vitamin D (cholecalciferol). Vitamin D metabolite data from wild primates living indigenously could suggest optimum levels. The purpose of this study was to: 1) to explore whether baboons, a speciose genus whose members have significant exposed skin, coat color variation and wide geographical distribution, mirrors the skin pigmentation-vitamin D relationship found in humans; 2) compare vitamin D metabolite levels in wild and captive members of the same or similar baboon species; and 3) apply a recently developed method currently used in humans for measuring multiple vitamin D metabolites as a panel to explore if/how these metabolites can inform us on vitamin D sufficiency. Serum samples from males of three baboon species in the wild: Papio anubis (olive baboon, dark exposed skin), P. cynocephalus (yellow baboon, brown exposed skin), and P. hamadryas (hamadryas baboon, pink exposed skin), were compared with vitamin D supplemented captive olive baboons with sun exposure. Liquid chromatography/tandem mass spectrometry (LC/MS/MS) measured vitamin D and its main metabolites. Cholecalciferol, 25 hydroxyvitamin D (25(OH)D ), and 24,25 dihydroxyvitamin D (24,25(OH) D ), showed significant differences by species. The levels of cholecalciferol due to supplements in the captive olive baboons did not convert to higher 25(OH)D while the wild olive baboons exhibited the lowest levels for both cholecalciferol and 25(OH)D . Further metabolic conversion of 25(OH)D to 24,25(OH) D indicated that all baboons had more similar conversion ratios and these were within the same range found for humans that are depicted as having adequate vitamin D levels. This study provided evidence that exposed skin color does influence vitamin D3 levels, with lower levels in darker skinned species, but these differences are eliminated in the downstream metabolite conversion indicating strong regulatory control.

%B Am J Primatol %V 80 %P e22935 %8 2018 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/30537386?dopt=Abstract %R 10.1002/ajp.22935 %0 Journal Article %J Genome Res %D 2018 %T Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. %A Nattestad, Maria %A Goodwin, Sara %A Ng, Karen %A Baslan, Timour %A Fritz J Sedlazeck %A Rescheneder, Philipp %A Garvin, Tyler %A Fang, Han %A Gurtowski, James %A Hutton, Elizabeth %A Tseng, Elizabeth %A Chin, Chen-Shan %A Beck, Timothy %A Sundaravadanam, Yogi %A Kramer, Melissa %A Antoniou, Eric %A McPherson, John D %A Hicks, James %A McCombie, W Richard %A Schatz, Michael C %K Breast Neoplasms %K Female %K Gene Amplification %K Gene Rearrangement %K Genome, Human %K Genomic Structural Variation %K High-Throughput Nucleotide Sequencing %K Humans %K MCF-7 Cells %K Oncogenes %K Receptor, ErbB-2 %K Repetitive Sequences, Nucleic Acid %K Transcriptome %X

The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged, although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available, with nearly 20,000 variants present, most of which were missed by short-read sequencing. Surrounding the important oncogene (also known as ), we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the genome and sheds new light on the complex mechanisms involved in cancer genome evolution.

%B Genome Res %V 28 %P 1126-1135 %8 2018 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/29954844?dopt=Abstract %R 10.1101/gr.231100.117 %0 Journal Article %J Cell %D 2018 %T Comprehensive Characterization of Cancer Driver Genes and Mutations. %A Bailey, Matthew H %A Tokheim, Collin %A Porta-Pardo, Eduard %A Sengupta, Sohini %A Bertrand, Denis %A Weerasinghe, Amila %A Colaprico, Antonio %A Wendl, Michael C %A Kim, Jaegil %A Reardon, Brendan %A Ng, Patrick Kwok-Shing %A Jeong, Kang Jin %A Cao, Song %A Wang, Zixing %A Gao, Jianjiong %A Gao, Qingsong %A Wang, Fang %A Liu, Eric Minwei %A Mularoni, Loris %A Rubio-Perez, Carlota %A Nagarajan, Niranjan %A Cortés-Ciriano, Isidro %A Zhou, Daniel Cui %A Liang, Wen-Wei %A Hess, Julian M %A Yellapantula, Venkata D %A Tamborero, David %A Gonzalez-Perez, Abel %A Suphavilai, Chayaporn %A Ko, Jia Yu %A Khurana, Ekta %A Park, Peter J %A Van Allen, Eliezer M %A Liang, Han %A Lawrence, Michael S %A Godzik, Adam %A Lopez-Bigas, Nuria %A Stuart, Josh %A Wheeler, David %A Getz, Gad %A Chen, Ken %A Lazar, Alexander J %A Mills, Gordon B %A Karchin, Rachel %A Ding, Li %K Algorithms %K B7-H1 Antigen %K Computational Biology %K Databases, Genetic %K Entropy %K Humans %K Microsatellite Instability %K Mutation %K Neoplasms %K Principal Component Analysis %K Programmed Cell Death 1 Receptor %X

Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%-85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors.

%B Cell %V 173 %P 371-385.e18 %8 2018 Apr 05 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/29625053?dopt=Abstract %R 10.1016/j.cell.2018.02.060 %0 Journal Article %J Am J Med Genet A %D 2018 %T A comprehensive clinical and genetic study in 127 patients with ID in Kinshasa, DR Congo. %A Lumaka, Aimé %A Race, Valerie %A Peeters, Hilde %A Corveleyn, Anniek %A Coban-Akdemir, Zeynep %A Jhangiani, Shalini N %A Song, Xiaofei %A Mubungu, Gerrye %A Posey, Jennifer %A Lupski, James R %A Vermeesch, Joris R %A Lukusa, Prosper %A Devriendt, Koenraad %K Adolescent %K Adult %K Algorithms %K Child %K Child, Preschool %K Comparative Genomic Hybridization %K Democratic Republic of the Congo %K Developmental Disabilities %K Disease Management %K Exome Sequencing %K Facies %K Female %K Genetic Association Studies %K Genetic Markers %K Genetic Predisposition to Disease %K Genetic Testing %K Homeodomain Proteins %K Humans %K Infant %K Intellectual Disability %K Male %K Phenotype %K Syndrome %K Transcription Factors %K Trinucleotide Repeat Expansion %K Trinucleotide Repeats %K Workflow %K X Chromosome Inactivation %K Young Adult %X

Pathogenic variants account for 4 to 41% of patients with intellectual disability (ID) or developmental delay (DD). In Sub-Saharan Africa, the prevalence of ID is thought to be higher, but data in Central Africa are limited to some case reports. In addition, clinical descriptions of some syndromes are not available for this population. This study aimed at providing an estimate for the fraction of ID/DD for which an underlying etiological genetic cause may be elucidated and provide insights into their clinical presentation in special institutions in a Central African country. A total of 127 patients (33 females and 94 males, mean age 10.03 ± 4.68 years), were recruited from six institutions across Kinshasa. A clinical diagnosis was achieved in 44 but molecular confirmation was achieved in 21 of the 22 patients with expected genetic defect (95% clinical sensitivity). Identified diseases included Down syndrome (15%), submicroscopic copy number variants (9%), aminoacylase deficiency (0.8%), Partington syndrome in one patient (0.8%) and his similarly affected brother, X-linked syndromic Mental Retardation type 33 (0.8%), and two conditions without clear underlying molecular genetic etiologies (Oculo-Auriculo-Vertebral and Amniotic Bands Sequence). We have shown that genetic etiologies, similar to those reported in Caucasian subjects, are a common etiologic cause of ID in African patients from Africa. We have confirmed the diagnostic utility of clinical characterization prior to genetic testing. Finally, our clinical descriptions provide insights into the presentation of these genetic diseases in African patients.

%B Am J Med Genet A %V 176 %P 1897-1909 %8 2018 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/30088852?dopt=Abstract %R 10.1002/ajmg.a.40382 %0 Journal Article %J Eur J Hum Genet %D 2018 %T Comprehensive genomic analysis of patients with disorders of cerebral cortical development. %A Wiszniewski, Wojciech %A Gawlinski, Pawel %A Gambin, Tomasz %A Bekiesinska-Figatowska, Monika %A Obersztyn, Ewa %A Antczak-Marach, Dorota %A Akdemir, Zeynep Hande Coban %A Harel, Tamar %A Karaca, Ender %A Jurek, Marta %A Sobecka, Katarzyna %A Nowakowska, Beata %A Kruk, Malgorzata %A Terczynska, Iwona %A Goszczanska-Ciuchta, Alicja %A Rudzka-Dybala, Mariola %A Jamroz, Ewa %A Pyrkosz, Antoni %A Jakubiuk-Tomaszuk, Anna %A Iwanowski, Piotr %A Gieruszczak-Bialek, Dorota %A Piotrowicz, Malgorzata %A Sasiadek, Maria %A Kochanowska, Iwona %A Gurda, Barbara %A Steinborn, Barbara %A Dawidziuk, Mateusz %A Castaneda, Jennifer %A Wlasienko, Pawel %A Bezniakow, Natalia %A Jhangiani, Shalini N %A Hoffman-Zacharska, Dorota %A Bal, Jerzy %A Szczepanik, Elzbieta %A Boerwinkle, Eric %A Gibbs, Richard A %A Lupski, James R %K Cadherins %K DNA Copy Number Variations %K Exome %K Female %K Genetic Heterogeneity %K Humans %K Male %K Malformations of Cortical Development %K Nerve Tissue Proteins %K Polymorphism, Single Nucleotide %K Receptors, Cell Surface %X

Malformations of cortical development (MCDs) manifest with structural brain anomalies that lead to neurologic sequelae, including epilepsy, cerebral palsy, developmental delay, and intellectual disability. To investigate the underlying genetic architecture of patients with disorders of cerebral cortical development, a cohort of 54 patients demonstrating neuroradiologic signs of MCDs was investigated. Individual genomes were interrogated for single-nucleotide variants (SNV) and copy number variants (CNV) with whole-exome sequencing and chromosomal microarray studies. Variation affecting known MCDs-associated genes was found in 16/54 cases, including 11 patients with SNV, 2 patients with CNV, and 3 patients with both CNV and SNV, at distinct loci. Diagnostic pathogenic SNV and potentially damaging variants of unknown significance (VUS) were identified in two groups of seven individuals each. We demonstrated that de novo variants are important among patients with MCDs as they were identified in 10/16 individuals with a molecular diagnosis. Three patients showed changes in known MCDs genes  and a clinical phenotype beyond the usual characteristics observed, i.e., phenotypic expansion, for a particular known disease gene clinical entity. We also discovered 2 likely candidate genes, CDH4, and ASTN1, with human and animal studies supporting their roles in brain development, and 5 potential candidate genes. Our findings emphasize genetic heterogeneity of MCDs disorders and postulate potential novel candidate genes involved in cerebral cortical development.

%B Eur J Hum Genet %V 26 %P 1121-1131 %8 2018 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/29706646?dopt=Abstract %R 10.1038/s41431-018-0137-z %0 Journal Article %J Cancer Cell %D 2018 %T A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. %A Berger, Ashton C %A Korkut, Anil %A Kanchi, Rupa S %A Hegde, Apurva M %A Lenoir, Walter %A Liu, Wenbin %A Liu, Yuexin %A Fan, Huihui %A Shen, Hui %A Ravikumar, Visweswaran %A Rao, Arvind %A Schultz, Andre %A Li, Xubin %A Sumazin, Pavel %A Williams, Cecilia %A Mestdagh, Pieter %A Gunaratne, Preethi H %A Yau, Christina %A Bowlby, Reanne %A Robertson, A Gordon %A Tiezzi, Daniel G %A Wang, Chen %A Cherniack, Andrew D %A Godwin, Andrew K %A Kuderer, Nicole M %A Rader, Janet S %A Zuna, Rosemary E %A Sood, Anil K %A Lazar, Alexander J %A Ojesina, Akinyemi I %A Adebamowo, Clement %A Adebamowo, Sally N %A Baggerly, Keith A %A Chen, Ting-Wen %A Chiu, Hua-Sheng %A Lefever, Steve %A Liu, Liang %A MacKenzie, Karen %A Orsulic, Sandra %A Roszik, Jason %A Shelley, Carl Simon %A Song, Qianqian %A Vellano, Christopher P %A Wentzensen, Nicolas %A Weinstein, John N %A Mills, Gordon B %A Levine, Douglas A %A Akbani, Rehan %K Breast Neoplasms %K Databases, Genetic %K DNA Copy Number Variations %K Female %K Gene Expression Profiling %K Gene Expression Regulation, Neoplastic %K Gene Regulatory Networks %K Genetic Predisposition to Disease %K Genital Neoplasms, Female %K Humans %K Mutation %K Organ Specificity %K Prognosis %K Receptors, Estrogen %K RNA, Long Noncoding %X

We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.

%B Cancer Cell %V 33 %P 690-705.e9 %8 2018 Apr 09 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/29622464?dopt=Abstract %R 10.1016/j.ccell.2018.03.014 %0 Journal Article %J Exp Eye Res %D 2018 %T Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice. %A Eblimit, Aiden %A Agrawal, Smriti Akshay %A Thomas, Kandace %A Anastassov, Ivan Assenov %A Abulikemu, Tajiguli %A Moayedi, Yalda %A Mardon, Graeme %A Chen, Rui %K Animals %K Cytoskeletal Proteins %K Disease Models, Animal %K DNA-Binding Proteins %K Electroretinography %K Mice %K Mice, Knockout %K Proteins %K Retina %K Retinal Cone Photoreceptor Cells %K Retinal Degeneration %K Retinal Rod Photoreceptor Cells %K Retinitis Pigmentosa %K Rhodopsin %X

The mammalian retina consists of multiple cell layers including photoreceptor cells, which are light sensing neurons that play essential functions in the visual process. Previously, we identified mutations in SPATA7, encoding spermatogenesis associated protein 7, in families with Leber Congenital Amaurosis (LCA) and juvenile Retinitis Pigmentosa (RP), and showed that Spata7 null mice recapitulate the human disease phenotype of retinal degeneration. SPATA7 is expressed in the connecting cilium of photoreceptor (PR) cells in the mouse retina, as well as in retinal pigment epithelium (RPE) cells, but the functional role of Spata7 in the RPE remains unknown. To investigate whether Spata7 is required in PRs, the RPE, or both, we conditionally knocked out Spata7 in photoreceptors and RPE cells using Crx-Cre and Best1-Cre transgenic mouse lines, respectively. In Spata7 photoreceptor-specific conditional (cKO) mice, both rod and cone photoreceptor dysfunction and degeneration is observed, characterized by progressive thinning of the outer nuclear layer and reduced response to light; however, RPE-specific deletion of Spata7 does not impair retinal function or cell survival. Furthermore, our findings show that both Rhodopsin and RPGRIP1 are mislocalized in the Spata7; Crx-Cre cKO mice, suggesting that loss of Spata7 in photoreceptors alone can result in altered trafficking of these proteins in the connecting cilium. Together, our findings suggest that loss of Spata7 in photoreceptors alone is sufficient to cause photoreceptor degeneration, but its function in the RPE is not required for photoreceptor survival; therefore, loss of Spata7 in photoreceptors alters both rod and cone function and survival, consistent with the clinical phenotypes observed in LCA and RP patients with mutations in SPATA7.

%B Exp Eye Res %V 166 %P 120-130 %8 2018 Jan %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/29100828?dopt=Abstract %R 10.1016/j.exer.2017.10.015 %0 Journal Article %J Medicine (Baltimore) %D 2018 %T Contributions of rare coding variants in hypotension syndrome genes to population blood pressure variation. %A Nandakumar, Priyanka %A Morrison, Alanna C %A Grove, Megan L %A Eric Boerwinkle %A Chakravarti, Aravinda %K Black People %K Blood Pressure %K Exome Sequencing %K Female %K Genetic Predisposition to Disease %K Genetic Variation %K Humans %K Hypertension %K Hypotension %K Male %K Middle Aged %K Phenotype %K Potassium Channels, Inwardly Rectifying %K Prospective Studies %K Reproducibility of Results %K Risk Factors %K Solute Carrier Family 12, Member 1 %K Solute Carrier Family 12, Member 3 %K White People %X

Rare variants, in particular renal salt handling genes, contribute to monogenic forms of hypertension and hypotension syndromes with electrolyte abnormalities. A study by Ji et al (2008) demonstrated this effect for rare loss-of-function coding variants in SLC12A3 (NCCT), SLC12A1 (NKCC2), and KCNJ1 (ROMK) that led to reduction of ∼6 mm Hg for SBP and ∼3 mm Hg for DBP among carriers in 2492 European ancestry Framingham Heart Study (FHS) subjects. These findings support a potentially large role for these variants in interindividual variation in systolic and diastolic blood pressure (SBP, DBP) in the population. The present study focuses on replicating the analyses completed by Ji et al to identify effects of rare variants in the population-based Atherosclerosis Risk in Communities (ARIC) study.We attempted to replicate the findings by Ji et al by applying their criteria to identify putative loss-of-function variants with allele frequency <0.001 and complete conservation across a set of orthologs, to exome sequencing data from 7444 European ancestry participants of the ARIC study.Although we failed to replicate the previous findings when applying their methods to the ARIC study data, we observed a similar effect when we restricted analyses to the subset of variants they observed.These results simultaneously support the utility of exome sequencing data for studying extremely rare coding variants in hypertension and underscore the need for improved filtering methods for identifying functional variants in human sequences.

%B Medicine (Baltimore) %V 97 %P e11865 %8 2018 Aug %G eng %N 33 %1 https://www.ncbi.nlm.nih.gov/pubmed/30113482?dopt=Abstract %R 10.1097/MD.0000000000011865 %0 Journal Article %J Exp Eye Res %D 2018 %T Corrigendum to "Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice" [Exp. Eye Res. 166 (2018) 120-130]. %A Eblimit, A %A Agrawal, S A %A Thomas, K %A Anastassov, I A %A Abulikemu, T %A Moayedi, Y %A Mardon, G %A Chen, R %B Exp Eye Res %V 171 %P 119 %8 2018 Jun %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/29579643?dopt=Abstract %R 10.1016/j.exer.2018.03.011 %0 Journal Article %J Hum Mutat %D 2017 %T Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. %A Chen, Yiyun %A Bartanus, Justin %A Liang, Desheng %A Zhu, Hongmin %A Breman, Amy M %A Smith, Janice L %A Wang, Hua %A Ren, Zhilin %A Patel, Ankita %A Stankiewicz, Pawel %A Cram, David S %A Cheung, Sau Wai %A Wu, Lingqian %A Yu, Fuli %K Animals %K Chromosome Aberrations %K Chromosome Disorders %K DNA Copy Number Variations %K Embryonic Development %K Female %K Genome, Human %K Humans %K Mice %K Microarray Analysis %K Pregnancy %K Transcription Factors %K Zebrafish %X

Detailed characterization of chromosomal abnormalities, a common cause for congenital abnormalities and pregnancy loss, is critical for elucidating genes for human fetal development. Here, 2,186 product-of-conception samples were tested for copy-number variations (CNVs) at two clinical diagnostic centers using whole-genome sequencing and high-resolution chromosomal microarray analysis. We developed a new gene discovery approach to predict potential developmental genes and identified 275 candidate genes from CNVs detected from both datasets. Based on Mouse Genome Informatics (MGI) and Zebrafish model organism database (ZFIN), 75% of identified genes could lead to developmental defects when mutated. Genes involved in embryonic development, gene transcription, and regulation of biological processes were significantly enriched. Especially, transcription factors and gene families sharing specific protein domains predominated, which included known developmental genes such as HOX, NKX homeodomain genes, and helix-loop-helix containing HAND2, NEUROG2, and NEUROD1 as well as potential novel developmental genes. We observed that developmental genes were denser in certain chromosomal regions, enabling identification of 31 potential genomic loci with clustered genes associated with development.

%B Hum Mutat %V 38 %P 669-677 %8 2017 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/28247551?dopt=Abstract %R 10.1002/humu.23207 %0 Journal Article %J J Child Adolesc Psychopharmacol %D 2017 %T CHRNA7 Deletions are Enriched in Risperidone-Treated Children and Adolescents. %A Gillentine, Madelyn A %A White, Janson J %A Grochowski, Christopher M %A Lupski, James R %A Schaaf, Christian P %A Calarge, Chadi A %K Adolescent %K alpha7 Nicotinic Acetylcholine Receptor %K Antipsychotic Agents %K Child %K Cohort Studies %K Female %K Gene Deletion %K Humans %K Male %K Neurodevelopmental Disorders %K Prospective Studies %K Risperidone %K Treatment Outcome %X

OBJECTIVE: Aggression is among the most common indications for referral to child and adolescent mental health services and is often challenging to treat. Understanding the biological underpinnings of aggression could help optimize treatment efficacy. Neuronal nicotinic acetylcholine receptors (nAChRs), specifically the α7 nAChR, encoded by the gene CHRNA7, have been implicated in aggressive behaviors in animal models as well as humans. Copy number variants (CNVs) of CHRNA7 are found in individuals with neuropsychiatric disorders, often with comorbid aggression. In this study, we aimed to determine the prevalence of CHRNA7 CNVs among individuals treated with risperidone, predominantly for irritability and aggression.

METHODS: Risperidone-treated children and adolescents were assessed for CHRNA7 copy number state using droplet digital PCR and genomic quantitative PCR. Demographic, anthropometric, and clinical data, including the Child Behavior Checklist (CBCL), were collected and compared across individuals with and without the CHRNA7 deletion.

RESULTS: Of 218 individuals (90% males, mean age: 12.3 ± 2.3 years), 7 (3.2%) were found to carry a CHRNA7 deletion and one proband carried a CHRNA7 duplication (0.46%). T-scores for rule breaking, aggression, and externalizing behavior factors of the CBCL were higher in the deletion group, despite taking 58% higher dose of risperidone.

CONCLUSIONS: CHRNA7 loss may contribute to a phenotype of severe aggression. Given the high prevalence of the deletion among risperidone-treated youth, future studies should examine the therapeutic potential of α7 nAChR-targeting drugs to target aggression associated with CHRNA7 deletions.

%B J Child Adolesc Psychopharmacol %V 27 %P 908-915 %8 2017 Dec %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/28817303?dopt=Abstract %R 10.1089/cap.2017.0068 %0 Journal Article %J Cell %D 2017 %T Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. %K Carcinoma, Hepatocellular %K DNA Methylation %K Genomics %K Humans %K Isocitrate Dehydrogenase %K Liver Neoplasms %K MicroRNAs %K Mutation %X

Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also. DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or downregulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed. Integrative molecular HCC subtyping incorporating unsupervised clustering of five data platforms identified three subtypes, one of which was associated with poorer prognosis in three HCC cohorts. Integrated analyses enabled development of a p53 target gene expression signature correlating with poor survival. Potential therapeutic targets for which inhibitors exist include WNT signaling, MDM4, MET, VEGFA, MCL1, IDH1, TERT, and immune checkpoint proteins CTLA-4, PD-1, and PD-L1.

%B Cell %V 169 %P 1327-1341.e23 %8 2017 Jun 15 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/28622513?dopt=Abstract %R 10.1016/j.cell.2017.05.046 %0 Journal Article %J Eur Urol %D 2017 %T Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma. %A Moss, Tyler J %A Qi, Yuan %A Xi, Liu %A Peng, Bo %A Kim, Tae-Beom %A Ezzedine, Nader E %A Mosqueda, Maribel E %A Guo, Charles C %A Czerniak, Bogdan A %A Ittmann, Michael %A Wheeler, David A %A Lerner, Seth P %A Matin, Surena F %K Aged %K Aged, 80 and over %K Biomarkers, Tumor %K Cluster Analysis %K Computational Biology %K Databases, Genetic %K DNA Mutational Analysis %K Exome Sequencing %K Female %K Gene Expression Profiling %K Genetic Predisposition to Disease %K Genomics %K Humans %K Kidney Neoplasms %K Kidney Pelvis %K Male %K Multigene Family %K Mutation %K Mutation Rate %K Phenotype %K Sequence Analysis, Protein %K Sequence Analysis, RNA %K Texas %K Treatment Outcome %K Ureter %K Ureteral Neoplasms %K Urinary Bladder Neoplasms %K Urothelium %X

BACKGROUND: Upper urinary tract urothelial cancer (UTUC) may have unique etiologic and genomic factors compared to bladder cancer.

OBJECTIVE: To characterize the genomic landscape of UTUC and provide insights into its biology using comprehensive integrated genomic analyses.

DESIGN, SETTING, AND PARTICIPANTS: We collected 31 untreated snap-frozen UTUC samples from two institutions and carried out whole-exome sequencing (WES) of DNA, RNA sequencing (RNAseq), and protein analysis.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Adjusting for batch effects, consensus mutation calls from independent pipelines identified DNA mutations, gene expression clusters using unsupervised consensus hierarchical clustering (UCHC), and protein expression levels that were correlated with relevant clinical variables, The Cancer Genome Atlas, and other published data.

RESULTS AND LIMITATIONS: WES identified mutations in FGFR3 (74.1%; 92% low-grade, 60% high-grade), KMT2D (44.4%), PIK3CA (25.9%), and TP53 (22.2%). APOBEC and CpG were the most common mutational signatures. UCHC of RNAseq data segregated samples into four molecular subtypes with the following characteristics. Cluster 1: no PIK3CA mutations, nonsmokers, high-grade

CONCLUSIONS: Mutations in UTUC occur at differing frequencies from bladder cancer, with four unique molecular and clinical subtypes. A novel SH3KBP1 fusion regulates RTK signaling. Further studies are needed to validate the described subtypes, explore their responses to therapy, and better define the novel fusion mutation.

PATIENT SUMMARY: We conducted a comprehensive study of the genetics of upper urinary tract urothelial cancer by evaluating DNA, RNA and protein expression in 31 tumors. We identified four molecular subtypes with distinct behaviors. Future studies will determine if these subtypes appear to have different responses to treatments.

%B Eur Urol %V 72 %P 641-649 %8 2017 Oct %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/28601352?dopt=Abstract %R 10.1016/j.eururo.2017.05.048 %0 Journal Article %J J Med Genet %D 2017 %T Congenital heart defects and left ventricular non-compaction in males with loss-of-function variants in NONO. %A Scott, Daryl A %A Hernandez-Garcia, Andres %A Azamian, Mahshid S %A Jordan, Valerie K %A Kim, Bum Jun %A Starkovich, Molly %A Zhang, Jinglan %A Wong, Lee-Jun %A Darilek, Sandra A %A Breman, Amy M %A Yang, Yaping %A Lupski, James R %A Jiwani, Amyn K %A Das, Bibhuti %A Lalani, Seema R %A Iglesias, Alejandro D %A Rosenfeld, Jill A %A Xia, Fan %K Child %K Child, Preschool %K Developmental Disabilities %K DNA-Binding Proteins %K Exome %K Heart Defects, Congenital %K Heart Ventricles %K Humans %K Infant %K Male %K Nuclear Matrix-Associated Proteins %K Octamer Transcription Factors %K RNA-Binding Proteins %X

BACKGROUND: The non-POU domain containing octamer-binding gene (NONO) is located on chromosome Xq13.1 and encodes a member of a small family of RNA-binding and DNA-binding proteins that perform a variety of tasks involved in RNA synthesis, transcriptional regulation and DNA repair. Loss-of-function variants in NONO have been described as a cause of intellectual disability in males but have not been described in association with congenital heart defects or cardiomyopathy. In this article, we seek to further define the phenotypic consequences of NONO depletion in human subjects.

METHODS: We searched a clinical database of over 6000 individuals referred for exome sequencing and over 60 000 individuals referred for CNV analysis.

RESULTS: We identified two males with atrial and ventricular septal defects, left ventricular non-compaction (LVNC), developmental delay and intellectual disability, who harboured de novo, loss-of-function variants in NONO. We also identified a male infant with developmental delay, congenital brain anomalies and severe LVNC requiring cardiac transplantation, who inherited a single-gene deletion of NONO from his asymptomatic mother.

CONCLUSIONS: We conclude that in addition to global developmental delay and intellectual disability, males with loss-of-function variants in NONO may also be predisposed to developing congenital heart defects and LVNC with the penetrance of these cardiac-related problems being influenced by genetic, epigenetic, environmental or stochastic factors. Brain imaging of males with NONO deficiency may reveal structural defects with abnormalities of the corpus callosum being the most common. Although dysmorphic features vary between affected individuals, relative macrocephaly is a common feature.

%B J Med Genet %V 54 %P 47-53 %8 2017 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27550220?dopt=Abstract %R 10.1136/jmedgenet-2016-104039 %0 Journal Article %J Mol Ecol %D 2017 %T Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. %A Dennenmoser, Stefan %A Sedlazeck, Fritz J %A Iwaszkiewicz, Elzbieta %A Li, Xiang-Yi %A Altmüller, Janine %A Nolte, Arne W %K Animals %K Biological Evolution %K DNA Copy Number Variations %K DNA Transposable Elements %K Hybridization, Genetic %K Introduced Species %K Perciformes %X

Evolutionary dynamics of structural genetic variation in lineages of hybrid origin is not well explored, although structural mutations may increase in controlled hybrid crosses. We therefore tested whether structural variants accumulate in a fish of recent hybrid origin, invasive Cottus, relative to both parental species Cottus rhenanus and Cottus perifretum. Copy-number variation in exons of 10,979 genes was assessed using comparative genome hybridization arrays. Twelve genes showed significantly higher copy numbers in invasive Cottus compared to both parents. This coincided with increased expression for three genes related to vision, detoxification and muscle development, suggesting possible gene dosage effects. Copy number increases of putative transposons were assessed by comparative mapping of genomic DNA reads against a de novo assembly of 1,005 repetitive elements. In contrast to exons, copy number increases of repetitive elements were common (20.7%) in invasive Cottus, whereas decrease was very rare (0.01%). Among the increased repetitive elements, 53.8% occurred at higher numbers in C. perifretum compared to C. rhenanus, while only 1.4% were more abundant in C. rhenanus. This implies a biased mutational process that amplifies genetic material from one ancestor. To assess the frequency of de novo mutations through hybridization, we screened 64 laboratory-bred F offspring between the parental species for copy-number changes at five candidate loci. We found no evidence for new structural variants, indicating that they are too rare to be detected given our sampling scheme. Instead, they must have accumulated over more generations than we observed in a controlled cross.

%B Mol Ecol %V 26 %P 4712-4724 %8 2017 Sep %G eng %N 18 %1 https://www.ncbi.nlm.nih.gov/pubmed/28390096?dopt=Abstract %R 10.1111/mec.14134 %0 Journal Article %J Am J Med Genet A %D 2017 %T Corner fracture type spondylometaphyseal dysplasia: Overlap with type II collagenopathies. %A Machol, Keren %A Jain, Mahim %A Almannai, Mohammed %A Orand, Thibault %A Lu, James T %A Tran, Alyssa %A Chen, Yuqing %A Schlesinger, Alan %A Gibbs, Richard %A Bonafe, Luisa %A Campos-Xavier, Ana Belinda %A Unger, Sheila %A Superti-Furga, Andrea %A Lee, Brendan H %A Campeau, Philippe M %A Burrage, Lindsay C %K Alleles %K Amino Acid Substitution %K Bone Diseases, Developmental %K Child, Preschool %K Collagen Type II %K Diagnosis, Differential %K Exome %K Genetic Association Studies %K Genotype %K Growth Disorders %K High-Throughput Nucleotide Sequencing %K Hip Joint %K Humans %K Infant %K Male %K Mutation %K Osteochondrodysplasias %K Phenotype %K Radiography %K Tibial Fractures %X

Spondylometaphyseal dysplasia (SMD) corner fracture type (also known as SMD "Sutcliffe" type, MIM 184255) is a rare skeletal dysplasia that presents with mild to moderate short stature, developmental coxa vara, mild platyspondyly, corner fracture-like lesions, and metaphyseal abnormalities with sparing of the epiphyses. The molecular basis for this disorder has yet to be clarified. We describe two patients with SMD corner fracture type and heterozygous pathogenic variants in COL2A1. These two cases together with a third case of SMD corner fracture type with a heterozygous COL2A1 pathogenic variant previously described suggest that this disorder overlaps with type II collagenopathies. The finding of one of the pathogenic variants in a previously reported case of spondyloepimetaphyseal dysplasia (SEMD) Strudwick type and the significant clinical similarity suggest an overlap between SMD corner fracture and SEMD Strudwick types. © 2016 Wiley Periodicals, Inc.

%B Am J Med Genet A %V 173 %P 733-739 %8 2017 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/27888646?dopt=Abstract %R 10.1002/ajmg.a.38059 %0 Journal Article %J Genome Med %D 2017 %T Creating a data resource: what will it take to build a medical information commons? %A Deverka, Patricia A %A Majumder, Mary A %A Villanueva, Angela G %A Anderson, Margaret %A Bakker, Annette C %A Bardill, Jessica %A Boerwinkle, Eric %A Bubela, Tania %A Evans, Barbara J %A Garrison, Nanibaa' A %A Gibbs, Richard A %A Gentleman, Robert %A Glazer, David %A Goldstein, Melissa M %A Greely, Hank %A Harris, Crane %A Knoppers, Bartha M %A Koenig, Barbara A %A Kohane, Isaac S %A La Rosa, Salvatore %A Mattison, John %A O'Donnell, Christopher J %A Rai, Arti K %A Rehm, Heidi L %A Rodriguez, Laura L %A Shelton, Robert %A Simoncelli, Tania %A Terry, Sharon F %A Watson, Michael S %A Wilbanks, John %A Cook-Deegan, Robert %A McGuire, Amy L %K Humans %K Information Dissemination %K Information Services %K Medical Informatics %X

National and international public-private partnerships, consortia, and government initiatives are underway to collect and share genomic, personal, and healthcare data on a massive scale. Ideally, these efforts will contribute to the creation of a medical information commons (MIC), a comprehensive data resource that is widely available for both research and clinical uses. Stakeholder participation is essential in clarifying goals, deepening understanding of areas of complexity, and addressing long-standing policy concerns such as privacy and security and data ownership. This article describes eight core principles proposed by a diverse group of expert stakeholders to guide the formation of a successful, sustainable MIC. These principles promote formation of an ethically sound, inclusive, participant-centric MIC and provide a framework for advancing the policy response to data-sharing opportunities and challenges.

%B Genome Med %V 9 %P 84 %8 2017 Sep 22 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28938910?dopt=Abstract %R 10.1186/s13073-017-0476-3 %0 Journal Article %J PLoS One %D 2016 %T Causal Role of Alcohol Consumption in an Improved Lipid Profile: The Atherosclerosis Risk in Communities (ARIC) Study. %A Vu, Khanh N %A Ballantyne, Christie M %A Hoogeveen, Ron C %A Nambi, Vijay %A Volcik, Kelly A %A Boerwinkle, Eric %A Morrison, Alanna C %K Alcohol Dehydrogenase %K Alcohol Drinking %K Atherosclerosis %K Female %K Humans %K Lipids %K Male %K Middle Aged %X

INTRODUCTION: Health benefits of low-to-moderate alcohol consumption may operate through an improved lipid profile. A Mendelian randomization (MR) approach was used to examine whether alcohol consumption causally affects lipid levels.

METHODS: This analysis involved 10,893 European Americans (EA) from the Atherosclerosis Risk in Communities (ARIC) study. Common and rare variants in alcohol dehydrogenase and acetaldehyde dehydrogenase genes were evaluated for MR assumptions. Five variants, residing in the ADH1B, ADH1C, and ADH4 genes, were selected as genetic instruments and were combined into an unweighted genetic score. Triglycerides (TG), total cholesterol, high-density lipoprotein cholesterol (HDL-c) and its subfractions (HDL2-c and HDL3-c), low-density lipoprotein cholesterol (LDL-c), small dense LDL-c (sdLDL-c), apolipoprotein B (apoB), and lipoprotein (a) (Lp(a)) levels were analyzed.

RESULTS: Alcohol consumption significantly increased HDL2-c and reduced TG, total cholesterol, LDL-c, sdLDL-c, and apoB levels. For each of these lipids a non-linear trend was observed. Compared to the first quartile of alcohol consumption, the third quartile had a 12.3% lower level of TG (p < 0.001), a 7.71 mg/dL lower level of total cholesterol (p = 0.007), a 10.3% higher level of HDL2-c (p = 0.007), a 6.87 mg/dL lower level of LDL-c (p = 0.012), a 7.4% lower level of sdLDL-c (p = 0.037), and a 3.5% lower level of apoB (p = 0.058, poverall = 0.022).

CONCLUSIONS: This study supports the causal role of regular low-to-moderate alcohol consumption in increasing HDL2-c, reducing TG, total cholesterol, and LDL-c, and provides evidence for the novel finding that low-to-moderate consumption of alcohol reduces apoB and sdLDL-c levels among EA. However, given the nonlinearity of the effect of alcohol consumption, even within the range of low-to-moderate drinking, increased consumption does not always result in a larger benefit.

%B PLoS One %V 11 %P e0148765 %8 2016 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/26849558?dopt=Abstract %R 10.1371/journal.pone.0148765 %0 Journal Article %J Neurol Neurochir Pol %D 2016 %T CAV3 mutation in a patient with transient hyperCKemia and myalgia. %A Macias, Anna %A Gambin, Tomasz %A Szafranski, Przemyslaw %A Jhangiani, Shalini N %A Kolasa, Anna %A Obersztyn, Ewa %A Lupski, James R %A Stankiewicz, Pawel %A Kaminska, Anna %K Caveolin 3 %K Colitis, Ulcerative %K Creatine Kinase %K Frameshift Mutation %K Humans %K Klinefelter Syndrome %K Magnetic Resonance Imaging %K Male %K Membrane Proteins %K Middle Aged %K Muscle, Skeletal %K Muscular Diseases %K Mutation, Missense %K Myalgia %K Phenotype %K Sjogren's Syndrome %K Thigh %X

Mutations in caveolin-3 (CAV3) can lead to different clinical phenotypes affecting skeletal or cardiac muscles. Here, we describe a patient with Klinefelter syndrome, ulcerative colitis and Sjögren syndrome, who developed transient hyperCKemia, myalgia and mild muscular weakness. Using whole exome sequencing (WES), a missense mutation G169A was found in the CAV3 gene. In addition, we identified a homozygous frameshift deletion in MS4A12 that may contribute to inflammatory bowel disease, further demonstrating usefulness of WES in dual molecular diagnoses.

%B Neurol Neurochir Pol %V 50 %P 468-473 %8 2016 Nov-Dec %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/27772553?dopt=Abstract %R 10.1016/j.pjnns.2016.06.008 %0 Journal Article %J PLoS Genet %D 2016 %T Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. %A Vij, Shubha %A Kuhl, Heiner %A Kuznetsova, Inna S %A Komissarov, Aleksey %A Yurchenko, Andrey A %A Van Heusden, Peter %A Singh, Siddharth %A Thevasagayam, Natascha M %A Prakki, Sai Rama Sridatta %A Purushothaman, Kathiresan %A Saju, Jolly M %A Jiang, Junhui %A Mbandi, Stanley Kimbung %A Jonas, Mario %A Hin Yan Tong, Amy %A Mwangi, Sarah %A Lau, Doreen %A Ngoh, Si Yan %A Liew, Woei Chang %A Shen, Xueyan %A Hon, Lawrence S %A Drake, James P %A Boitano, Matthew %A Hall, Richard %A Chin, Chen-Shan %A Lachumanan, Ramkumar %A Korlach, Jonas %A Trifonov, Vladimir %A Kabilov, Marsel %A Tupikin, Alexey %A Green, Darrell %A Moxon, Simon %A Garvin, Tyler %A Sedlazeck, Fritz J %A Vurture, Gregory W %A Gopalapillai, Gopikrishna %A Kumar Katneni, Vinaya %A Noble, Tansyn H %A Scaria, Vinod %A Sivasubbu, Sridhar %A Jerry, Dean R %A O'Brien, Stephen J %A Schatz, Michael C %A Dalmay, Tamas %A Turner, Stephen W %A Lok, Si %A Christoffels, Alan %A Orbán, László %K Animals %K Bass %K Chromosome Mapping %K Genome %K In Situ Hybridization, Fluorescence %K Phylogeny %X

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics.

%B PLoS Genet %V 12 %P e1005954 %8 2016 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/27082250?dopt=Abstract %R 10.1371/journal.pgen.1005954 %0 Journal Article %J Hum Genet %D 2016 %T Clinical genomics: from a truly personal genome viewpoint. %A Lupski, James R %K Genetic Diseases, Inborn %K Genetic Variation %K Genome, Human %K Genomics %K Humans %K Informed Consent %K Precision Medicine %K Privacy %K Sequence Analysis, DNA %X

The path to Clinical Genomics is punctuated by our understanding of what types of DNA structural and sequence variation contribute to disease, the many technical challenges to detect such variation genome-wide, and the initial struggles to interpret personal genome variation in the context of disease. This review describes one perspective of the development of clinical genomics; whereas the experimental challenges, and hurdles to overcoming them, might be deemed readily apparent, the non-technical issues for clinical implementation may be less obvious. Some of these latter challenges, including: (1) informed consent, (2) privacy, (3) what constitutes potentially pathogenic variation contributing to disease, (4) disease penetrance in populations, and (5) the genetic architecture of disease, and the struggles sometimes faced for solutions, are highlighted using illustrative examples.

%B Hum Genet %V 135 %P 591-601 %8 2016 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/27221143?dopt=Abstract %R 10.1007/s00439-016-1682-6 %0 Journal Article %J Am J Hum Genet %D 2016 %T Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine. %A Green, Robert C %A Goddard, Katrina A B %A Jarvik, Gail P %A Amendola, Laura M %A Appelbaum, Paul S %A Berg, Jonathan S %A Bernhardt, Barbara A %A Biesecker, Leslie G %A Biswas, Sawona %A Blout, Carrie L %A Bowling, Kevin M %A Brothers, Kyle B %A Burke, Wylie %A Caga-Anan, Charlisse F %A Chinnaiyan, Arul M %A Chung, Wendy K %A Clayton, Ellen W %A Cooper, Gregory M %A East, Kelly %A Evans, James P %A Fullerton, Stephanie M %A Garraway, Levi A %A Garrett, Jeremy R %A Gray, Stacy W %A Henderson, Gail E %A Hindorff, Lucia A %A Holm, Ingrid A %A Lewis, Michelle Huckaby %A Hutter, Carolyn M %A Janne, Pasi A %A Joffe, Steven %A Kaufman, David %A Knoppers, Bartha M %A Koenig, Barbara A %A Krantz, Ian D %A Manolio, Teri A %A McCullough, Laurence %A McEwen, Jean %A McGuire, Amy %A Muzny, Donna %A Myers, Richard M %A Nickerson, Deborah A %A Ou, Jeffrey %A Parsons, Donald W %A Petersen, Gloria M %A Plon, Sharon E %A Rehm, Heidi L %A Roberts, J Scott %A Robinson, Dan %A Salama, Joseph S %A Scollon, Sarah %A Sharp, Richard R %A Shirts, Brian %A Spinner, Nancy B %A Tabor, Holly K %A Tarczy-Hornoch, Peter %A Veenstra, David L %A Wagle, Nikhil %A Weck, Karen %A Wilfond, Benjamin S %A Wilhelmsen, Kirk %A Wolf, Susan M %A Wynn, Julia %A Yu, Joon-Ho %K Adult %K Biomedical Research %K Cardiovascular Diseases %K Child %K Clinical Trials as Topic %K Evidence-Based Practice %K Exome %K Genome, Human %K Genomics %K High-Throughput Nucleotide Sequencing %K Humans %K National Human Genome Research Institute (U.S.) %K Polymorphism, Single Nucleotide %K Population Groups %K Software %K United States %X

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.

%B Am J Hum Genet %V 98 %P 1051-1066 %8 2016 Jun 02 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/27181682?dopt=Abstract %R 10.1016/j.ajhg.2016.04.011 %0 Journal Article %J Blood %D 2016 %T Coexistence of gain-of-function JAK2 germ line mutations with JAK2V617F in polycythemia vera. %A Lanikova, Lucie %A Babosova, Olga %A Swierczek, Sabina %A Wang, Linghua %A Wheeler, David A %A Divoky, Vladimir %A Korinek, Vladimir %A Prchal, Josef T %K Amino Acid Substitution %K Cells, Cultured %K Cohort Studies %K DNA Mutational Analysis %K Germ-Line Mutation %K Humans %K Janus Kinase 2 %K Mutation, Missense %K Phenylalanine %K Polycythemia Vera %K Polymorphism, Single Nucleotide %K Valine %B Blood %V 128 %P 2266-2270 %8 2016 Nov 03 %G eng %N 18 %1 https://www.ncbi.nlm.nih.gov/pubmed/27647865?dopt=Abstract %R 10.1182/blood-2016-04-711283 %0 Journal Article %J J Evol Biol %D 2016 %T Comparative genomic study of arachnid immune systems indicates loss of beta-1,3-glucanase-related proteins and the immune deficiency pathway. %A Bechsgaard, J %A Vanthournout, B %A Funch, P %A Vestbo, S %A Gibbs, R A %A Richards, S %A Sanggaard, K W %A Enghild, J J %A Bilde, T %K Amino Acid Sequence %K Animals %K Antimicrobial Cationic Peptides %K Arachnida %K Blood Proteins %K Defensins %K Gene Dosage %K Genome %K Genomics %K Hemolymph %K Immune System %K Immunity, Innate %K Protein Domains %K Sequence Alignment %K Signal Transduction %X

Analyses of arthropod genomes have shown that the genes in the different innate humoral immune responses are conserved. These genes encode proteins that are involved in immune signalling pathways that recognize pathogens and activate immune responses. These immune responses include phagocytosis, encapsulation of the pathogen and production of effector molecules for pathogen elimination. So far, most studies have focused on insects leaving other major arthropod groups largely unexplored. Here, we annotate the immune-related genes of six arachnid genomes and present evidence for a conserved pattern of some immune genes, but also evolutionary changes in the arachnid immune system. Specifically, our results suggest that the family of recognition molecules of beta-1,3-glucanase-related proteins (βGRPs) and the genes from the immune deficiency (IMD) signalling pathway have been lost in a common ancestor of arachnids. These findings are consistent with previous work suggesting that the humoral immune effector proteins are constitutively produced in arachnids in contrast to insects, where these have to be induced. Further functional studies are needed to verify this. We further show that the full haemolymph clotting cascade found in the horseshoe crab is retrieved in most arachnid genomes. Tetranychus lacks at least one major component, although it is possible that this cascade could still function through recruitment of a different protein. The gel-forming protein in horseshoe crabs, coagulogen, was not recovered in any of the arachnid genomes; however, it is possible that the arachnid clot consists of a related protein, spätzle, that is present in all of the genomes.

%B J Evol Biol %V 29 %P 277-91 %8 2016 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/26528622?dopt=Abstract %R 10.1111/jeb.12780 %0 Journal Article %J G3 (Bethesda) %D 2016 %T Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont. %A Lindsey, Amelia R I %A Werren, John H %A Richards, Stephen %A Stouthamer, Richard %K Animals %K Ankyrin Repeat %K Bacterial Proteins %K Biological Evolution %K Culicidae %K Drosophila %K Frameshift Mutation %K Genome, Bacterial %K Genomics %K Host Specificity %K Open Reading Frames %K Parthenogenesis %K Phylogeny %K Symbiosis %K Wasps %K Wolbachia %X

Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain.

%B G3 (Bethesda) %V 6 %P 2113-23 %8 2016 Jul 07 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/27194801?dopt=Abstract %R 10.1534/g3.116.028449 %0 Journal Article %J Genome Biol Evol %D 2016 %T Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts. %A Newton, Irene L G %A Clark, Michael E %A Kent, Bethany N %A Bordenstein, Seth R %A Qu, Jiaxin %A Richards, Stephen %A Kelkar, Yogeshwar D %A Werren, John H %K Animals %K Arthropods %K Cytoplasm %K Drosophila %K Genome, Bacterial %K Genomics %K Host Specificity %K Male %K Mutation %K Phylogeny %K Reproduction %K Selection, Genetic %K Wolbachia %X

Wolbachia pipientis are obligate intracellular bacteria commonly found in many arthropods. They can induce various reproductive alterations in hosts, including cytoplasmic incompatibility, male-killing, feminization, and parthenogenetic development, and can provide host protection against some viruses and other pathogens. Wolbachia differ from many other primary endosymbionts in arthropods because they undergo frequent horizontal transmission between hosts and are well known for an abundance of mobile elements and relatively high recombination rates. Here, we compare the genomes of two closely related Wolbachia (with 0.57% genome-wide synonymous divergence) that differ in their reproductive effects on hosts. wVitA induces a sperm-egg incompatibility (also known as cytoplasmic incompatibility) in the parasitoid insect Nasonia vitripennis, whereas wUni causes parthenogenetic development in a different parasitoid, Muscidifurax uniraptor Although these bacteria are closely related, the genomic comparison reveals rampant rearrangements, protein truncations (particularly in proteins predicted to be secreted), and elevated substitution rates. These changes occur predominantly in the wUni lineage, and may be due in part to adaptations by wUni to a new host environment, or its phenotypic shift to parthenogenesis induction. However, we conclude that the approximately 8-fold elevated synonymous substitution rate in wUni is due to a either an elevated mutation rate or a greater number of generations per year in wUni, which occurs in semitropical host species. We identify a set of genes whose loss or pseudogenization in the wUni lineage implicates them in the phenotypic shift from cytoplasmic incompatibility to parthenogenesis induction. Finally, comparison of these closely related strains allows us to determine the fine-scale mutation patterns in Wolbachia Although Wolbachia are AT rich, mutation probabilities estimated from 4-fold degenerate sites are not AT biased, and predict an equilibrium AT content much less biased than observed (57-50% AT predicted vs. 76% current content at degenerate sites genome wide). The contrast suggests selection for increased AT content within Wolbachia genomes.

%B Genome Biol Evol %V 8 %P 1526-42 %8 2016 Jun 03 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/27189996?dopt=Abstract %R 10.1093/gbe/evw096 %0 Journal Article %J mSphere %D 2016 %T Comparison of the Gene Coding Contents and Other Unusual Features of the GC-Rich and AT-Rich Branch Probosciviruses. %A Ling, Paul D %A Long, Simon Y %A Zong, Jian-Chao %A Heaggans, Sarah Y %A Qin, Xiang %A Hayward, Gary S %X

Nearly 100 cases of lethal acute hemorrhagic disease in young Asian elephants have been reported worldwide. All tested cases contained high levels of elephant endotheliotropic herpesvirus (EEHV) DNA in pathological blood or tissue samples. Seven known major types of EEHVs have been partially characterized and shown to all belong to the novel Proboscivirus genus. However, the recently determined 206-kb EEHV4 genome proved to represent the prototype of a GC-rich branch virus that is very distinct from the previously published 180-kb EEHV1A, EEHV1B, and EEHV5A genomes, which all fall within an alternative AT-rich branch. Although EEHV4 retains the large family of 7xTM and vGPCR-like genes, six are unique to either just one or the other branch. While both branches display a highly enriched distribution of A and T tracts in intergenic domains, they are generally much larger within the GC-rich branch. Both branches retain the vGCNT1 acetylglucosamine transferase and at least one vOX-2 gene, but the two branches differ by 25 genes overall, with the AT-rich branch encoding a fucosyl transferase (vFUT9) plus two or three more vOX2 proteins and an immunoglobulin-like gene family that are all absent from the GC-rich branch. Several envelope glycoproteins retain only 15 to 20% protein identity or less across the two branches. Finally, the two plausible predicted transcriptional regulatory proteins display no homology at all to those in the alpha-, beta-, or gammaherpesvirus subfamilies. These results reinforce our previous proposal that the probosciviruses should be designated a new subfamily of mammalian herpesviruses. IMPORTANCE Multiple species of herpesviruses from three different lineages of the Proboscivirus genus (EEHV1/6, EEHV2/5, and EEHV3/4/7) infect either Asian or African elephants, but the highly lethal hemorrhagic disease is largely confined to Asian elephant calves and is predominantly associated with EEHV1. In the accompanying paper [P. D. Ling et al., mSphere 1(3):e00081-15, 10.1128/mSphere.00081-15], we report the complete 206-kb genome of EEHV4, the third different species causing disease in Asian elephants and the first example of a GC-rich branch proboscivirus. To gain insights into the nature and differential properties of these two very anciently diverged lineages of elephant herpesviruses, we describe here several additional unusual features found in the complete GC-rich genome of EEHV4 with particular emphasis on patterns of divergence as well as common unique features that are distinct from those of all other herpesviruses, such as the enlarged AT-rich intergenic domains and gene families, including the large number of vGPCR-like proteins.

%B mSphere %V 1 %8 2016 May-Jun %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/27340696?dopt=Abstract %R 10.1128/mSphere.00091-16 %0 Journal Article %J mSphere %D 2016 %T Complete Genome Sequence of Elephant Endotheliotropic Herpesvirus 4, the First Example of a GC-Rich Branch Proboscivirus. %A Ling, Paul D %A Long, Simon Y %A Fuery, Angela %A Peng, Rong-Sheng %A Heaggans, Sarah Y %A Qin, Xiang %A Worley, Kim C %A Dugan, Shannon %A Hayward, Gary S %X

A novel group of mammalian DNA viruses called elephant endotheliotropic herpesviruses (EEHVs) belonging to the Proboscivirus genus has been associated with nearly 100 cases of highly lethal acute hemorrhagic disease in young Asian elephants worldwide. The complete 180-kb genomes of prototype strains from three AT-rich branch viruses, EEHV1A, EEHV1B, and EEHV5, have been published. However, less than 6 kb of DNA sequence each from EEHV3, EEHV4, and EEHV7 showed them to be a hugely diverged second major branch with GC-rich characteristics. Here, we determined the complete 206-kb genome of EEHV4(Baylor) directly from trunk wash DNA by next-generation sequencing and de novo assembly procedures. Among a total of 119 genes with an overall colinear organization similar to those of the AT-rich EEHVs, major features of EEHV4 include a family of 26 paralogous 7xTM and vGPCR-like genes plus 25 novel or missing genes. The genome also contains an unusual distribution of tracts of 5 to 11 successive A or T nucleotides in intergenic domains between the mostly much higher GC content protein coding regions. Furthermore, an extremely high GC-rich bias in the third wobble position of codons clearly delineates the coding regions for many but not all proteins. There are also two novel captured cellular genes, including a C-type lectin (vECTL) and an O-linked acetylglucosamine transferase (vOGT), as well as an unusually large and complex Ori-Lyt dyad symmetry domain. Finally, 30 kb from a second strain proved to include three small chimeric domains, indicating the existence of distinct EEHV4A and EEHV4B subtypes. IMPORTANCE Multiple species of herpesviruses from three different lineages of the Proboscivirus genus (EEHV1/6, EEHV2/5, and EEHV3/4/7) infect both Asian and African elephants, but lethal hemorrhagic disease is largely confined to Asian elephant calves and is predominantly associated with EEHV1. Milder disease caused by EEHV5 or EEHV4 is being increasingly recognized as well, but little is known about the latter, which is estimated to have diverged at least 35 million years ago from the others within a distinctive GC-rich branch of the Proboscivirus genus. Here, we have determined the complete genomic DNA sequence of a strain of EEHV4 obtained from a trunk wash sample collected from a surviving Asian elephant calf undergoing asymptomatic shedding during convalescence after an acute hemorrhagic disease episode. This represents the first example from among the three known GC-rich branch Proboscivirus species to be assembled and fully annotated. Several distinctive features of EEHV4 compared to AT-rich branch genomes are described.

%B mSphere %V 1 %8 2016 May-Jun %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/27340695?dopt=Abstract %R 10.1128/mSphere.00081-15 %0 Journal Article %J Hum Genet %D 2016 %T Complex inheritance of ABCA4 disease: four mutations in a family with multiple macular phenotypes. %A Lee, Winston %A Xie, Yajing %A Zernant, Jana %A Bo Yuan %A Bearelly, Srilaxmi %A Tsang, Stephen H %A James R Lupski %A Allikmets, Rando %K Adult %K Aged %K ATP-Binding Cassette Transporters %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K Electroretinography %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Macula Lutea %K Macular Degeneration %K Male %K Middle Aged %K Mutation %K Pedigree %K Phenotype %K Stargardt Disease %X

Over 800 mutations in the ABCA4 gene cause autosomal recessive Stargardt disease. Due to extensive genetic heterogeneity, observed variant-associated phenotypes can manifest tremendous variability of expression. Furthermore, the high carrier frequency of pathogenic ABCA4 alleles in the general population (~1:20) often results in pseudo-dominant inheritance patterns further complicating the diagnosis and characterization of affected individuals. This study describes a genotype/phenotype analysis of an unusual family with multiple macular disease phenotypes spanning across two generations and segregating four distinct ABCA4 mutant alleles. Complete sequencing of ABCA4 discovered two known missense mutations, p.C54Y and p.G1961E. Array comparative genomic hybridization revealed a large novel deletion combined with a small insertion, c.6148-698_c.6670del/insTGTGCACCTCCCTAG, and complete sequencing of the entire ABCA4 genomic locus uncovered a new deep intronic variant, c.302+68C>T. Patients with the p.G1961E mutation had the mildest, confined maculopathy phenotype with peripheral flecks while those with all other mutant allele combinations exhibited a more advanced stage of generalized retinal and choriocapillaris atrophy. This family epitomizes the clinical and genetic complexity of ABCA4-associated diseases. It contained variants from all classes of mutations, in the coding region, deep intronic, both single nucleotide variants and copy number variants that accounted for varying phenotypes segregating in an apparent dominant fashion. Unequivocally defining disease-associated alleles in the ABCA4 locus requires a multifaceted approach that includes advanced mutation detection methods and a thorough analysis of clinical phenotypes.

%B Hum Genet %V 135 %P 9-19 %8 2016 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26527198?dopt=Abstract %R 10.1007/s00439-015-1605-y %0 Journal Article %J Cancer Cell %D 2016 %T Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. %A Zheng, Siyuan %A Cherniack, Andrew D %A Dewal, Ninad %A Moffitt, Richard A %A Danilova, Ludmila %A Murray, Bradley A %A Lerario, Antonio M %A Else, Tobias %A Knijnenburg, Theo A %A Ciriello, Giovanni %A Kim, Seungchan %A Assie, Guillaume %A Morozova, Olena %A Akbani, Rehan %A Shih, Juliann %A Hoadley, Katherine A %A Choueiri, Toni K %A Waldmann, Jens %A Mete, Ozgur %A Robertson, A Gordon %A Wu, Hsin-Ta %A Raphael, Benjamin J %A Shao, Lina %A Meyerson, Matthew %A Demeure, Michael J %A Beuschlein, Felix %A Gill, Anthony J %A Sidhu, Stan B %A Almeida, Madson Q %A Fragoso, Maria C B V %A Cope, Leslie M %A Kebebew, Electron %A Habra, Mouhammed A %A Whitsett, Timothy G %A Bussey, Kimberly J %A Rainey, William E %A Asa, Sylvia L %A Bertherat, Jérôme %A Fassnacht, Martin %A Wheeler, David A %A Hammer, Gary D %A Giordano, Thomas J %A Verhaak, Roel G W %K Adolescent %K Adrenal Cortex Neoplasms %K Adrenocortical Carcinoma %K Adult %K Aged %K Aged, 80 and over %K Child %K Disease-Free Survival %K DNA Methylation %K Female %K Gene Expression Profiling %K Gene Expression Regulation, Neoplastic %K Genetic Predisposition to Disease %K Genome, Human %K Genomics %K Humans %K Male %K Middle Aged %K Mutation %K Outcome Assessment, Health Care %K Prognosis %K Young Adult %X

We describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers.

%B Cancer Cell %V 29 %P 723-736 %8 2016 May 09 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/27165744?dopt=Abstract %R 10.1016/j.ccell.2016.04.002 %0 Journal Article %J Nature %D 2016 %T A comprehensive transcriptional map of primate brain development. %A Bakken, Trygve E %A Miller, Jeremy A %A Ding, Song-Lin %A Sunkin, Susan M %A Smith, Kimberly A %A Ng, Lydia %A Szafer, Aaron %A Dalley, Rachel A %A Royall, Joshua J %A Lemon, Tracy %A Shapouri, Sheila %A Aiona, Kaylynn %A Arnold, James %A Bennett, Jeffrey L %A Bertagnolli, Darren %A Bickley, Kristopher %A Boe, Andrew %A Brouner, Krissy %A Butler, Stephanie %A Byrnes, Emi %A Caldejon, Shiella %A Carey, Anita %A Cate, Shelby %A Chapin, Mike %A Chen, Jefferey %A Dee, Nick %A Desta, Tsega %A Dolbeare, Tim A %A Dotson, Nadia %A Ebbert, Amanda %A Fulfs, Erich %A Gee, Garrett %A Gilbert, Terri L %A Goldy, Jeff %A Gourley, Lindsey %A Gregor, Ben %A Gu, Guangyu %A Hall, Jon %A Haradon, Zeb %A Haynor, David R %A Hejazinia, Nika %A Hoerder-Suabedissen, Anna %A Howard, Robert %A Jochim, Jay %A Kinnunen, Marty %A Kriedberg, Ali %A Kuan, Chihchau L %A Lau, Christopher %A Lee, Chang-Kyu %A Lee, Felix %A Luong, Lon %A Mastan, Naveed %A May, Ryan %A Melchor, Jose %A Mosqueda, Nerick %A Mott, Erika %A Ngo, Kiet %A Nyhus, Julie %A Oldre, Aaron %A Olson, Eric %A Parente, Jody %A Parker, Patrick D %A Parry, Sheana %A Pendergraft, Julie %A Potekhina, Lydia %A Reding, Melissa %A Riley, Zackery L %A Roberts, Tyson %A Rogers, Brandon %A Roll, Kate %A Rosen, David %A Sandman, David %A Sarreal, Melaine %A Shapovalova, Nadiya %A Shi, Shu %A Sjoquist, Nathan %A Sodt, Andy J %A Townsend, Robbie %A Velasquez, Lissette %A Wagley, Udi %A Wakeman, Wayne B %A White, Cassandra %A Bennett, Crissa %A Wu, Jennifer %A Young, Rob %A Youngstrom, Brian L %A Wohnoutka, Paul %A Gibbs, Richard A %A Rogers, Jeffrey %A Hohmann, John G %A Hawrylycz, Michael J %A Hevner, Robert F %A Molnár, Zoltán %A Phillips, John W %A Dang, Chinh %A Jones, Allan R %A Amaral, David G %A Bernard, Amy %A Lein, Ed S %K Aging %K Animals %K Autism Spectrum Disorder %K Brain %K Cell Adhesion %K Conserved Sequence %K Female %K Humans %K Intellectual Disability %K Macaca mulatta %K Male %K Microcephaly %K Neocortex %K Neurodevelopmental Disorders %K Neurogenesis %K Risk Factors %K Schizophrenia %K Spatio-Temporal Analysis %K Species Specificity %K Transcription, Genetic %K Transcriptome %X

The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.

%B Nature %V 535 %P 367-75 %8 2016 Jul 21 %G eng %N 7612 %1 https://www.ncbi.nlm.nih.gov/pubmed/27409810?dopt=Abstract %R 10.1038/nature18637 %0 Journal Article %J FEBS J %D 2016 %T Conditional knockout of retinal determination genes in differentiating cells in Drosophila. %A Jin, Meng %A Eblimit, Aiden %A Pulikkathara, Merlyn %A Corr, Stuart %A Chen, Rui %A Mardon, Graeme %K Alleles %K Animals %K Cell Differentiation %K Drosophila %K Drosophila Proteins %K Eye %K Eye Proteins %K Gene Knockout Techniques %K Homeodomain Proteins %K Larva %K Photoreceptor Cells, Invertebrate %K Retina %X

Conditional gene knockout in postmitotic cells is a valuable technique which allows the study of gene function with spatiotemporal control. Surprisingly, in contrast to its long-term and extensive use in mouse studies, this technology is lacking in Drosophila. Here, we use a novel method for generating complete loss of eyes absent (eya) or sine oculis (so) function in postmitotic cells posterior to the morphogenetic furrow (MF). Specifically, genomic rescue constructs with flippase recognition target (FRT) sequences flanking essential exons are used to generate conditional null alleles. By removing gene function in differentiating cells, we show that eya and so are dispensable for larval photoreceptor differentiation, but are required for differentiation during pupal development. Both eya and so are necessary for photoreceptor survival and the apoptosis caused by loss of eya or so function is likely a secondary consequence of inappropriate differentiation. We also confirm their requirement for cone cell development and reveal a novel role in interommatidial bristle (IOB) formation. In addition, so is required for normal eye disc morphology. This is the first report of a knockout method to study eya and so function in postmitotic cells. This technology will open the door to a large array of new functional studies in virtually any tissue and at any stage of development or in adults.

%B FEBS J %V 283 %P 2754-66 %8 2016 Aug %G eng %N 15 %1 https://www.ncbi.nlm.nih.gov/pubmed/27257739?dopt=Abstract %R 10.1111/febs.13772 %0 Journal Article %J Genom Data %D 2016 %T Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization. %A Yuan, Bo %A Liu, Pengfei %A Rogers, Jeffrey %A Lupski, James R %X

Array comparative genomic hybridization (aCGH) has been widely used to detect copy number variants (CNVs) in both research and clinical settings. A customizable aCGH platform may greatly facilitate copy number analyses in genomic regions with higher-order complexity, such as low-copy repeats (LCRs). Here we present the aCGH analyses focusing on the 45 kb LCRs [1] at the NPHP1 region with diverse copy numbers in humans. Also, the interspecies aCGH analysis comparing human and nonhuman primates revealed dynamic copy number transitions of the human 45 kb LCR orthologues during primate evolution and therefore shed light on the origin of complexity at this locus. The original aCGH data are available at GEO under GSE73962.

%B Genom Data %V 8 %P 106-9 %8 2016 Jun %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/27222811?dopt=Abstract %R 10.1016/j.gdata.2016.04.008 %0 Journal Article %J Am J Hum Genet %D 2016 %T Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome. %A Lindstrand, Anna %A Frangakis, Stephan %A Carvalho, Claudia M B %A Richardson, Ellen B %A McFadden, Kelsey A %A Willer, Jason R %A Pehlivan, Davut %A Liu, Pengfei %A Pediaditakis, Igor L %A Sabo, Aniko %A Lewis, Richard Alan %A Banin, Eyal %A Lupski, James R %A Davis, Erica E %A Katsanis, Nicholas %K Adolescent %K Adult %K Alleles %K Animals %K Bardet-Biedl Syndrome %K Child %K Child, Preschool %K Chromosome Breakpoints %K Cytoskeletal Proteins %K DNA Copy Number Variations %K Exons %K Female %K Gastrulation %K Genes, Recessive %K Humans %K Infant %K Male %K Mutation %K Pedigree %K Young Adult %K Zebrafish %K Zebrafish Proteins %X

Bardet-Biedl syndrome (BBS) is a defining ciliopathy, notable for extensive allelic and genetic heterogeneity, almost all of which has been identified through sequencing. Recent data have suggested that copy-number variants (CNVs) also contribute to BBS. We used a custom oligonucleotide array comparative genomic hybridization (aCGH) covering 20 genes that encode intraflagellar transport (IFT) components and 74 ciliopathy loci to screen 92 unrelated individuals with BBS, irrespective of their known mutational burden. We identified 17 individuals with exon-disruptive CNVs (18.5%), including 13 different deletions in eight BBS genes (BBS1, BBS2, ARL6/BBS3, BBS4, BBS5, BBS7, BBS9, and NPHP1) and a deletion and a duplication in other ciliopathy-associated genes (ALMS1 and NPHP4, respectively). By contrast, we found a single heterozygous exon-disruptive event in a BBS-associated gene (BBS9) in 229 control subjects. Superimposing these data with resequencing revealed CNVs to (1) be sufficient to cause disease, (2) Mendelize heterozygous deleterious alleles, and (3) contribute oligogenic alleles by combining point mutations and exonic CNVs in multiple genes. Finally, we report a deletion and a splice site mutation in IFT74, inherited under a recessive paradigm, defining a candidate BBS locus. Our data suggest that CNVs contribute pathogenic alleles to a substantial fraction of BBS-affected individuals and highlight how either deletions or point mutations in discrete splice isoforms can induce hypomorphic mutations in genes otherwise intolerant to deleterious variation. Our data also suggest that CNV analyses and resequencing studies unbiased for previous mutational burden is necessary to delineate the complexity of disease architecture.

%B Am J Hum Genet %V 99 %P 318-36 %8 2016 Aug 04 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/27486776?dopt=Abstract %R 10.1016/j.ajhg.2015.04.023 %0 Journal Article %J PLoS Genet %D 2016 %T Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. %A Vij, Shubha %A Kuhl, Heiner %A Kuznetsova, Inna S %A Komissarov, Aleksey %A Yurchenko, Andrey A %A Van Heusden, Peter %A Singh, Siddharth %A Thevasagayam, Natascha M %A Prakki, Sai Rama Sridatta %A Purushothaman, Kathiresan %A Saju, Jolly M %A Jiang, Junhui %A Mbandi, Stanley Kimbung %A Jonas, Mario %A Hin Yan Tong, Amy %A Mwangi, Sarah %A Lau, Doreen %A Ngoh, Si Yan %A Liew, Woei Chang %A Shen, Xueyan %A Hon, Lawrence S %A Drake, James P %A Boitano, Matthew %A Hall, Richard %A Chin, Chen-Shan %A Lachumanan, Ramkumar %A Korlach, Jonas %A Trifonov, Vladimir %A Kabilov, Marsel %A Tupikin, Alexey %A Green, Darrell %A Moxon, Simon %A Garvin, Tyler %A Sedlazeck, Fritz J %A Vurture, Gregory W %A Gopalapillai, Gopikrishna %A Katneni, Vinaya Kumar %A Noble, Tansyn H %A Scaria, Vinod %A Sivasubbu, Sridhar %A Jerry, Dean R %A O'Brien, Stephen J %A Schatz, Michael C %A Dalmay, Tamas %A Turner, Stephen W %A Lok, Si %A Christoffels, Alan %A Orbán, László %X

[This corrects the article DOI: 10.1371/journal.pgen.1005954.].

%B PLoS Genet %V 12 %P e1006500 %8 2016 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/27935956?dopt=Abstract %R 10.1371/journal.pgen.1006500 %0 Journal Article %J Am J Med Genet A %D 2016 %T CRIPT exonic deletion and a novel missense mutation in a female with short stature, dysmorphic features, microcephaly, and pigmentary abnormalities. %A Leduc, Magalie S %A Niu, Zhiyv %A Bi, Weimin %A Zhu, Wenmiao %A Miloslavskaya, Irene %A Chiang, Theodore %A Streff, Haley %A Seavitt, John R %A Murray, Stephen A %A Eng, Christine %A Chan, Audrey %A Yang, Yaping %A Lalani, Seema R %K Abnormalities, Multiple %K Adaptor Proteins, Signal Transducing %K Alleles %K Amino Acid Substitution %K Child, Preschool %K DNA Mutational Analysis %K Dwarfism %K Exons %K Facies %K Female %K Genetic Association Studies %K Humans %K Microcephaly %K Mutation, Missense %K Pedigree %K Phenotype %K Sequence Deletion %X

Mutations in CRIPT encoding cysteine-rich PDZ domain-binding protein are rare, and to date have been reported in only two patients with autosomal recessive primordial dwarfism and distinctive facies. Here, we describe a female with biallelic mutations in CRIPT presenting with postnatal growth retardation, global developmental delay, and dysmorphic features including frontal bossing, high forehead, and sparse hair and eyebrows. Additional clinical features included high myopia, admixed hyper- and hypopigmented macules primarily on the face, arms, and legs, and syndactyly of 4-5 toes bilaterally. Using whole exome sequencing (WES) and chromosomal microarray analysis (CMA), we detected a c.8G>A (p.C3Y) missense variant in exon 1 of the CRIPT gene inherited from the mother and a 1,331 bp deletion encompassing exon 1, inherited from the father. The c.8G>A (p.C3Y) missense variant in CRIPT was apparently homozygous in the proband due to the exon 1 deletion. Our findings illustrate the clinical utility of combining WES with copy number variant (CNV) analysis to provide a molecular diagnosis to patients with rare Mendelian disorders. Our findings also illustrate the clinical spectrum of CRIPT related mutations. © 2016 Wiley Periodicals, Inc.

%B Am J Med Genet A %V 170 %P 2206-11 %8 2016 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/27250922?dopt=Abstract %R 10.1002/ajmg.a.37780 %0 Journal Article %J Nat Commun %D 2016 %T Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. %A Chitsazzadeh, Vida %A Coarfa, Cristian %A Drummond, Jennifer A %A Nguyen, Tri %A Joseph, Aaron %A Chilukuri, Suneel %A Charpiot, Elizabeth %A Adelmann, Charles H %A Ching, Grace %A Nguyen, Tran N %A Nicholas, Courtney %A Thomas, Valencia D %A Migden, Michael %A MacFarlane, Deborah %A Thompson, Erika %A Shen, Jianjun %A Takata, Yoko %A McNiece, Kayla %A Polansky, Maxim A %A Abbas, Hussein A %A Rajapakshe, Kimal %A Gower, Adam %A Spira, Avrum %A Covington, Kyle R %A Xiao, Weimin %A Gunaratne, Preethi %A Pickering, Curtis %A Frederick, Mitchell %A Myers, Jeffrey N %A Shen, Li %A Yao, Hui %A Su, Xiaoping %A Rapini, Ronald P %A Wheeler, David A %A Hawk, Ernest T %A Flores, Elsa R %A Tsai, Kenneth Y %K Animals %K Antineoplastic Agents %K Carcinogenesis %K Carcinoma, Squamous Cell %K Disease Progression %K DNA Mutational Analysis %K Exome Sequencing %K Female %K Gene Expression Profiling %K Genomics %K High-Throughput Nucleotide Sequencing %K Humans %K Keratosis, Actinic %K Mice %K Mice, Hairless %K Molecular Targeted Therapy %K Precancerous Conditions %K Sequence Analysis, RNA %K Skin %K Skin Neoplasms %K Ultraviolet Rays %X

Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in USA annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). To identify potential targets for molecularly targeted chemoprevention, here we perform integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar ultraviolet radiation-driven Hairless mouse model. We identify the major transcriptional drivers of this progression sequence, showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this ultraviolet radiation-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible.

%B Nat Commun %V 7 %P 12601 %8 2016 Aug 30 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/27574101?dopt=Abstract %R 10.1038/ncomms12601 %0 Journal Article %J PLoS Pathog %D 2015 %T The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways. %A Tscherner, Michael %A Zwolanek, Florian %A Jenull, Sabrina %A Fritz J Sedlazeck %A Petryshyn, Andriy %A Frohner, Ingrid E %A Mavrianos, John %A Chauhan, Neeraj %A von Haeseler, Arndt %A Kuchler, Karl %K Adaptation, Physiological %K Animals %K Candida albicans %K Candidiasis %K Chromatin Assembly and Disassembly %K Chromatin Immunoprecipitation %K Histone Acetyltransferases %K Immunoblotting %K Mass Spectrometry %K Mice %K Mice, Inbred C57BL %K Oxidative Stress %K Polymerase Chain Reaction %K Virulence %X

Human fungal pathogens like Candida albicans respond to host immune surveillance by rapidly adapting their transcriptional programs. Chromatin assembly factors are involved in the regulation of stress genes by modulating the histone density at these loci. Here, we report a novel role for the chromatin assembly-associated histone acetyltransferase complex NuB4 in regulating oxidative stress resistance, antifungal drug tolerance and virulence in C. albicans. Strikingly, depletion of the NuB4 catalytic subunit, the histone acetyltransferase Hat1, markedly increases resistance to oxidative stress and tolerance to azole antifungals. Hydrogen peroxide resistance in cells lacking Hat1 results from higher induction rates of oxidative stress gene expression, accompanied by reduced histone density as well as subsequent increased RNA polymerase recruitment. Furthermore, hat1Δ/Δ cells, despite showing growth defects in vitro, display reduced susceptibility to reactive oxygen-mediated killing by innate immune cells. Thus, clearance from infected mice is delayed although cells lacking Hat1 are severely compromised in killing the host. Interestingly, increased oxidative stress resistance and azole tolerance are phenocopied by the loss of histone chaperone complexes CAF-1 and HIR, respectively, suggesting a central role for NuB4 in the delivery of histones destined for chromatin assembly via distinct pathways. Remarkably, the oxidative stress phenotype of hat1Δ/Δ cells is a species-specific trait only found in C. albicans and members of the CTG clade. The reduced azole susceptibility appears to be conserved in a wider range of fungi. Thus, our work demonstrates how highly conserved chromatin assembly pathways can acquire new functions in pathogenic fungi during coevolution with the host.

%B PLoS Pathog %V 11 %P e1005218 %8 2015 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/26473952?dopt=Abstract %R 10.1371/journal.ppat.1005218 %0 Journal Article %J Eur J Hum Genet %D 2015 %T Cerebral visual impairment and intellectual disability caused by PGAP1 variants. %A Bosch, Daniëlle G M %A Boonstra, F Nienke %A Kinoshita, Taroh %A Jhangiani, Shalini %A de Ligt, Joep %A Cremers, Frans P M %A Lupski, James R %A Murakami, Yoshiko %A de Vries, Bert B A %K Animals %K Cell Line, Tumor %K Child %K CHO Cells %K Cricetinae %K Cricetulus %K Humans %K Intellectual Disability %K Male %K Membrane Proteins %K Mutation %K Phosphoinositide Phospholipase C %K Phosphoric Monoester Hydrolases %K Syndrome %K Vision Disorders %K Visual Perception %X

Homozygous variants in PGAP1 (post-GPI attachment to proteins 1) have recently been identified in two families with developmental delay, seizures and/or spasticity. PGAP1 is a member of the glycosylphosphatidylinositol anchor biosynthesis and remodeling pathway and defects in this pathway are a subclass of congenital disorders of glycosylation. Here we performed whole-exome sequencing in an individual with cerebral visual impairment (CVI), intellectual disability (ID), and factor XII deficiency and revealed compound heterozygous variants in PGAP1, c.274_276del (p.(Pro92del)) and c.921_925del (p.(Lys308Asnfs*25)). Subsequently, PGAP1-deficient Chinese hamster ovary (CHO)-cell lines were transfected with either mutant or wild-type constructs and their sensitivity to phosphatidylinositol-specific phospholipase C (PI-PLC) treatment was measured. The mutant constructs could not rescue the PGAP1-deficient CHO cell lines resistance to PI-PLC treatment. In addition, lymphoblastoid cell lines (LCLs) of the affected individual showed no sensitivity to PI-PLC treatment, whereas the LCLs of the heterozygous carrier parents were partially resistant. In conclusion, we report novel PGAP1 variants in a boy with CVI and ID and a proven functional loss of PGAP1 and show, to our knowledge, for the first time this genetic association with CVI.

%B Eur J Hum Genet %V 23 %P 1689-93 %8 2015 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/25804403?dopt=Abstract %R 10.1038/ejhg.2015.42 %0 Journal Article %J NPJ Schizophr %D 2015 %T Characterization of molecular and cellular phenotypes associated with a heterozygous deletion using patient-derived hiPSC neural cells. %A Lee, Inkyu S %A Carvalho, Claudia M B %A Douvaras, Panagiotis %A Ho, Seok-Man %A Hartley, Brigham J %A Zuccherato, Luciana W %A Ladran, Ian G %A Siegel, Arthur J %A McCarthy, Shane %A Malhotra, Dheeraj %A Sebat, Jonathan %A Rapoport, Judith %A Fossati, Valentina %A Lupski, James R %A Levy, Deborah L %A Brennand, Kristen J %X

Neurodevelopmental disorders, such as autism spectrum disorders (ASD) and schizophrenia (SZ), are complex disorders with a high degree of heritability. Genetic studies have identified several candidate genes associated with these disorders, including contactin-associated protein-like 2 (). Traditionally, in animal models or , the function of has been studied by genetic deletion or transcriptional knockdown, which reduce the expression of the entire gene; however, it remains unclear whether the mutations identified in clinical settings are sufficient to alter expression in human neurons. Here, using human induced pluripotent stem cells (hiPSCs) derived from two individuals with a large (289kb) and heterozygous deletion in (affecting exons 14-15) and discordant clinical outcomes, we have characterized expression patterns in hiPSC neural progenitor cells (NPCs), two independent populations of hiPSC-derived neurons and hiPSC-derived oligodendrocyte precursor cells (OPCs). First, we observed exon-specific changes in expression in both carriers; although the expression of exons 14-15 is significantly decreased, the expression of other exons is upregulated. Second, we observed significant differences in patterns of allele-specific expression in carriers that were consistent with clinical outcome. Third, we observed a robust neural migration phenotype that correlated with diagnosis and exon- and allele-specific expression patterns, but not with genotype. In all, our data highlight the importance of considering the nature, location and regulation of mutated alleles when attempting to connect GWAS studies to gene function.

%B NPJ Schizophr %V 1 %P 15019- %8 2015 Jun 24 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26985448?dopt=Abstract %R 10.1038/npjschz.2015.19 %0 Journal Article %J J Inherit Metab Dis %D 2015 %T Clinical, morphological, biochemical, imaging and outcome parameters in 21 individuals with mitochondrial maintenance defect related to FBXL4 mutations. %A Huemer, Martina %A Karall, Daniela %A Schossig, Anna %A Abdenur, Jose E %A Al Jasmi, Fatma %A Biagosch, Caroline %A Distelmaier, Felix %A Freisinger, Peter %A Graham, Brett H %A Haack, Tobias B %A Hauser, Natalie %A Hertecant, Jozef %A Ebrahimi-Fakhari, Darius %A Konstantopoulou, Vassiliki %A Leydiker, Karen %A Lourenco, Charles M %A Scholl-Bürgi, Sabine %A Wilichowski, Ekkehard %A Wolf, Nicole I %A Wortmann, Saskia B %A Taylor, Robert W %A Mayr, Johannes A %A Bonnen, Penelope E %A Sperl, Wolfgang %A Prokisch, Holger %A McFarland, Robert %K Acidosis, Lactic %K Child %K Child, Preschool %K Disease Progression %K F-Box Proteins %K Facial Asymmetry %K Family %K Female %K Genetic Association Studies %K Humans %K Infant %K Infant, Newborn %K Male %K Mitochondrial Diseases %K Muscle Hypotonia %K Mutation %K Neuroimaging %K Prognosis %K Retrospective Studies %K Ubiquitin-Protein Ligases %X

FBXL4 deficiency is a recently described disorder of mitochondrial maintenance associated with a loss of mitochondrial DNA in cells. To date, the genetic diagnosis of FBXL4 deficiency has been established in 28 individuals. This paper retrospectively reviews proxy-reported clinical and biochemical findings and evaluates brain imaging, morphological and genetic data in 21 of those patients. Neonatal/early-onset severe lactic acidosis, muscular hypotonia, feeding problems and failure to thrive is the characteristic pattern at first presentation. Facial dysmorphic features are present in 67% of cases. Seven children died (mean age 37 months); 11 children were alive (mean age at follow-up 46 months), three children were lost to follow-up. All survivors developed severe psychomotor retardation. Brain imaging was non-specific in neonates but a later-onset, rapidly progressive brain atrophy was noted. Elevated blood lactate and metabolic acidosis were observed in all individuals; creatine kinase was elevated in 45% of measurements. Diagnostic workup in patient tissues and cells revealed a severe combined respiratory chain defect with a general decrease of enzymes associated with mitochondrial energy metabolism and a relative depletion of mitochondrial DNA content. Mutations were detected throughout the FBXL4 gene albeit with no clear delineation of a genotype-phenotype correlation. Treatment with "mitochondrial medications" did not prove effective. In conclusion, a clinical pattern of early-onset encephalopathy, persistent lactic acidosis, profound muscular hypotonia and typical facial dysmorphism should prompt initiation of molecular genetic analysis of FBXL4. Establishment of the diagnosis permits genetic counselling, prevents patients undergoing unhelpful diagnostic procedures and allows for accurate prognosis.

%B J Inherit Metab Dis %V 38 %P 905-14 %8 2015 Sep %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/25868664?dopt=Abstract %R 10.1007/s10545-015-9836-6 %0 Journal Article %J JAMA %D 2015 %T Cognitive phenotypes and genomic copy number variations. %A Lupski, James R %K DNA Copy Number Variations %K Female %K Heterozygote %K Humans %K Intellectual Disability %K Male %K Mental Disorders %B JAMA %V 313 %P 2029-30 %8 2015 May 26 %G eng %N 20 %1 https://www.ncbi.nlm.nih.gov/pubmed/26010630?dopt=Abstract %R 10.1001/jama.2015.4846 %0 Journal Article %J PLoS Genet %D 2015 %T Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. %A Yuan, Bo %A Liu, Pengfei %A Gupta, Aditya %A Beck, Christine R %A Tejomurtula, Anusha %A Campbell, Ian M %A Gambin, Tomasz %A Simmons, Alexandra D %A Withers, Marjorie A %A Harris, R Alan %A Rogers, Jeffrey %A Schwartz, David C %A Lupski, James R %K Adaptor Proteins, Signal Transducing %K Alleles %K Animals %K Comparative Genomic Hybridization %K Cytoskeletal Proteins %K Evolution, Molecular %K Gene Dosage %K Gene Rearrangement %K Genome, Human %K Genomic Structural Variation %K Haplotypes %K Humans %K Kidney Diseases, Cystic %K Membrane Proteins %K Primates %X

Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases-about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual's susceptibility to acquiring disease-associated alleles.

%B PLoS Genet %V 11 %P e1005686 %8 2015 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/26641089?dopt=Abstract %R 10.1371/journal.pgen.1005686 %0 Journal Article %J Hum Mol Genet %D 2015 %T Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. %A Dong, Chengliang %A Wei, Peng %A Jian, Xueqiu %A Gibbs, Richard %A Boerwinkle, Eric %A Wang, Kai %A Liu, Xiaoming %K Computational Biology %K Exome %K Genome, Human %K Humans %K Polymorphism, Single Nucleotide %K Software %X

Accurate deleteriousness prediction for nonsynonymous variants is crucial for distinguishing pathogenic mutations from background polymorphisms in whole exome sequencing (WES) studies. Although many deleteriousness prediction methods have been developed, their prediction results are sometimes inconsistent with each other and their relative merits are still unclear in practical applications. To address these issues, we comprehensively evaluated the predictive performance of 18 current deleteriousness-scoring methods, including 11 function prediction scores (PolyPhen-2, SIFT, MutationTaster, Mutation Assessor, FATHMM, LRT, PANTHER, PhD-SNP, SNAP, SNPs&GO and MutPred), 3 conservation scores (GERP++, SiPhy and PhyloP) and 4 ensemble scores (CADD, PON-P, KGGSeq and CONDEL). We found that FATHMM and KGGSeq had the highest discriminative power among independent scores and ensemble scores, respectively. Moreover, to ensure unbiased performance evaluation of these prediction scores, we manually collected three distinct testing datasets, on which no current prediction scores were tuned. In addition, we developed two new ensemble scores that integrate nine independent scores and allele frequency. Our scores achieved the highest discriminative power compared with all the deleteriousness prediction scores tested and showed low false-positive prediction rate for benign yet rare nonsynonymous variants, which demonstrated the value of combining information from multiple orthologous approaches. Finally, to facilitate variant prioritization in WES studies, we have pre-computed our ensemble scores for 87 347 044 possible variants in the whole-exome and made them publicly available through the ANNOVAR software and the dbNSFP database.

%B Hum Mol Genet %V 24 %P 2125-37 %8 2015 Apr 15 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/25552646?dopt=Abstract %R 10.1093/hmg/ddu733 %0 Journal Article %J PLoS Genet %D 2015 %T Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication. %A Beck, Christine R %A Carvalho, Claudia M B %A Banser, Linda %A Gambin, Tomasz %A Stubbolo, Danielle %A Yuan, Bo %A Sperle, Karen %A McCahan, Suzanne M %A Henneke, Marco %A Seeman, Pavel %A Garbern, James Y %A Hobson, Grace M %A Lupski, James R %K Chromosome Breakpoints %K Chromosome Inversion %K Gene Dosage %K Gene Duplication %K Humans %K Myelin Proteolipid Protein %K Pelizaeus-Merzbacher Disease %X

Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology-or homeology-driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

%B PLoS Genet %V 11 %P e1005050 %8 2015 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/25749076?dopt=Abstract %R 10.1371/journal.pgen.1005050 %0 Journal Article %J J Thromb Haemost %D 2015 %T Complexity and diversity of F8 genetic variations in the 1000 genomes. %A Li, J N %A Carrero, I G %A Dong, J F %A Yu, F L %K Alleles %K Cohort Studies %K Computational Biology %K Ethnicity %K Factor VIII %K Female %K Gene Frequency %K Genetic Association Studies %K Genetic Variation %K Hemophilia A %K Human Genome Project %K Humans %K INDEL Mutation %K Male %K Mutation, Missense %K Polymorphism, Single Nucleotide %K RNA, Messenger %K Sequence Deletion %K Transcription, Genetic %X

BACKGROUND: Hemophilia A (HA) is an X-linked bleeding disorder caused by deleterious mutations in the coagulation factor VIII gene (F8). To date, F8 mutations have been documented predominantly in European subjects and in American subjects of European descent. Information on F8 variants in individuals of more diverse ethnic backgrounds is limited.

OBJECTIVES: To discover novel and rare F8 variants, and to characterize F8 variants in diverse population backgrounds.

PATIENTS/METHODS: We analyzed 2535 subjects, including 26 different ethnicities, whose data were available from the 1000 Genomes Project (1000G) phase 3 dataset, for F8 variants and their potential functional impact.

RESULTS: We identified 3030 single nucleotide variants, 31 short deletions and insertions (Indels) and a large, 497 kb, deletion. Among all variants, 86.4% were rare variants and 55.6% were novel. Eighteen variants previously associated with HA were found in our study. Most of these 'HA variants' were ethnic-specific with low allele frequency; however, one variant (p.M2257V) was present in 27% of African subjects. The p.E132D, p.T281A, p.A303V and p.D422H 'HA variants' were identified only in males. Twelve novel missense variants were predicted to be deleterious. The large deletion was discovered in eight female subjects without affecting F8 transcription and the transcription of genes on the X chromosome.

CONCLUSION: Characterizing F8 in the 1000G project highlighted the complexity of F8 variants and the importance of interrogating genetic variants on multiple ethnic backgrounds for associations with bleeding and thrombosis. The haplotype analysis and the orientation of duplicons that flank the large deletion suggested that the deletion was recurrent and originated by homologous recombination.

%B J Thromb Haemost %V 13 %P 2031-40 %8 2015 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/26383047?dopt=Abstract %R 10.1111/jth.13144 %0 Journal Article %J Nat Genet %D 2015 %T A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease. %A Nikpay, Majid %A Goel, Anuj %A Won, Hong-Hee %A Hall, Leanne M %A Willenborg, Christina %A Kanoni, Stavroula %A Saleheen, Danish %A Kyriakou, Theodosios %A Nelson, Christopher P %A Hopewell, Jemma C %A Webb, Thomas R %A Zeng, Lingyao %A Dehghan, Abbas %A Alver, Maris %A Armasu, Sebastian M %A Auro, Kirsi %A Bjonnes, Andrew %A Chasman, Daniel I %A Chen, Shufeng %A Ford, Ian %A Franceschini, Nora %A Gieger, Christian %A Grace, Christopher %A Gustafsson, Stefan %A Huang, Jie %A Hwang, Shih-Jen %A Kim, Yun Kyoung %A Kleber, Marcus E %A Lau, King Wai %A Lu, Xiangfeng %A Lu, Yingchang %A Lyytikäinen, Leo-Pekka %A Mihailov, Evelin %A Morrison, Alanna C %A Pervjakova, Natalia %A Qu, Liming %A Rose, Lynda M %A Salfati, Elias %A Saxena, Richa %A Scholz, Markus %A Smith, Albert V %A Tikkanen, Emmi %A Uitterlinden, Andre %A Yang, Xueli %A Zhang, Weihua %A Zhao, Wei %A de Andrade, Mariza %A de Vries, Paul S %A Van Zuydam, Natalie R %A Anand, Sonia S %A Bertram, Lars %A Beutner, Frank %A Dedoussis, George %A Frossard, Philippe %A Gauguier, Dominique %A Goodall, Alison H %A Gottesman, Omri %A Haber, Marc %A Han, Bok-Ghee %A Huang, Jianfeng %A Jalilzadeh, Shapour %A Kessler, Thorsten %A König, Inke R %A Lannfelt, Lars %A Lieb, Wolfgang %A Lind, Lars %A Lindgren, Cecilia M %A Lokki, Marja-Liisa %A Magnusson, Patrik K %A Mallick, Nadeem H %A Mehra, Narinder %A Meitinger, Thomas %A Memon, Fazal-Ur-Rehman %A Morris, Andrew P %A Nieminen, Markku S %A Pedersen, Nancy L %A Peters, Annette %A Rallidis, Loukianos S %A Rasheed, Asif %A Samuel, Maria %A Shah, Svati H %A Sinisalo, Juha %A Stirrups, Kathleen E %A Trompet, Stella %A Wang, Laiyuan %A Zaman, Khan S %A Ardissino, Diego %A Eric Boerwinkle %A Borecki, Ingrid B %A Bottinger, Erwin P %A Buring, Julie E %A Chambers, John C %A Collins, Rory %A Cupples, L Adrienne %A Danesh, John %A Demuth, Ilja %A Elosua, Roberto %A Epstein, Stephen E %A Esko, Tõnu %A Feitosa, Mary F %A Franco, Oscar H %A Franzosi, Maria Grazia %A Granger, Christopher B %A Gu, Dongfeng %A Gudnason, Vilmundur %A Hall, Alistair S %A Hamsten, Anders %A Harris, Tamara B %A Hazen, Stanley L %A Hengstenberg, Christian %A Hofman, Albert %A Ingelsson, Erik %A Iribarren, Carlos %A Jukema, J Wouter %A Karhunen, Pekka J %A Kim, Bong-Jo %A Kooner, Jaspal S %A Kullo, Iftikhar J %A Lehtimäki, Terho %A Loos, Ruth J F %A Melander, Olle %A Metspalu, Andres %A Marz, Winfried %A Palmer, Colin N %A Perola, Markus %A Quertermous, Thomas %A Rader, Daniel J %A Ridker, Paul M %A Ripatti, Samuli %A Roberts, Robert %A Salomaa, Veikko %A Sanghera, Dharambir K %A Schwartz, Stephen M %A Seedorf, Udo %A Stewart, Alexandre F %A Stott, David J %A Thiery, Joachim %A Zalloua, Pierre A %A O'Donnell, Christopher J %A Reilly, Muredach P %A Assimes, Themistocles L %A Thompson, John R %A Erdmann, Jeanette %A Clarke, Robert %A Watkins, Hugh %A Kathiresan, Sekar %A McPherson, Ruth %A Deloukas, Panos %A Schunkert, Heribert %A Samani, Nilesh J %A Farrall, Martin %K Coronary Artery Disease %K Genome, Human %K Genome-Wide Association Study %K Humans %K Phenotype %X

Existing knowledge of genetic variants affecting risk of coronary artery disease (CAD) is largely based on genome-wide association study (GWAS) analysis of common SNPs. Leveraging phased haplotypes from the 1000 Genomes Project, we report a GWAS meta-analysis of ∼185,000 CAD cases and controls, interrogating 6.7 million common (minor allele frequency (MAF) > 0.05) and 2.7 million low-frequency (0.005 < MAF < 0.05) variants. In addition to confirming most known CAD-associated loci, we identified ten new loci (eight additive and two recessive) that contain candidate causal genes newly implicating biological processes in vessel walls. We observed intralocus allelic heterogeneity but little evidence of low-frequency variants with larger effects and no evidence of synthetic association. Our analysis provides a comprehensive survey of the fine genetic architecture of CAD, showing that genetic susceptibility to this common disease is largely determined by common SNPs of small effect size.

%B Nat Genet %V 47 %P 1121-1130 %8 2015 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/26343387?dopt=Abstract %R 10.1038/ng.3396 %0 Journal Article %J Genet Med %D 2015 %T Comprehensive analysis of patients with Stargardt macular dystrophy reveals new genotype-phenotype correlations and unexpected diagnostic revisions. %A Zaneveld, Jacques %A Siddiqui, Sorath %A Li, Huajin %A Wang, Xia %A Wang, Hui %A Wang, Keqing %A Li, Hui %A Ren, Huanan %A Lopez, Irma %A Dorfman, Allison %A Khan, Ayesha %A Wang, Feng %A Salvo, Jason %A Gelowani, Violet %A Li, Yumei %A Sui, Ruifang %A Koenekoop, Robert %A Chen, Rui %K Adult %K ATP-Binding Cassette Transporters %K DNA Copy Number Variations %K DNA Mutational Analysis %K Female %K Genetic Association Studies %K High-Throughput Nucleotide Sequencing %K Humans %K Macular Degeneration %K Male %K Middle Aged %K Sequence Deletion %K Stargardt Disease %X

PURPOSE: Stargardt macular dystrophy (STGD) results in early central vision loss. We sought to explain the genetic cause of STGD in a cohort of 88 patients from three different cultural backgrounds.

METHODS: Next-generation sequencing using a novel capture panel was used to search for disease-causing mutations. Patients with undetermined causes were clinically reexamined and tested for copy-number variations as well as intronic mutations.

RESULTS: We determined the cause of disease in 67% of our patients. Our analysis identified 35 novel ABCA4 alleles. Eleven patients had mutations in genes not previously reported to cause STGD. Finally, 45% of our patients with unsolved causes had single deleterious mutations in ABCA4, a recessive disease gene. No likely pathogenic copy-number variations were identified.

CONCLUSION: This study expands our knowledge of STGD by identifying dozens of novel alleles that cause the disease. The frequency of single mutations in ABCA4 among STGD patients is higher than that among controls, indicating that these mutations contribute to disease. Disease in 11 patients was explained by mutations outside ABCA4, underlining the need to genotype all retinal disease genes to maximize genetic diagnostic rates. Few ABCA4 mutations were observed in our French Canadian patients. This population may contain an unidentified founder mutation. Our results indicate that copy-number variations are unlikely to be a major cause of STGD.

%B Genet Med %V 17 %P 262-70 %8 2015 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/25474345?dopt=Abstract %R 10.1038/gim.2014.174 %0 Journal Article %J Nat Commun %D 2015 %T A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. %A Alioto, Tyler S %A Buchhalter, Ivo %A Derdak, Sophia %A Hutter, Barbara %A Eldridge, Matthew D %A Hovig, Eivind %A Heisler, Lawrence E %A Beck, Timothy A %A Simpson, Jared T %A Tonon, Laurie %A Sertier, Anne-Sophie %A Patch, Ann-Marie %A Jäger, Natalie %A Ginsbach, Philip %A Drews, Ruben %A Paramasivam, Nagarajan %A Kabbe, Rolf %A Chotewutmontri, Sasithorn %A Diessl, Nicolle %A Previti, Christopher %A Schmidt, Sabine %A Brors, Benedikt %A Feuerbach, Lars %A Heinold, Michael %A Gröbner, Susanne %A Korshunov, Andrey %A Tarpey, Patrick S %A Butler, Adam P %A Hinton, Jonathan %A Jones, David %A Menzies, Andrew %A Raine, Keiran %A Shepherd, Rebecca %A Stebbings, Lucy %A Teague, Jon W %A Ribeca, Paolo %A Giner, Francesc Castro %A Beltran, Sergi %A Raineri, Emanuele %A Dabad, Marc %A Heath, Simon C %A Gut, Marta %A Denroche, Robert E %A Harding, Nicholas J %A Yamaguchi, Takafumi N %A Fujimoto, Akihiro %A Nakagawa, Hidewaki %A Quesada, Victor %A Valdés-Mas, Rafael %A Nakken, Sigve %A Vodák, Daniel %A Bower, Lawrence %A Lynch, Andrew G %A Anderson, Charlotte L %A Waddell, Nicola %A Pearson, John V %A Grimmond, Sean M %A Peto, Myron %A Spellman, Paul %A He, Minghui %A Kandoth, Cyriac %A Lee, Semin %A Zhang, John %A Létourneau, Louis %A Ma, Singer %A Seth, Sahil %A Torrents, David %A Xi, Liu %A Wheeler, David A %A López-Otín, Carlos %A Campo, Elías %A Campbell, Peter J %A Boutros, Paul C %A Puente, Xose S %A Gerhard, Daniela S %A Pfister, Stefan M %A McPherson, John D %A Hudson, Thomas J %A Schlesner, Matthias %A Lichter, Peter %A Eils, Roland %A Jones, David T W %A Gut, Ivo G %K Genome, Human %K High-Throughput Nucleotide Sequencing %K Humans %K Leukemia, Lymphoid %K Medulloblastoma %K Mutation %X

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.

%B Nat Commun %V 6 %P 10001 %8 2015 Dec 09 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26647970?dopt=Abstract %R 10.1038/ncomms10001 %0 Journal Article %J Nature %D 2015 %T Comprehensive genomic characterization of head and neck squamous cell carcinomas. %K Carcinoma, Squamous Cell %K DNA Copy Number Variations %K DNA, Neoplasm %K Female %K Gene Expression Regulation, Neoplastic %K Genome, Human %K Genomics %K Head and Neck Neoplasms %K Humans %K Male %K Molecular Targeted Therapy %K Mutation %K Oncogenes %K RNA, Neoplasm %K Signal Transduction %K Squamous Cell Carcinoma of Head and Neck %K Transcription Factors %X

The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.

%B Nature %V 517 %P 576-82 %8 2015 Jan 29 %G eng %N 7536 %1 https://www.ncbi.nlm.nih.gov/pubmed/25631445?dopt=Abstract %R 10.1038/nature14129 %0 Journal Article %J Orphanet J Rare Dis %D 2015 %T Comprehensive molecular diagnosis of 67 Chinese Usher syndrome probands: high rate of ethnicity specific mutations in Chinese USH patients. %A Jiang, Lichun %A Liang, Xiaofang %A Li, Yumei %A Wang, Jing %A Zaneveld, Jacques Eric %A Wang, Hui %A Xu, Shan %A Wang, Keqing %A Wang, Binbin %A Chen, Rui %A Sui, Ruifang %K China %K Cohort Studies %K Ethnicity %K Female %K Humans %K Male %K Molecular Diagnostic Techniques %K Mutation %K Pedigree %K Phenotype %K Usher Syndromes %X

BACKGROUND: Usher syndrome (USH) is the most common disease causing combined deafness and blindness. It is predominantly an autosomal recessive genetic disorder with occasionally digenic cases. Molecular diagnosis of USH patients is important for disease management. Few studies have tried to find the genetic cause of USH in Chinese patients. This study was designed to determine the mutation spectrum of Chinese USH patients.

METHODS: We applied next generation sequencing to characterize the mutation spectrum in 67 independent Chinese families with at least one member diagnosed with USH. Blood was collected at Peking Union Medical College Hospital. This cohort is one of the largest USH cohorts reported. We utilized customized panel and whole exome sequencing, variant analysis, Sanger validation and segregation tests to find disease causing mutations in these families.

RESULTS: We identified biallelic disease causing mutations in known USH genes in 70 % (49) of our patients. As has been previously reported, MYO7A is the most frequently mutated gene in our USH type I patients while USH2A is the most mutated gene in our USH type II patients. In addition, we identify mutations in CLRN1, DFNB31, GPR98 and PCDH15 for the first time in Chinese USH patients. Together, mutations in CLRN1, DNFB31, GPR98 and PCDH15 account for 11.4 % of disease in our cohort. Interestingly, although the spectrum of disease genes is quite similar between our Chinese patient cohort and other patient cohorts from different (and primarily Caucasian) ethnic backgrounds, the mutations themselves are dramatically different. In particular, 76 % (52/68) of alleles found in this study have never been previously reported. Interestingly, we observed a strong enrichment for severe protein truncating mutations expected to have severe functional consequence on the protein in USH II patients compared to the reported mutation spectrum in RP patients, who often carry partial protein truncating mutations.

CONCLUSIONS: Our study provides the first comprehensive genetic characterization of a large collection of Chinese USH patients. Up to 90 % of USH patients have disease caused by mutations in known USH disease genes. By combining NGS-based molecular diagnosis and patient clinical information, a more accurate diagnosis, prognosis and personalized treatment of USH patients can be achieved.

%B Orphanet J Rare Dis %V 10 %P 110 %8 2015 Sep 04 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26338283?dopt=Abstract %R 10.1186/s13023-015-0329-3 %0 Journal Article %J Invest Ophthalmol Vis Sci %D 2015 %T Comprehensive Molecular Diagnosis of a Large Chinese Leber Congenital Amaurosis Cohort. %A Wang, Hui %A Wang, Xia %A Zou, Xuan %A Xu, Shan %A Li, Hui %A Soens, Zachry Tore %A Wang, Keqing %A Li, Yumei %A Dong, Fangtian %A Chen, Rui %A Sui, Ruifang %K Adolescent %K Adult %K Asian People %K Child %K Child, Preschool %K Female %K Humans %K Infant %K Leber Congenital Amaurosis %K Male %K Molecular Diagnostic Techniques %K Mutation %K Pedigree %K Phenotype %X

PURPOSE: Leber congenital amaurosis (LCA) is an inherited retinal disease that causes early-onset severe visual impairment. To evaluate the mutation spectrum in the Chinese population, we performed a mutation screen in 145 Chinese LCA families.

METHODS: First, we performed direct Sanger sequencing of 7 LCA disease genes in 81 LCA families. Next, we developed a capture panel that enriches the entire coding exons and splicing sites of 163 known retinal disease genes and other candidate retinal disease genes. The capture panel allowed us to quickly identify disease-causing mutations in a large number of genes at a relatively low cost. Thus, this method was applied to the 53 LCA families that were unsolved by direct Sanger sequencing of 7 LCA disease genes and an additional 64 LCA families. Systematic next-generation sequencing (NGS) data analysis, Sanger sequencing validation, and segregation analysis were used to identify pathogenic mutations.

RESULTS: Homozygous or compound heterozygous mutations were identified in 107 families, heterozygous autosomal dominant mutations were identified in 3 families and an X-linked mutation was found in 1 family, for a combined solving rate of 76.6%. In total, 136 novel pathogenic mutations were found in this study. In combination with two previous studies carried out in Chinese LCA patients, we concluded that the mutation spectrum in the Chinese population is distinct compared to that in the European population. After revisiting, we also refined the clinical diagnosis of 10 families based on their molecular diagnosis.

CONCLUSIONS: Our results highlight the importance of a molecular diagnosis as an integral part of the clinical diagnostic process.

%B Invest Ophthalmol Vis Sci %V 56 %P 3642-55 %8 2015 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/26047050?dopt=Abstract %R 10.1167/iovs.14-15972 %0 Journal Article %J Nat Genet %D 2015 %T Convergent evolution of the genomes of marine mammals. %A Foote, Andrew D %A Liu, Yue %A Thomas, Gregg W C %A Vinar, Tomas %A Alföldi, Jessica %A Deng, Jixin %A Dugan, Shannon %A van Elk, Cornelis E %A Hunter, Margaret E %A Joshi, Vandita %A Khan, Ziad %A Kovar, Christie %A Lee, Sandra L %A Lindblad-Toh, Kerstin %A Mancia, Annalaura %A Nielsen, Rasmus %A Qin, Xiang %A Qu, Jiaxin %A Raney, Brian J %A Vijay, Nagarjun %A Wolf, Jochen B W %A Hahn, Matthew W %A Muzny, Donna M %A Worley, Kim C %A Gilbert, M Thomas P %A Gibbs, Richard A %K Adaptation, Physiological %K Amino Acid Substitution %K Animals %K Evolution, Molecular %K Genome %K Humans %K Mammals %K Phenotype %K Phylogeny %K Selection, Genetic %X

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

%B Nat Genet %V 47 %P 272-5 %8 2015 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/25621460?dopt=Abstract %R 10.1038/ng.3198 %0 Journal Article %J Nat Genet %D 2015 %T COPA mutations impair ER-Golgi transport and cause hereditary autoimmune-mediated lung disease and arthritis. %A Watkin, Levi B %A Jessen, Birthe %A Wiszniewski, Wojciech %A Vece, Timothy J %A Jan, Max %A Sha, Youbao %A Thamsen, Maike %A Santos-Cortez, Regie L P %A Lee, Kwanghyuk %A Gambin, Tomasz %A Forbes, Lisa R %A Law, Christopher S %A Stray-Pedersen, Asbjørg %A Cheng, Mickie H %A Mace, Emily M %A Anderson, Mark S %A Liu, Dongfang %A Tang, Ling Fung %A Nicholas, Sarah K %A Nahmod, Karen %A Makedonas, George %A Canter, Debra L %A Kwok, Pui-Yan %A Hicks, John %A Jones, Kirk D %A Penney, Samantha %A Jhangiani, Shalini N %A Rosenblum, Michael D %A Dell, Sharon D %A Waterfield, Michael R %A Papa, Feroz R %A Muzny, Donna M %A Zaitlen, Noah %A Leal, Suzanne M %A Gonzaga-Jauregui, Claudia %A Boerwinkle, Eric %A Eissa, N Tony %A Gibbs, Richard A %A Lupski, James R %A Orange, Jordan S %A Shum, Anthony K %K Amino Acid Sequence %K Arthritis %K Autoimmune Diseases %K Child, Preschool %K Coatomer Protein %K Endoplasmic Reticulum %K Endoplasmic Reticulum Stress %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Golgi Apparatus %K HEK293 Cells %K Humans %K Infant %K Lod Score %K Lung Diseases, Interstitial %K Male %K Molecular Sequence Data %K Pedigree %K Protein Transport %X

Unbiased genetic studies have uncovered surprising molecular mechanisms in human cellular immunity and autoimmunity. We performed whole-exome sequencing and targeted sequencing in five families with an apparent mendelian syndrome of autoimmunity characterized by high-titer autoantibodies, inflammatory arthritis and interstitial lung disease. We identified four unique deleterious variants in the COPA gene (encoding coatomer subunit α) affecting the same functional domain. Hypothesizing that mutant COPA leads to defective intracellular transport via coat protein complex I (COPI), we show that COPA variants impair binding to proteins targeted for retrograde Golgi-to-ER transport. Additionally, expression of mutant COPA results in ER stress and the upregulation of cytokines priming for a T helper type 17 (TH17) response. Patient-derived CD4(+) T cells also demonstrate significant skewing toward a TH17 phenotype that is implicated in autoimmunity. Our findings uncover an unexpected molecular link between a vesicular transport protein and a syndrome of autoimmunity manifested by lung and joint disease.

%B Nat Genet %V 47 %P 654-60 %8 2015 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/25894502?dopt=Abstract %R 10.1038/ng.3279 %0 Journal Article %J N Engl J Med %D 2015 %T Coronary heart disease and genetic variants with low phospholipase A2 activity. %A Polfus, Linda M %A Gibbs, Richard A %A Boerwinkle, Eric %K Aged %K Black or African American %K Coronary Disease %K Exome %K Female %K Genetic Variation %K Heterozygote %K Humans %K Male %K Middle Aged %K Mutation %K Phospholipases A2 %K Risk Factors %K White People %B N Engl J Med %V 372 %P 295-6 %8 2015 Jan 15 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/25587968?dopt=Abstract %R 10.1056/NEJMc1409673 %0 Journal Article %J Genetics %D 2015 %T Cortical Folding of the Primate Brain: An Interdisciplinary Examination of the Genetic Architecture, Modularity, and Evolvability of a Significant Neurological Trait in Pedigreed Baboons (Genus Papio). %A Atkinson, Elizabeth G %A Rogers, Jeffrey %A Mahaney, Michael C %A Cox, Laura A %A Cheverud, James M %K Animals %K Biological Evolution %K Brain %K Cerebral Cortex %K Chromosome Mapping %K Cluster Analysis %K Papio %K Pedigree %K Primates %K Quantitative Trait Loci %K Reproducibility of Results %X

Folding of the primate brain cortex allows for improved neural processing power by increasing cortical surface area for the allocation of neurons. The arrangement of folds (sulci) and ridges (gyri) across the cerebral cortex is thought to reflect the underlying neural network. Gyrification, an adaptive trait with a unique evolutionary history, is affected by genetic factors different from those affecting brain volume. Using a large pedigreed population of ∼1000 Papio baboons, we address critical questions about the genetic architecture of primate brain folding, the interplay between genetics, brain anatomy, development, patterns of cortical-cortical connectivity, and gyrification's potential for future evolution. Through Mantel testing and cluster analyses, we find that the baboon cortex is quite evolvable, with high integration between the genotype and phenotype. We further find significantly similar partitioning of variation between cortical development, anatomy, and connectivity, supporting the predictions of tension-based models for sulcal development. We identify a significant, moderate degree of genetic control over variation in sulcal length, with gyrus-shape features being more susceptible to environmental effects. Finally, through QTL mapping, we identify novel chromosomal regions affecting variation in brain folding. The most significant QTL contain compelling candidate genes, including gene clusters associated with Williams and Down syndromes. The QTL distribution suggests a complex genetic architecture for gyrification with both polygeny and pleiotropy. Our results provide a solid preliminary characterization of the genetic basis of primate brain folding, a unique and biomedically relevant phenotype with significant implications in primate brain evolution.

%B Genetics %V 200 %P 651-65 %8 2015 Jun %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25873632?dopt=Abstract %R 10.1534/genetics.114.173443 %0 Journal Article %J Sci Rep %D 2015 %T CRISPR-engineered mosaicism rapidly reveals that loss of Kcnj13 function in mice mimics human disease phenotypes. %A Zhong, Hua %A Chen, Yiyun %A Li, Yumei %A Chen, Rui %A Mardon, Graeme %K Animals %K CRISPR-Cas Systems %K Humans %K Leber Congenital Amaurosis %K Mice %K Mice, Transgenic %K Mosaicism %K Potassium Channels, Inwardly Rectifying %K Retinal Pigment Epithelium %X

The era of genomics has demanded the development of more efficient and timesaving approaches to validate gene function in disease. Here, we utilized the CRISPR-Cas9 system to generate Kcnj13 mutant mice by zygote injection to verify the pathogenic role of human KCNJ13, mutations of which are thought to cause Leber congenital amaurosis (LCA), an early-onset form of blindness. We found that complete loss of Kcnj13 is likely postnatal lethal. Among surviving F0-generation mice examined, 80% show mosaic KCNJ13 expression in the retinal pigment epithelium (RPE). Mosaic expression correlates with decreased response to light and photoreceptor degeneration, indicating that Kcnj13 mutant mice mimic human KCNJ13-related LCA disease. Importantly, mosaic animals enable us to directly compare Kcnj13 mutant and wild-type RPE cells in the same eye. We found that RPE cells lacking KCNJ13 protein still survive but overlying photoreceptors exhibit cell degeneration. At the same time, wild-type RPE cells can rescue neighboring photoreceptor cells that overlie mutant RPE cells. These results suggest that KCNJ13 expression is required for RPE cells to maintain photoreceptor survival. Moreover, we show that CRISPR-Cas9 engineered mosaicism can be used to rapidly test candidate gene function in vivo.

%B Sci Rep %V 5 %P 8366 %8 2015 Feb 10 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/25666713?dopt=Abstract %R 10.1038/srep08366 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2014 %T Characterization of HPV and host genome interactions in primary head and neck cancers. %A Parfenov, Michael %A Pedamallu, Chandra Sekhar %A Gehlenborg, Nils %A Freeman, Samuel S %A Danilova, Ludmila %A Bristow, Christopher A %A Lee, Semin %A Hadjipanayis, Angela G %A Ivanova, Elena V %A Wilkerson, Matthew D %A Protopopov, Alexei %A Yang, Lixing %A Seth, Sahil %A Song, Xingzhi %A Tang, Jiabin %A Ren, Xiaojia %A Zhang, Jianhua %A Pantazi, Angeliki %A Santoso, Netty %A Xu, Andrew W %A Mahadeshwar, Harshad %A Wheeler, David A %A Haddad, Robert I %A Jung, Joonil %A Ojesina, Akinyemi I %A Issaeva, Natalia %A Yarbrough, Wendell G %A Hayes, D Neil %A Grandis, Jennifer R %A El-Naggar, Adel K %A Meyerson, Matthew %A Park, Peter J %A Chin, Lynda %A Seidman, J G %A Hammerman, Peter S %A Kucherlapati, Raju %K Base Sequence %K DNA Methylation %K Gene Expression Regulation, Neoplastic %K Genes, Neoplasm %K Genome, Human %K Head and Neck Neoplasms %K Host-Pathogen Interactions %K Humans %K Molecular Sequence Data %K Papillomaviridae %K Virus Integration %X

Previous studies have established that a subset of head and neck tumors contains human papillomavirus (HPV) sequences and that HPV-driven head and neck cancers display distinct biological and clinical features. HPV is known to drive cancer by the actions of the E6 and E7 oncoproteins, but the molecular architecture of HPV infection and its interaction with the host genome in head and neck cancers have not been comprehensively described. We profiled a cohort of 279 head and neck cancers with next generation RNA and DNA sequencing and show that 35 (12.5%) tumors displayed evidence of high-risk HPV types 16, 33, or 35. Twenty-five cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for genic regions. Integrations had a marked impact on the human genome and were associated with alterations in DNA copy number, mRNA transcript abundance and splicing, and both inter- and intrachromosomal rearrangements. Many of these events involved genes with documented roles in cancer. Cancers with integrated vs. nonintegrated HPV displayed different patterns of DNA methylation and both human and viral gene expressions. Together, these data provide insight into the mechanisms by which HPV interacts with the human genome beyond expression of viral oncoproteins and suggest that specific integration events are an integral component of viral oncogenesis.

%B Proc Natl Acad Sci U S A %V 111 %P 15544-9 %8 2014 Oct 28 %G eng %N 43 %1 https://www.ncbi.nlm.nih.gov/pubmed/25313082?dopt=Abstract %R 10.1073/pnas.1416074111 %0 Journal Article %J Nat Genet %D 2014 %T The common marmoset genome provides insight into primate biology and evolution. %K Amino Acid Sequence %K Animals %K Callithrix %K Evolution, Molecular %K Female %K Genome %K MicroRNAs %K Molecular Sequence Data %K Phylogeny %K Polymorphism, Single Nucleotide %K Reproduction %K Sequence Analysis, DNA %X

We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application.

%B Nat Genet %V 46 %P 850-7 %8 2014 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/25038751?dopt=Abstract %R 10.1038/ng.3042 %0 Journal Article %J Nat Rev Genet %D 2014 %T Comparative primate genomics: emerging patterns of genome content and dynamics. %A Rogers, Jeffrey %A Gibbs, Richard A %K Animals %K Base Sequence %K Evolution, Molecular %K Genetic Speciation %K Genetic Variation %K Genome %K Genome, Human %K Genomics %K Humans %K Primates %X

Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future.

%B Nat Rev Genet %V 15 %P 347-59 %8 2014 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/24709753?dopt=Abstract %R 10.1038/nrg3707 %0 Journal Article %J Genome Res %D 2014 %T Comparative validation of the D. melanogaster modENCODE transcriptome annotation. %A Chen, Zhen-Xia %A Sturgill, David %A Qu, Jiaxin %A Jiang, Huaiyang %A Park, Soo %A Boley, Nathan %A Suzuki, Ana Maria %A Fletcher, Anthony R %A Plachetzki, David C %A FitzGerald, Peter C %A Artieri, Carlo G %A Atallah, Joel %A Barmina, Olga %A Brown, James B %A Blankenburg, Kerstin P %A Clough, Emily %A Dasgupta, Abhijit %A Gubbala, Sai %A Han, Yi %A Jayaseelan, Joy C %A Kalra, Divya %A Kim, Yoo-Ah %A Kovar, Christie L %A Lee, Sandra L %A Li, Mingmei %A Malley, James D %A Malone, John H %A Mathew, Tittu %A Mattiuzzo, Nicolas R %A Munidasa, Mala %A Muzny, Donna M %A Ongeri, Fiona %A Perales, Lora %A Przytycka, Teresa M %A Pu, Ling-Ling %A Robinson, Garrett %A Thornton, Rebecca L %A Saada, Nehad %A Scherer, Steven E %A Smith, Harold E %A Vinson, Charles %A Warner, Crystal B %A Worley, Kim C %A Wu, Yuan-Qing %A Zou, Xiaoyan %A Cherbas, Peter %A Kellis, Manolis %A Eisen, Michael B %A Piano, Fabio %A Kionte, Karin %A Fitch, David H %A Sternberg, Paul W %A Cutter, Asher D %A Duff, Michael O %A Hoskins, Roger A %A Graveley, Brenton R %A Gibbs, Richard A %A Bickel, Peter J %A Kopp, Artyom %A Carninci, Piero %A Celniker, Susan E %A Oliver, Brian %A Richards, Stephen %K Animals %K Cluster Analysis %K Computational Biology %K Drosophila melanogaster %K Evolution, Molecular %K Exons %K Female %K Gene Expression Profiling %K Genome, Insect %K Humans %K Male %K Molecular Sequence Annotation %K Nucleotide Motifs %K Phylogeny %K Position-Specific Scoring Matrices %K Promoter Regions, Genetic %K Reproducibility of Results %K RNA Editing %K RNA Splice Sites %K RNA Splicing %K Transcription Initiation Site %K Transcriptome %X

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

%B Genome Res %V 24 %P 1209-23 %8 2014 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/24985915?dopt=Abstract %R 10.1101/gr.159384.113 %0 Journal Article %J Nat Genet %D 2013 %T The Cancer Genome Atlas Pan-Cancer analysis project. %A Weinstein, John N %A Collisson, Eric A %A Mills, Gordon B %A Shaw, Kenna R Mills %A Ozenberger, Brad A %A Ellrott, Kyle %A Shmulevich, Ilya %A Sander, Chris %A Stuart, Joshua M %K Gene Expression Profiling %K Genome %K Humans %K Neoplasms %X

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

%B Nat Genet %V 45 %P 1113-20 %8 2013 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/24071849?dopt=Abstract %R 10.1038/ng.2764 %0 Journal Article %J Mol Ecol Resour %D 2013 %T Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum). %A Wilton, Peter R %A Sloan, Daniel B %A Logsdon, John M %A Harshavardhan Doddapaneni %A Neiman, Maurine %K Animals %K Expressed Sequence Tags %K Microsatellite Repeats %K Phylogeny %K Reproduction %K Reproduction, Asexual %K Sequence Analysis, DNA %K Snails %K Transcriptome %X

Understanding the evolution and maintenance of sexual reproduction is one of the central challenges of evolutionary biology, yet we know very little about how sex influences molecular evolution. The New Zealand freshwater snail Potamopyrgus antipodarum is ideally suited to address this knowledge gap because obligately sexual individuals often coexist with multiple independently derived obligately asexual lineages. This unusual situation allows direct comparisons both between sexual and asexual P. antipodarum and across populations that differ in the relative frequency of sexual individuals. As such, P. antipodarum has received a great deal of attention as a model system for the maintenance of sex in nature and is also used as a model for environmental toxicology and biological invasions. Molecular genetic resources for P. antipodarum will thus be useful to investigators in a variety of biological fields. We used 454 sequencing of cDNA libraries to generate transcriptomes from two sexual and two asexual P. antipodarum lineages. A de novo assembly of 116.7 Mb of sequence reads produced 41 396 contigs, and sequence similarity-based Gene Ontology annotations were obtained for 3740 contigs. We detected 408 315 SNP loci and 7315 microsatellite loci, which together represent the first genome-scale resource available for P. antipodarum. Raw 454 read sequences, contig sequences, annotation data and polymorphism data are publicly available in a searchable online database and for download at http://www.biology.uiowa.edu/neiman/transcriptome.php.

%B Mol Ecol Resour %V 13 %P 289-94 %8 2013 Mar %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23280235?dopt=Abstract %R 10.1111/1755-0998.12051 %0 Journal Article %J J Thromb Haemost %D 2013 %T Characterizing polymorphisms and allelic diversity of von Willebrand factor gene in the 1000 Genomes. %A Wang, Q Y %A Song, J %A Gibbs, R A %A Boerwinkle, E %A Dong, J F %A Yu, F L %K Asian People %K Black or African American %K Black People %K Databases, Genetic %K DNA Mutational Analysis %K Ethnicity %K Gene Frequency %K Genetic Predisposition to Disease %K Hemostasis %K Human Genome Project %K Humans %K Incidence %K Mutation %K Phenotype %K Polymorphism, Single Nucleotide %K von Willebrand Diseases %K von Willebrand Factor %K White People %X

BACKGROUND: The von Willebrand factor (VWF) gene is highly polymorphic, with variants correlated with VWF antigen levels, adhesion activity, clearance and factor VIII binding. VWF mutations are detected in patients with von Willebrand disease (VWD), whereas polymorphic variants could be associated with thrombosis. However, information on the ethnic diversity of VWF variants and their association with diseases is limited.

OBJECTIVES: To characterize novel VWF variants from different ethnicities in the general population.

PATIENTS/METHODS: We analyzed samples from 1092 subjects of 14 ethnicities available in the 1000 Genomes database for VWF variants and their potential functional impacts.

RESULTS: We identified 2728 SNPs and 91 insertions and deletions that had a high level of ethnic diversity, with Africans having the highest number of variants. The highest level of diversity was found in the D' and D2 domains. Among 94 non-synonymous variants, 31 were predicted to be deleterious, including 19 that were previously associated with VWD. Most of these 'VWD variants' had allele frequencies consistent with disease incidence in European subjects, but some had a significantly higher frequency in other ethnicities. The mutations R2185Q, H817Q and M740I associated with type 1 and type 2N VWD were present in more than 13% of African subjects.

CONCLUSIONS: These results highlight the complexity of VWF variations in different ethnic groups and emphasize the importance of interrogating variations on multiple ethnic backgrounds for associations with bleeding and thrombosis.

%B J Thromb Haemost %V 11 %P 261-9 %8 2013 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23216583?dopt=Abstract %R 10.1111/jth.12093 %0 Journal Article %J Nat Genet %D 2013 %T Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. %A Baud, Amelie %A Hermsen, Roel %A Guryev, Victor %A Stridh, Pernilla %A Graham, Delyth %A McBride, Martin W %A Foroud, Tatiana %A Calderari, Sophie %A Diez, Margarita %A Ockinger, Johan %A Beyeen, Amennai D %A Gillett, Alan %A Abdelmagid, Nada %A Guerreiro-Cacais, Andre Ortlieb %A Jagodic, Maja %A Tuncel, Jonatan %A Norin, Ulrika %A Beattie, Elisabeth %A Huynh, Ngan %A Miller, William H %A Koller, Daniel L %A Alam, Imranul %A Falak, Samreen %A Osborne-Pellegrin, Mary %A Martinez-Membrives, Esther %A Canete, Toni %A Blazquez, Gloria %A Vicens-Costa, Elia %A Mont-Cardona, Carme %A Diaz-Moran, Sira %A Tobena, Adolf %A Hummel, Oliver %A Zelenika, Diana %A Saar, Kathrin %A Patone, Giannino %A Bauerfeind, Anja %A Bihoreau, Marie-Therese %A Heinig, Matthias %A Lee, Young-Ae %A Rintisch, Carola %A Schulz, Herbert %A Wheeler, David A %A Worley, Kim C %A Muzny, Donna M %A Gibbs, Richard A %A Lathrop, Mark %A Lansu, Nico %A Toonen, Pim %A Ruzius, Frans Paul %A de Bruijn, Ewart %A Hauser, Heidi %A Adams, David J %A Keane, Thomas %A Atanur, Santosh S %A Aitman, Tim J %A Flicek, Paul %A Malinauskas, Tomas %A Jones, E Yvonne %A Ekman, Diana %A Lopez-Aumatell, Regina %A Dominiczak, Anna F %A Johannesson, Martina %A Holmdahl, Rikard %A Olsson, Tomas %A Gauguier, Dominique %A Hübner, Norbert %A Fernandez-Teruel, Alberto %A Cuppen, Edwin %A Mott, Richard %A Flint, Jonathan %K Animals %K Animals, Outbred Strains %K Anxiety %K Chromosome Mapping %K Genetic Variation %K Genotype %K Heart Diseases %K Humans %K Mice %K Mice, Inbred C57BL %K Models, Molecular %K Multiple Sclerosis %K Phenotype %K Polymorphism, Single Nucleotide %K Quantitative Trait Loci %K Rats %K Sequence Analysis, DNA %X

Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating new genes in models of anxiety, heart disease and multiple sclerosis. The relationship between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci, a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show that the extent and spatial pattern of variation in inbred rats differ substantially from those of inbred mice and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species.

%B Nat Genet %V 45 %P 767-75 %8 2013 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/23708188?dopt=Abstract %R 10.1038/ng.2644 %0 Journal Article %J Fungal Genet Biol %D 2013 %T A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus. %A Harshavardhan Doddapaneni %A Subramanian, Venkataramanan %A Fu, Bolei %A Cullen, Dan %K Agaricus %K Biotransformation %K Computational Biology %K Fungal Proteins %K Genetic Variation %K Genome, Fungal %K Lignin %K Metabolic Networks and Pathways %K Oxidoreductases %X

The oxidative enzymatic machinery for degradation of organic substrates in Agaricus bisporus (Ab) is at the core of the carbon recycling mechanisms in this fungus. To date, 156 genes have been tentatively identified as part of this oxidative enzymatic machinery, which includes 26 peroxidase encoding genes, nine copper radical oxidase [including three putative glyoxal oxidase-encoding genes (GLXs)], 12 laccases sensu stricto and 109 cytochrome P450 monooxygenases. Comparative analyses of these enzymes in Ab with those of the white-rot fungus, Phanerochaete chrysosporium, the brown-rot fungus, Postia placenta, the coprophilic litter fungus, Coprinopsis cinerea and the ectomychorizal fungus, Laccaria bicolor, revealed enzyme diversity consistent with adaptation to substrates rich in humic substances and partially degraded plant material. For instance, relative to wood decay fungi, Ab cytochrome P450 genes were less numerous (109 gene models), distributed among distinctive families, and lacked extensive duplication and clustering. Viewed together with P450 transcript accumulation patterns in three tested growth conditions, these observations were consistent with the unique Ab lifestyle. Based on tandem gene arrangements, a certain degree of gene duplication seems to have occurred in this fungus in the copper radical oxidase (CRO) and the laccase gene families. In Ab, high transcript levels and regulation of the heme-thiolate peroxidases, two manganese peroxidases and the three GLX-like genes are likely in response to complex natural substrates, including lignocellulose and its derivatives, thereby suggesting an important role in lignin degradation. On the other hand, the expression patterns of the related CROs suggest a developmental role in this fungus. Based on these observations, a brief comparative genomic overview of the Ab oxidative enzyme machinery is presented.

%B Fungal Genet Biol %V 55 %P 22-31 %8 2013 Jun %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/23583597?dopt=Abstract %R 10.1016/j.fgb.2013.03.004 %0 Journal Article %J Genome Announc %D 2013 %T Complete Genome Sequence of Elephant Endotheliotropic Herpesvirus 1A. %A Ling, Paul D %A Reid, Jeffrey G %A Qin, Xiang %A Muzny, Donna M %A Gibbs, Richard %A Petrosino, Joseph %A Peng, Rongsheng %A Zong, Jian-Chao %A Heaggans, Sarah Y %A Hayward, Gary S %X

Elephant endotheliotropic herpesvirus 1A is a member of the Proboscivirus genus and is a major cause of fatal hemorrhagic disease in endangered juvenile Asian elephants worldwide. Here, we report the first complete genome sequence from this genus, obtained directly from necropsy DNA, in which 60 of the 115 predicted genes are not found in any known herpesvirus.

%B Genome Announc %V 1 %P e0010613 %8 2013 Apr 11 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23580705?dopt=Abstract %R 10.1128/genomeA.00106-13 %0 Journal Article %J Nature %D 2013 %T Comprehensive molecular characterization of clear cell renal cell carcinoma. %K Acetyl-CoA Carboxylase %K AMP-Activated Protein Kinases %K Carcinoma, Renal Cell %K Chromatin %K Chromatin Assembly and Disassembly %K Citric Acid Cycle %K DNA Methylation %K DNA Mutational Analysis %K Epigenesis, Genetic %K Gene Expression Profiling %K Gene Expression Regulation, Neoplastic %K Genome, Human %K Genomics %K GRB10 Adaptor Protein %K Histone-Lysine N-Methyltransferase %K Humans %K Metabolic Networks and Pathways %K MicroRNAs %K Mutation %K Pentose Phosphate Pathway %K Phosphatidylinositol 3-Kinases %K Proto-Oncogene Proteins c-akt %K PTEN Phosphohydrolase %K RNA, Neoplasm %K Signal Transduction %K Survival Analysis %X

Genetic changes underlying clear cell renal cell carcinoma (ccRCC) include alterations in genes controlling cellular oxygen sensing (for example, VHL) and the maintenance of chromatin states (for example, PBRM1). We surveyed more than 400 tumours using different genomic platforms and identified 19 significantly mutated genes. The PI(3)K/AKT pathway was recurrently mutated, suggesting this pathway as a potential therapeutic target. Widespread DNA hypomethylation was associated with mutation of the H3K36 methyltransferase SETD2, and integrative analysis suggested that mutations involving the SWI/SNF chromatin remodelling complex (PBRM1, ARID1A, SMARCA4) could have far-reaching effects on other pathways. Aggressive cancers demonstrated evidence of a metabolic shift, involving downregulation of genes involved in the TCA cycle, decreased AMPK and PTEN protein levels, upregulation of the pentose phosphate pathway and the glutamine transporter genes, increased acetyl-CoA carboxylase protein, and altered promoter methylation of miR-21 (also known as MIR21) and GRB10. Remodelling cellular metabolism thus constitutes a recurrent pattern in ccRCC that correlates with tumour stage and severity and offers new views on the opportunities for disease treatment.

%B Nature %V 499 %P 43-9 %8 2013 Jul 04 %G eng %N 7456 %1 https://www.ncbi.nlm.nih.gov/pubmed/23792563?dopt=Abstract %R 10.1038/nature12222 %0 Journal Article %J J Med Genet %D 2013 %T Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. %A Wang, Xia %A Wang, Hui %A Sun, Vincent %A Tuan, Han-Fang %A Keser, Vafa %A Wang, Keqing %A Ren, Huanan %A Lopez, Irma %A Zaneveld, Jacques E %A Siddiqui, Sorath %A Bowles, Stephanie %A Khan, Ayesha %A Salvo, Jason %A Jacobson, Samuel G %A Iannaccone, Alessandro %A Wang, Feng %A Birch, David %A Heckenlively, John R %A Fishman, Gerald A %A Traboulsi, Elias I %A Li, Yumei %A Wheaton, Dianna %A Koenekoop, Robert K %A Chen, Rui %K Alleles %K Amino Acid Sequence %K Base Sequence %K Exome %K Female %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Leber Congenital Amaurosis %K Mutation %K Pedigree %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Retinitis Pigmentosa %K Sensitivity and Specificity %X

BACKGROUND: Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are inherited retinal diseases that cause early onset severe visual impairment. An accurate molecular diagnosis can refine the clinical diagnosis and allow gene specific treatments.

METHODS: We developed a capture panel that enriches the exonic DNA of 163 known retinal disease genes. Using this panel, we performed targeted next generation sequencing (NGS) for a large cohort of 179 unrelated and prescreened patients with the clinical diagnosis of LCA or juvenile RP. Systematic NGS data analysis, Sanger sequencing validation, and segregation analysis were utilised to identify the pathogenic mutations. Patients were revisited to examine the potential phenotypic ambiguity at the time of initial diagnosis.

RESULTS: Pathogenic mutations for 72 patients (40%) were identified, including 45 novel mutations. Of these 72 patients, 58 carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis. We revisited patients in the latter case and found that homozygous mutations in PRPH2 can cause LCA/juvenile RP. Guided by the molecular diagnosis, we reclassified the clinical diagnosis in two patients.

CONCLUSIONS: We have identified a novel gene and a large number of novel mutations that are associated with LCA/juvenile RP. Our results highlight the importance of molecular diagnosis as an integral part of clinical diagnosis.

%B J Med Genet %V 50 %P 674-88 %8 2013 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/23847139?dopt=Abstract %R 10.1136/jmedgenet-2013-101558 %0 Journal Article %J Mol Psychiatry %D 2013 %T CRHR1 genotypes, neural circuits and the diathesis for anxiety and depression. %A Rogers, J %A Raveendran, M %A Fawcett, G L %A Fox, A S %A Shelton, S E %A Oler, J A %A Cheverud, J %A Muzny, D M %A Gibbs, R A %A Davidson, R J %A Kalin, N H %K Animals %K Anxiety %K Brain %K Depression %K Disease Models, Animal %K Female %K Fluorodeoxyglucose F18 %K Genetic Association Studies %K Genetic Predisposition to Disease %K Genotype %K Macaca mulatta %K Male %K Polymorphism, Single Nucleotide %K Positron-Emission Tomography %K Receptors, Corticotropin-Releasing Hormone %X

The corticotrophin-releasing hormone (CRH) system integrates the stress response and is associated with stress-related psychopathology. Previous reports have identified interactions between childhood trauma and sequence variation in the CRH receptor 1 gene (CRHR1) that increase risk for affective disorders. However, the underlying mechanisms that connect variation in CRHR1 to psychopathology are unknown. To explore potential mechanisms, we used a validated rhesus macaque model to investigate association between genetic variation in CRHR1, anxious temperament (AT) and brain metabolic activity. In young rhesus monkeys, AT is analogous to the childhood risk phenotype that predicts the development of human anxiety and depressive disorders. Regional brain metabolism was assessed with (18)F-labeled fluoro-2-deoxyglucose (FDG) positron emission tomography in 236 young, normally reared macaques that were also characterized for AT. We show that single nucleotide polymorphisms (SNPs) affecting exon 6 of CRHR1 influence both AT and metabolic activity in the anterior hippocampus and amygdala, components of the neural circuit underlying AT. We also find evidence for association between SNPs in CRHR1 and metabolism in the intraparietal sulcus and precuneus. These translational data suggest that genetic variation in CRHR1 affects the risk for affective disorders by influencing the function of the neural circuit underlying AT and that differences in gene expression or the protein sequence involving exon 6 may be important. These results suggest that variation in CRHR1 may influence brain function before any childhood adversity and may be a diathesis for the interaction between CRHR1 genotypes and childhood trauma reported to affect human psychopathology.

%B Mol Psychiatry %V 18 %P 700-7 %8 2013 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/23147386?dopt=Abstract %R 10.1038/mp.2012.152 %0 Journal Article %J Am J Med Genet A %D 2012 %T The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. %A Bamshad, Michael J %A Shendure, Jay A %A Valle, David %A Hamosh, Ada %A Lupski, James R %A Gibbs, Richard A %A Boerwinkle, Eric %A Lifton, Richard P %A Gerstein, Mark %A Gunel, Murat %A Mane, Shrikant %A Nickerson, Deborah A %K Academies and Institutes %K Genetic Diseases, Inborn %K Genetics, Medical %K Genome, Human %K Genome-Wide Association Study %K Genomics %K High-Throughput Nucleotide Sequencing %K Humans %X

Next generation exome sequencing (ES) and whole genome sequencing (WGS) are new powerful tools for discovering the gene(s) that underlie Mendelian disorders. To accelerate these discoveries, the National Institutes of Health has established three Centers for Mendelian Genomics (CMGs): the Center for Mendelian Genomics at the University of Washington; the Center for Mendelian Genomics at Yale University; and the Baylor-Johns Hopkins Center for Mendelian Genomics at Baylor College of Medicine and Johns Hopkins University. The CMGs will provide ES/WGS and extensive analysis expertise at no cost to collaborating investigators where the causal gene(s) for a Mendelian phenotype has yet to be uncovered. Over the next few years and in collaboration with the global human genetics community, the CMGs hope to facilitate the identification of the genes underlying a very large fraction of all Mendelian disorders; see http://mendelian.org.

%B Am J Med Genet A %V 158A %P 1523-5 %8 2012 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/22628075?dopt=Abstract %R 10.1002/ajmg.a.35470 %0 Journal Article %J Genome Biol %D 2012 %T Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms. %A Lu, James T %A Wang, Yi %A Gibbs, Richard A %A Yu, Fuli %K Gene Frequency %K Genetics, Population %K Genome, Human %K Genome-Wide Association Study %K HapMap Project %K Heterozygote %K Humans %K INDEL Mutation %K Linkage Disequilibrium %K Polymorphism, Genetic %K Polymorphism, Single Nucleotide %X

BACKGROUND: Indels are an important cause of human variation and central to the study of human disease. The 1000 Genomes Project Low-Coverage Pilot identified over 1.3 million indels shorter than 50 bp, of which over 890 were identified as potentially disruptive variants. Yet, despite their ubiquity, the local genomic characteristics of indels remain unexplored.

RESULTS: Herein we describe population- and minor allele frequency-based differences in linkage disequilibrium and imputation characteristics for indels included in the 1000 Genomes Project Low-Coverage Pilot for the CEU, YRI and CHB+JPT populations. Common indels were well tagged by nearby SNPs in all studied populations, and were also tagged at a similar rate to common SNPs. Both neutral and functionally deleterious common indels were imputed with greater than 95% concordance from HapMap Phase 3 and OMNI SNP sites. Further, 38 to 56% of low frequency indels were tagged by low frequency SNPs. We were able to impute heterozygous low frequency indels with over 50% concordance. Lastly, our analysis also revealed evidence of ascertainment bias. This bias prevents us from extending the applicability of our results to highly polymorphic indels that could not be identified in the Low-Coverage Pilot.

CONCLUSIONS: Although further scope exists to improve the imputation of low frequency indels, our study demonstrates that there are already ample opportunities to retrospectively impute indels for prior genome-wide association studies and to incorporate indel imputation into future case/control studies.

%B Genome Biol %V 13 %P R15 %8 2012 Feb 29 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/22377349?dopt=Abstract %R 10.1186/gb-2012-13-2-r15 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2012 %T Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. %A Fernandez-Fueyo, Elena %A Ruiz-Duenas, Francisco J %A Ferreira, Patricia %A Floudas, Dimitrios %A Hibbett, David S %A Canessa, Paulo %A Larrondo, Luis F %A James, Tim Y %A Seelenfreund, Daniela %A Lobos, Sergio %A Polanco, Rubén %A Tello, Mario %A Honda, Yoichi %A Watanabe, Takahito %A Watanabe, Takashi %A Ryu, Jae San %A Kubicek, Christian P %A Schmoll, Monika %A Gaskell, Jill %A Hammel, Kenneth E %A St John, Franz J %A Vanden Wymelenberg, Amber %A Sabat, Grzegorz %A Splinter BonDurant, Sandra %A Syed, Khajamohiddin %A Yadav, Jagjit S %A Doddapaneni, Harshavardhan %A Subramanian, Venkataramanan %A Lavín, José L %A Oguiza, José A %A Perez, Gumer %A Pisabarro, Antonio G %A Ramirez, Lucia %A Santoyo, Francisco %A Master, Emma %A Coutinho, Pedro M %A Henrissat, Bernard %A Lombard, Vincent %A Magnuson, Jon Karl %A Kües, Ursula %A Hori, Chiaki %A Igarashi, Kiyohiko %A Samejima, Masahiro %A Held, Benjamin W %A Barry, Kerrie W %A LaButti, Kurt M %A Lapidus, Alla %A Lindquist, Erika A %A Lucas, Susan M %A Riley, Robert %A Salamov, Asaf A %A Hoffmeister, Dirk %A Schwenk, Daniel %A Hadar, Yitzhak %A Yarden, Oded %A de Vries, Ronald P %A Wiebenga, Ad %A Stenlid, Jan %A Eastwood, Daniel %A Grigoriev, Igor V %A Berka, Randy M %A Blanchette, Robert A %A Kersten, Phil %A Martinez, Angel T %A Vicuna, Rafael %A Cullen, Dan %K Basidiomycota %K Genomics %K Hydrolysis %K Lignin %K Molecular Sequence Data %K Oxidation-Reduction %K Phylogeny %K Species Specificity %X

Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn(2+). Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.

%B Proc Natl Acad Sci U S A %V 109 %P 5458-63 %8 2012 Apr 03 %G eng %N 14 %1 https://www.ncbi.nlm.nih.gov/pubmed/22434909?dopt=Abstract %R 10.1073/pnas.1119912109 %0 Journal Article %J BMC Microbiol %D 2012 %T Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. %A Qin, Xiang %A Galloway-Peña, Jessica R %A Sillanpaa, Jouko %A Roh, Jung Hyeob %A Nallapareddy, Sreedhar R %A Chowdhury, Shahreen %A Bourgogne, Agathe %A Choudhury, Tina %A Muzny, Donna M %A Buhay, Christian J %A Ding, Yan %A Dugan-Rocha, Shannon %A Liu, Wen %A Kovar, Christie %A Sodergren, Erica %A Highlander, Sarah %A Petrosino, Joseph F %A Worley, Kim C %A Gibbs, Richard A %A Weinstock, George M %A Murray, Barbara E %K DNA, Bacterial %K Enterococcus faecium %K Genome, Bacterial %K Humans %K Molecular Sequence Data %K Sequence Analysis, DNA %X

BACKGROUND: Enterococci are among the leading causes of hospital-acquired infections in the United States and Europe, with Enterococcus faecalis and Enterococcus faecium being the two most common species isolated from enterococcal infections. In the last decade, the proportion of enterococcal infections caused by E. faecium has steadily increased compared to other Enterococcus species. Although the underlying mechanism for the gradual replacement of E. faecalis by E. faecium in the hospital environment is not yet understood, many studies using genotyping and phylogenetic analysis have shown the emergence of a globally dispersed polyclonal subcluster of E. faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references.

RESULTS: In this study, we report the complete genome sequence of the E. faecium strain TX16, also known as DO, which belongs to multilocus sequence type (ST) 18, and was the first E. faecium strain ever sequenced. Whole genome comparison of the TX16 genome with 21 E. faecium draft genomes confirmed that most clinical, outbreak, and hospital-associated (HA) strains (including STs 16, 17, 18, and 78), in addition to strains of non-hospital origin, group in the same clade (referred to as the HA clade) and are evolutionally considerably more closely related to each other by phylogenetic and gene content similarity analyses than to isolates in the community-associated (CA) clade with approximately a 3-4% average nucleotide sequence difference between the two clades at the core genome level. Our study also revealed that many genomic loci in the TX16 genome are unique to the HA clade. 380 ORFs in TX16 are HA-clade specific and antibiotic resistance genes are enriched in HA-clade strains. Mobile elements such as IS16 and transposons were also found almost exclusively in HA strains, as previously reported.

CONCLUSIONS: Our findings along with other studies show that HA clonal lineages harbor specific genetic elements as well as sequence differences in the core genome which may confer selection advantages over the more heterogeneous CA E. faecium isolates. Which of these differences are important for the success of specific E. faecium lineages in the hospital environment remain(s) to be determined.

%B BMC Microbiol %V 12 %P 135 %8 2012 Jul 07 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/22769602?dopt=Abstract %R 10.1186/1471-2180-12-135 %0 Journal Article %J Stand Genomic Sci %D 2012 %T Complete genome sequence of Treponema pallidum strain DAL-1. %A Zobaníková, Marie %A Mikolka, Pavol %A Čejková, Darina %A Pospíšilová, Petra %A Chen, Lei %A Strouhal, Michal %A Qin, Xiang %A Weinstock, George M %A Smajs, David %X

Treponema pallidum strain DAL-1 is a human uncultivable pathogen causing the sexually transmitted disease syphilis. Strain DAL-1 was isolated from the amniotic fluid of a pregnant woman in the secondary stage of syphilis. Here we describe the 1,139,971 bp long genome of T. pallidum strain DAL-1 which was sequenced using two independent sequencing methods (454 pyrosequencing and Illumina). In rabbits, strain DAL-1 replicated better than the T. pallidum strain Nichols. The comparison of the complete DAL-1 genome sequence with the Nichols sequence revealed a list of genetic differences that are potentially responsible for the increased rabbit virulence of the DAL-1 strain.

%B Stand Genomic Sci %V 7 %P 12-21 %8 2012 Oct 10 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/23449808?dopt=Abstract %R 10.4056/sigs.2615838 %0 Journal Article %J Nature %D 2012 %T Comprehensive molecular characterization of human colon and rectal cancer. %K Colonic Neoplasms %K DNA Copy Number Variations %K DNA Methylation %K Exome %K Gene Expression Profiling %K Humans %K Mutation %K Mutation Rate %K Polymorphism, Single Nucleotide %K Rectal Neoplasms %K Sequence Analysis, DNA %X

To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase ε (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.

%B Nature %V 487 %P 330-7 %8 2012 Jul 18 %G eng %N 7407 %1 https://www.ncbi.nlm.nih.gov/pubmed/22810696?dopt=Abstract %R 10.1038/nature11252 %0 Journal Article %J Science %D 2012 %T Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. %A Price, Dana C %A Chan, Cheong Xin %A Yoon, Hwan Su %A Yang, Eun Chan %A Qiu, Huan %A Weber, Andreas P M %A Schwacke, Rainer %A Gross, Jeferson %A Blouin, Nicolas A %A Lane, Chris %A Reyes-Prieto, Adrián %A Durnford, Dion G %A Neilson, Jonathan A D %A Lang, B Franz %A Burger, Gertraud %A Steiner, Jürgen M %A Löffelhardt, Wolfgang %A Meuser, Jonathan E %A Posewitz, Matthew C %A Ball, Steven %A Arias, Maria Cecilia %A Henrissat, Bernard %A Coutinho, Pedro M %A Rensing, Stefan A %A Symeonidi, Aikaterini %A Harshavardhan Doddapaneni %A Green, Beverley R %A Rajah, Veeran D %A Boore, Jeffrey %A Bhattacharya, Debashish %K Biological Evolution %K Cyanobacteria %K Cyanophora %K Evolution, Molecular %K Gene Transfer, Horizontal %K Genes, Bacterial %K Genome, Plant %K Molecular Sequence Data %K Photosynthesis %K Phylogeny %K Symbiosis %X

The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to the evolution of algae and plants. We analyzed draft genome and transcriptome data from the basally diverging alga Cyanophora paradoxa and provide evidence for a single origin of the primary plastid in the eukaryote supergroup Plantae. C. paradoxa retains ancestral features of starch biosynthesis, fermentation, and plastid protein translocation common to plants and algae but lacks typical eukaryotic light-harvesting complex proteins. Traces of an ancient link to parasites such as Chlamydiae were found in the genomes of C. paradoxa and other Plantae. Apparently, Chlamydia-like bacteria donated genes that allow export of photosynthate from the plastid and its polymerization into storage polysaccharide in the cytosol.

%B Science %V 335 %P 843-7 %8 2012 Feb 17 %G eng %N 6070 %1 https://www.ncbi.nlm.nih.gov/pubmed/22344442?dopt=Abstract %R 10.1126/science.1213561 %0 Journal Article %J BMC Genomics %D 2011 %T Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). %A Fawcett, Gloria L %A Raveendran, Muthuswamy %A Deiros, David Rio %A Chen, David %A Yu, Fuli %A Harris, Ronald Alan %A Ren, Yanru %A Muzny, Donna M %A Reid, Jeffrey G %A Wheeler, David A %A Worley, Kimberly C %A Shelton, Steven E %A Kalin, Ned H %A Milosavljevic, Aleksandar %A Gibbs, Richard %A Rogers, Jeffrey %K Animals %K Genetic Variation %K India %K Macaca mulatta %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %K Species Specificity %X

BACKGROUND: Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits opportunities for genetic studies related to health and disease. Extensive information about SNPs and other genetic variation in rhesus macaques would facilitate valuable genetic analyses, as well as provide markers for genome-wide linkage analysis and the genetic management of captive breeding colonies.

RESULTS: We used the available rhesus macaque draft genome sequence, new sequence data from unrelated individuals and existing published sequence data to create a genome-wide SNP resource for Indian-origin rhesus monkeys. The original reference animal and two additional Indian-origin individuals were resequenced to low coverage using SOLiD™ sequencing. We then used three strategies to validate SNPs: comparison of potential SNPs found in the same individual using two different sequencing chemistries, and comparison of potential SNPs in different individuals identified with either the same or different sequencing chemistries. Our approach validated approximately 3 million SNPs distributed across the genome. Preliminary analysis of SNP annotations suggests that a substantial number of these macaque SNPs may have functional effects. More than 700 non-synonymous SNPs were scored by Polyphen-2 as either possibly or probably damaging to protein function and these variants now constitute potential models for studying functional genetic variation relevant to human physiology and disease.

CONCLUSIONS: Resequencing of a small number of animals identified greater than 3 million SNPs. This provides a significant new information resource for rhesus macaques, an important research animal. The data also suggests that overall genetic variation is high in this species. We identified many potentially damaging non-synonymous coding SNPs, providing new opportunities to identify rhesus models for human disease.

%B BMC Genomics %V 12 %P 311 %8 2011 Jun 13 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/21668978?dopt=Abstract %R 10.1186/1471-2164-12-311 %0 Journal Article %J Hum Mol Genet %D 2011 %T Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. %A Palmieri, Michela %A Impey, Soren %A Kang, Hyojin %A di Ronza, Alberto %A Pelz, Carl %A Sardiello, Marco %A Ballabio, Andrea %K Basic Helix-Loop-Helix Leucine Zipper Transcription Factors %K Gene Expression Regulation %K Gene Regulatory Networks %K HeLa Cells %K Humans %K Lysosomes %K Promoter Regions, Genetic %K Protein Binding %K Proteins %X

In metazoans, lysosomes are the center for the degradation of macromolecules and play a key role in a variety of cellular processes, such as autophagy, exocytosis and membrane repair. Defects of lysosomal pathways are associated with lysosomal storage disorders and with several late onset neurodegenerative diseases. We recently discovered the CLEAR (Coordinated Lysosomal Expression and Regulation) gene network and its master gene transcription factor EB (TFEB), which regulates lysosomal biogenesis and function. Here, we used a combination of genomic approaches, including ChIP-seq (sequencing of chromatin immunoprecipitate) analysis, profiling of TFEB-mediated transcriptional induction, genome-wide mapping of TFEB target sites and recursive expression meta-analysis of TFEB targets, to identify 471 TFEB direct targets that represent essential components of the CLEAR network. This analysis revealed a comprehensive system regulating the expression, import and activity of lysosomal enzymes that control the degradation of proteins, glycosaminoglycans, sphingolipids and glycogen. Interestingly, the CLEAR network appears to be involved in the regulation of additional lysosome-associated processes, including autophagy, exo- and endocytosis, phagocytosis and immune response. Furthermore, non-lysosomal enzymes involved in the degradation of essential proteins such as hemoglobin and chitin are also part of the CLEAR network. Finally, we identified nine novel lysosomal proteins by using the CLEAR network as a tool for prioritizing candidates. This study provides potential therapeutic targets to modulate cellular clearance in a variety of disease conditions.

%B Hum Mol Genet %V 20 %P 3852-66 %8 2011 Oct 01 %G eng %N 19 %1 https://www.ncbi.nlm.nih.gov/pubmed/21752829?dopt=Abstract %R 10.1093/hmg/ddr306 %0 Journal Article %J Cell %D 2011 %T Clan genomics and the complex architecture of human disease. %A Lupski, James R %A Belmont, John W %A Boerwinkle, Eric %A Gibbs, Richard A %K Genetic Predisposition to Disease %K Genetic Variation %K Genetics, Population %K Genome, Human %K Genomics %K Humans %K Pedigree %K Pilot Projects %K Precision Medicine %X

Human diseases are caused by alleles that encompass the full range of variant types, from single-nucleotide changes to copy-number variants, and these variations span a broad frequency spectrum, from the very rare to the common. The picture emerging from analysis of whole-genome sequences, the 1000 Genomes Project pilot studies, and targeted genomic sequencing derived from very large sample sizes reveals an abundance of rare and private variants. One implication of this realization is that recent mutation may have a greater influence on disease susceptibility or protection than is conferred by variations that arose in distant ancestors.

%B Cell %V 147 %P 32-43 %8 2011 Sep 30 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/21962505?dopt=Abstract %R 10.1016/j.cell.2011.09.008 %0 Journal Article %J Nature %D 2011 %T Comparative and demographic analysis of orang-utan genomes. %A Locke, Devin P %A Hillier, LaDeana W %A Warren, Wesley C %A Worley, Kim C %A Nazareth, Lynne V %A Muzny, Donna M %A Yang, Shiaw-Pyng %A Wang, Zhengyuan %A Chinwalla, Asif T %A Minx, Pat %A Mitreva, Makedonka %A Cook, Lisa %A Delehaunty, Kim D %A Fronick, Catrina %A Schmidt, Heather %A Fulton, Lucinda A %A Fulton, Robert S %A Nelson, Joanne O %A Magrini, Vincent %A Pohl, Craig %A Graves, Tina A %A Markovic, Chris %A Cree, Andy %A Dinh, Huyen H %A Hume, Jennifer %A Kovar, Christie L %A Fowler, Gerald R %A Lunter, Gerton %A Meader, Stephen %A Heger, Andreas %A Ponting, Chris P %A Marques-Bonet, Tomas %A Alkan, Can %A Chen, Lin %A Cheng, Ze %A Kidd, Jeffrey M %A Eichler, Evan E %A White, Simon %A Searle, Stephen %A Vilella, Albert J %A Chen, Yuan %A Flicek, Paul %A Ma, Jian %A Raney, Brian %A Suh, Bernard %A Burhans, Richard %A Herrero, Javier %A Haussler, David %A Faria, Rui %A Fernando, Olga %A Darré, Fleur %A Farré, Domènec %A Gazave, Elodie %A Oliva, Meritxell %A Navarro, Arcadi %A Roberto, Roberta %A Capozzi, Oronzo %A Archidiacono, Nicoletta %A Della Valle, Giuliano %A Purgato, Stefania %A Rocchi, Mariano %A Konkel, Miriam K %A Walker, Jerilyn A %A Ullmer, Brygg %A Batzer, Mark A %A Smit, Arian F A %A Hubley, Robert %A Casola, Claudio %A Schrider, Daniel R %A Hahn, Matthew W %A Quesada, Victor %A Puente, Xose S %A Ordoñez, Gonzalo R %A López-Otín, Carlos %A Vinar, Tomas %A Brejova, Brona %A Ratan, Aakrosh %A Harris, Robert S %A Miller, Webb %A Kosiol, Carolin %A Lawson, Heather A %A Taliwal, Vikas %A Martins, André L %A Siepel, Adam %A Roychoudhury, Arindam %A Ma, Xin %A Degenhardt, Jeremiah %A Bustamante, Carlos D %A Gutenkunst, Ryan N %A Mailund, Thomas %A Dutheil, Julien Y %A Hobolth, Asger %A Schierup, Mikkel H %A Ryder, Oliver A %A Yoshinaga, Yuko %A De Jong, Pieter J %A Weinstock, George M %A Rogers, Jeffrey %A Mardis, Elaine R %A Gibbs, Richard A %A Wilson, Richard K %K Animals %K Centromere %K Cerebrosides %K Chromosomes %K Evolution, Molecular %K Female %K Gene Rearrangement %K Genetic Speciation %K Genetic Variation %K Genetics, Population %K Genome %K Humans %K Male %K Phylogeny %K Pongo abelii %K Pongo pygmaeus %K Population Density %K Population Dynamics %K Species Specificity %X

'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

%B Nature %V 469 %P 529-33 %8 2011 Jan 27 %G eng %N 7331 %1 https://www.ncbi.nlm.nih.gov/pubmed/21270892?dopt=Abstract %R 10.1038/nature09687 %0 Journal Article %J PLoS One %D 2011 %T The complete genome sequence of 'Candidatus Liberibacter solanacearum', the bacterium associated with potato zebra chip disease. %A Lin, Hong %A Lou, Binghai %A Glynn, Jonathan M %A Doddapaneni, Harshavardhan %A Civerolo, Edwin L %A Chen, Chuanwu %A Duan, Yongping %A Zhou, Lijuan %A Vahling, Cheryl M %K Amino Acids %K Biological Transport %K Carbohydrate Metabolism %K Cell Division %K Cell Proliferation %K Citrus %K DNA Replication %K DNA, Bacterial %K Energy Metabolism %K Genome, Bacterial %K Genomics %K Nitrogen %K Nucleotides %K Plant Diseases %K Prophages %K Proteobacteria %K Solanum tuberosum %K Sulfur %K Vitamins %X

Zebra Chip (ZC) is an emerging plant disease that causes aboveground decline of potato shoots and generally results in unusable tubers. This disease has led to multi-million dollar losses for growers in the central and western United States over the past decade and impacts the livelihood of potato farmers in Mexico and New Zealand. ZC is associated with 'Candidatus Liberibacter solanacearum', a fastidious alpha-proteobacterium that is transmitted by a phloem-feeding psyllid vector, Bactericera cockerelli Sulc. Research on this disease has been hampered by a lack of robust culture methods and paucity of genome sequence information for 'Ca. L. solanacearum'. Here we present the sequence of the 1.26 Mbp metagenome of 'Ca. L. solanacearum', based on DNA isolated from potato psyllids. The coding inventory of the 'Ca. L. solanacearum' genome was analyzed and compared to related Rhizobiaceae to better understand 'Ca. L. solanacearum' physiology and identify potential targets to develop improved treatment strategies. This analysis revealed a number of unique transporters and pathways, all potentially contributing to ZC pathogenesis. Some of these factors may have been acquired through horizontal gene transfer. Taxonomically, 'Ca. L. solanacearum' is related to 'Ca. L. asiaticus', a suspected causative agent of citrus huanglongbing, yet many genome rearrangements and several gene gains/losses are evident when comparing these two Liberibacter. species. Relative to 'Ca. L. asiaticus', 'Ca. L. solanacearum' probably has reduced capacity for nucleic acid modification, increased amino acid and vitamin biosynthesis functionalities, and gained a high-affinity iron transport system characteristic of several pathogenic microbes.

%B PLoS One %V 6 %P e19135 %8 2011 Apr 28 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/21552483?dopt=Abstract %R 10.1371/journal.pone.0019135 %0 Journal Article %J PLoS One %D 2011 %T Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: the loss of infectivity to humans is associated with genome decay. %A Smajs, David %A Zobaníková, Marie %A Strouhal, Michal %A Čejková, Darina %A Dugan-Rocha, Shannon %A Pospíšilová, Petra %A Norris, Steven J %A Albert, Tom %A Qin, Xiang %A Hallsworth-Pepin, Kym %A Buhay, Christian %A Muzny, Donna M %A Chen, Lei %A Gibbs, Richard A %A Weinstock, George M %K Genome %K Humans %K Molecular Sequence Data %K Sequence Analysis, DNA %K Treponema %X

Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not infectious to humans, although its genome structure is very closely related to other pathogenic Treponema species including Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a combination of several high-throughput sequencing strategies. Whereas the overall size (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded proteins of known or predicted function in the Nichols genome. These proteins included virulence factors, gene regulators and components of DNA repair and recombination. The majority (52 or 61.9%) of the Cuniculi A pseudogenes and divergent genes were of unknown function. Our results indicate that T. paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized host-associated niche (rabbits) during loss of infectivity to humans. The genes that are inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important in the infectivity and pathogenesis of T. pallidum subspecies.

%B PLoS One %V 6 %P e20415 %8 2011 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/21655244?dopt=Abstract %R 10.1371/journal.pone.0020415 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2011 %T Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. %A Xi, Ruibin %A Hadjipanayis, Angela G %A Luquette, Lovelace J %A Kim, Tae-Min %A Lee, Eunjung %A Zhang, Jianhua %A Johnson, Mark D %A Muzny, Donna M %A Wheeler, David A %A Gibbs, Richard A %A Kucherlapati, Raju %A Park, Peter J %K Algorithms %K Bayes Theorem %K Brain Neoplasms %K Comparative Genomic Hybridization %K Computer Simulation %K DNA Copy Number Variations %K Female %K Gene Dosage %K Genome %K Genome, Human %K Glioblastoma %K Humans %K Models, Genetic %K Models, Statistical %K Sequence Analysis, DNA %X

DNA copy number variations (CNVs) play an important role in the pathogenesis and progression of cancer and confer susceptibility to a variety of human disorders. Array comparative genomic hybridization has been used widely to identify CNVs genome wide, but the next-generation sequencing technology provides an opportunity to characterize CNVs genome wide with unprecedented resolution. In this study, we developed an algorithm to detect CNVs from whole-genome sequencing data and applied it to a newly sequenced glioblastoma genome with a matched control. This read-depth algorithm, called BIC-seq, can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion. Using BIC-seq, we identified hundreds of CNVs as small as 40 bp in the cancer genome sequenced at 10× coverage, whereas we could only detect large CNVs (> 15 kb) in the array comparative genomic hybridization profiles for the same genome. Eighty percent (14/16) of the small variants tested (110 bp to 14 kb) were experimentally validated by quantitative PCR, demonstrating high sensitivity and true positive rate of the algorithm. We also extended the algorithm to detect recurrent CNVs in multiple samples as well as deriving error bars for breakpoints using a Gibbs sampling approach. We propose this statistical approach as a principled yet practical and efficient method to estimate CNVs in whole-genome sequencing data.

%B Proc Natl Acad Sci U S A %V 108 %P E1128-36 %8 2011 Nov 15 %G eng %N 46 %1 https://www.ncbi.nlm.nih.gov/pubmed/22065754?dopt=Abstract %R 10.1073/pnas.1110574108 %0 Journal Article %J Epilepsy Res %D 2011 %T Cortical sulcal areas in baboons (Papio hamadryas spp.) with generalized interictal epileptic discharges on scalp EEG. %A Szabó, C A %A Kochunov, P %A Knape, K D %A McCoy, K J M %A Leland, M M %A Lancaster, J L %A Fox, P T %A Williams, J T %A Rogers, J %K Animals %K Brain %K Cerebral Cortex %K Data Interpretation, Statistical %K Electroencephalography %K Epilepsy %K Female %K Functional Laterality %K Image Processing, Computer-Assisted %K Magnetic Resonance Imaging %K Male %K Papio %K Parietal Lobe %K Seizures %X

Brain MRI studies in people with idiopathic generalized epilepsies demonstrate regional morphometric differences, though variable in magnitude and location. As the baboon provides an excellent electroclinical and neuroimaging model for photosensitive generalized epilepsy in humans, this study evaluated MRI volumetric and morphometric differences between baboons with interictal epileptic discharges (IEDs) on scalp EEG and baboons with normal EEG studies. Seventy-seven baboons underwent high-resolution brain MRI and scalp EEG studies. The scans were acquired using an 8-channel primate head coil (Siemens TRIO 3T scanner, Erlangen, Germany). After spatial normalization, sulcal measurements were obtained by object-based-morphology methods. One-hour scalp EEG studies were performed in animals sedated with ketamine. Thirty-eight (22F/16M) baboons had normal EEGs (IED-), while 39 (22F/17M) had generalized IEDs (IED+). The two groups were compared for age, total brain volume, and sulcal areas (Hotelling's Trace) as well as between-subjects comparison of 11 individual sulcal areas (averaged between left and right hemispheres). There were no differences between IED- and IED+ groups with respect to age or total brain (gray or white matter) volume, and multivariate tests demonstrated a marginally significant decrease of sulcal areas in IED+ baboons (p=0.075). Tests of between-subjects effects showed statistically significant decreases in the intraparietal (p=0.002), central (p=0.03) and cingulate sulci (p=0.02), and marginal decreases involving the lunate (p=0.07) and superior temporal sulci (p=0.08). Differences in sulcal areas in IED+ baboons may reflect global developmental abnormalities, while decreases of areas of specific sulci reflect anatomical markers for potential generators or cortical nodes of the networks underlying spontaneous seizures and photosensitivity in the baboon.

%B Epilepsy Res %V 93 %P 91-5 %8 2011 Feb %G eng %N 2-3 %1 https://www.ncbi.nlm.nih.gov/pubmed/21256716?dopt=Abstract %R 10.1016/j.eplepsyres.2010.10.016 %0 Journal Article %J J Lipid Res %D 2010 %T Calpain-10 is a component of the obesity-related quantitative trait locus Adip1. %A Cheverud, James M %A Fawcett, Gloria L %A Jarvis, Joseph P %A Norgard, Elizabeth A %A Pavlicev, Mihaela %A Pletscher, L Susan %A Polonsky, Kenneth S %A Ye, Honggang %A Bell, Graeme I %A Semenkovich, Clay F %K Alleles %K Animals %K Calpain %K Female %K Gene Knockout Techniques %K Genetic Complementation Test %K Genetic Variation %K Hybridization, Genetic %K Male %K Mice %K Obesity %K Quantitative Trait Loci %X

We previously mapped Adip1, an obesity quantitative trait locus (QTL), to the central portion of murine chromosome 1 containing the calpain-10 (Capn10) gene. Human studies have associated calpain-10 (CAPN10) variants with type 2 diabetes and various metabolic traits. We performed a quantitative hybrid complementation test (QHCT) to determine whether differences attributed to Adip1 are the result of variant Capn10 alleles in LG/J and SM/J mice. We crossed LG/J and SM/J to wild-type (C57BL/6J) and Capn10 knockout (Capn10(-/-)) mice to form four F(1) hybrid groups: LG/J by wild-type, LG/J by Capn10(-/-), SM/J by wild-type, and SM/J by Capn10(-/-). We performed a two-way ANOVA with the experimental strain, tester strain, and their interaction as the factors. Significant interaction indicates a quantitative failure to complement. We found failure to complement for fat, organ, and body weights, and leptin, female free fatty acid, and triglyceride levels. Capn10(-/-) resulted in heavier weights and higher serum levels in LG/J crosses but not in SM/J crosses. For glucose tolerance and insulin response tests, the Capn10(-/-) allele resulted in lower glucose levels in crosses with SM/J but had no effect in the LG/J crosses. Differences between the LG/J and SM/J Capn10 alleles are the likely source of some of the QTL effects mapped to Adip1 in the LG/J-by-SM/J cross. Capn10 plays an important role in regulating obesity and diabetes in mice.

%B J Lipid Res %V 51 %P 907-13 %8 2010 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/20388922?dopt=Abstract %R 10.1194/jlr.M900128 %0 Journal Article %J Science %D 2010 %T A catalog of reference genomes from the human microbiome. %A Nelson, Karen E %A Weinstock, George M %A Highlander, Sarah K %A Worley, Kim C %A Creasy, Heather Huot %A Wortman, Jennifer Russo %A Rusch, Douglas B %A Mitreva, Makedonka %A Sodergren, Erica %A Chinwalla, Asif T %A Feldgarden, Michael %A Gevers, Dirk %A Haas, Brian J %A Madupu, Ramana %A Ward, Doyle V %A Birren, Bruce W %A Gibbs, Richard A %A Methe, Barbara %A Petrosino, Joseph F %A Strausberg, Robert L %A Sutton, Granger G %A White, Owen R %A Wilson, Richard K %A Durkin, Scott %A Giglio, Michelle Gwinn %A Gujja, Sharvari %A Howarth, Clint %A Kodira, Chinnappa D %A Kyrpides, Nikos %A Mehta, Teena %A Muzny, Donna M %A Pearson, Matthew %A Pepin, Kymberlie %A Pati, Amrita %A Qin, Xiang %A Yandava, Chandri %A Zeng, Qiandong %A Zhang, Lan %A Berlin, Aaron M %A Chen, Lei %A Hepburn, Theresa A %A Johnson, Justin %A McCorrison, Jamison %A Miller, Jason %A Minx, Pat %A Nusbaum, Chad %A Russ, Carsten %A Sykes, Sean M %A Tomlinson, Chad M %A Young, Sarah %A Warren, Wesley C %A Badger, Jonathan %A Crabtree, Jonathan %A Markowitz, Victor M %A Orvis, Joshua %A Cree, Andrew %A Ferriera, Steve %A Fulton, Lucinda L %A Fulton, Robert S %A Gillis, Marcus %A Hemphill, Lisa D %A Joshi, Vandita %A Kovar, Christie %A Torralba, Manolito %A Wetterstrand, Kris A %A Abouellleil, Amr %A Wollam, Aye M %A Buhay, Christian J %A Ding, Yan %A Dugan, Shannon %A FitzGerald, Michael G %A Holder, Mike %A Hostetler, Jessica %A Clifton, Sandra W %A Allen-Vercoe, Emma %A Earl, Ashlee M %A Farmer, Candace N %A Liolios, Konstantinos %A Surette, Michael G %A Xu, Qiang %A Pohl, Craig %A Wilczek-Boney, Katarzyna %A Zhu, Dianhui %K Bacteria %K Bacterial Proteins %K Biodiversity %K Computational Biology %K Databases, Genetic %K Gastrointestinal Tract %K Genes, Bacterial %K Genetic Variation %K Genome, Archaeal %K Genome, Bacterial %K Humans %K Metagenome %K Metagenomics %K Mouth %K Peptides %K Phylogeny %K Respiratory System %K Sequence Analysis, DNA %K Skin %K Urogenital System %X

The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.

%B Science %V 328 %P 994-9 %8 2010 May 21 %G eng %N 5981 %1 https://www.ncbi.nlm.nih.gov/pubmed/20489017?dopt=Abstract %R 10.1126/science.1183605 %0 Journal Article %J Metabolism %D 2010 %T Common INSIG2 polymorphisms are associated with age-related changes in body size and high-density lipoprotein cholesterol from young adulthood to middle age. %A Fornage, Myriam %A Papanicolaou, George %A Lewis, Cora E %A Boerwinkle, Eric %A Siscovick, David S %K Adolescent %K Adult %K Age Factors %K Body Mass Index %K Body Size %K Cholesterol, HDL %K Cross-Sectional Studies %K Female %K Humans %K Intracellular Signaling Peptides and Proteins %K Male %K Membrane Proteins %K Polymorphism, Single Nucleotide %K Young Adult %X

Insulin-induced gene 2 (INSIG2) plays an important role in the regulation of cholesterol and fatty acids synthesis. A polymorphism, rs7566605, located 10 kilobases upstream of the INSIG2 gene, was identified in a genomewide association study of obesity. We conducted an association study of 12 INSIG2 tag-single nucleotide polymorphisms with longitudinal measures of body size (body mass index and waist circumference) and lipid metabolism (plasma high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides levels). We investigated their interaction with age in 4304 Coronary Artery Risk Development in Young Adults participants (49.5% blacks, 50.5% whites) followed prospectively for 20 years. rs7566605 was not associated with variation in body size or lipid metabolism at any age in either racial group. However, rs1352083 and rs10185316 were associated with age-related decline in high-density lipoprotein cholesterol in whites (P = .0005 and .04, respectively). A similar trend was observed in blacks who consistently maintained a body mass index less than 25 kg/m(2) over the study period. These data support a role of INSIG2 sequence variation in the regulation of cholesterol metabolism.

%B Metabolism %V 59 %P 1084-91 %8 2010 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/20045156?dopt=Abstract %R 10.1016/j.metabol.2009.11.005 %0 Journal Article %J PLoS One %D 2010 %T Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. %A Yeoman, Carl J %A Yildirim, Suleyman %A Thomas, Susan M %A Durkin, A Scott %A Torralba, Manolito %A Sutton, Granger %A Buhay, Christian J %A Ding, Yan %A Dugan-Rocha, Shannon P %A Muzny, Donna M %A Qin, Xiang %A Gibbs, Richard A %A Leigh, Steven R %A Stumpf, Rebecca %A White, Bryan A %A Highlander, Sarah K %A Nelson, Karen E %A Wilson, Brenda A %K Bacterial Proteins %K Female %K Gardnerella vaginalis %K Genomics %K Humans %K Male %K Molecular Sequence Data %K Phylogeny %K Vagina %K Vaginosis, Bacterial %K Virulence %X

BACKGROUND: Gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (BV). Here we report the genome sequencing and comparative analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and 594 (ATCC 14018) were isolated from the vaginal tracts of women with symptomatic BV, while Strain 409-05 was isolated from a healthy, asymptomatic individual with a Nugent score of 9.

PRINCIPAL FINDINGS: Substantial genomic rearrangement and heterogeneity were observed that appeared to have resulted from both mobile elements and substantial lateral gene transfer. These genomic differences translated to differences in metabolic potential. All strains are equipped with significant virulence potential, including genes encoding the previously described vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm formation, and antimicrobial resistance systems, We also observed systems promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains possess a large number of genes that may enhance their ability to compete with and exclude other vaginal colonists. These include up to six toxin-antitoxin systems and up to nine additional antitoxins lacking cognate toxins, several of which are clustered within each genome. All strains encode bacteriocidal toxins, including two lysozyme-like toxins produced uniquely by strain 409-05. Interestingly, the BV isolates encode numerous proteins not found in strain 409-05 that likely increase their pathogenic potential. These include enzymes enabling mucin degradation, a trait previously described to strongly correlate with BV, although commonly attributed to non-G. vaginalis species.

CONCLUSIONS: Collectively, our results indicate that all three strains are able to thrive in vaginal environments, and therein the BV isolates are capable of occupying a niche that is unique from 409-05. Each strain has significant virulence potential, although genomic and metabolic differences, such as the ability to degrade mucin, indicate that the detection of G. vaginalis in the vaginal tract provides only partial information on the physiological potential of the organism.

%B PLoS One %V 5 %P e12411 %8 2010 Aug 26 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/20865041?dopt=Abstract %R 10.1371/journal.pone.0012411 %0 Journal Article %J Nature %D 2010 %T Complete Khoisan and Bantu genomes from southern Africa. %A Schuster, Stephan C %A Miller, Webb %A Ratan, Aakrosh %A Tomsho, Lynn P %A Giardine, Belinda %A Kasson, Lindsay R %A Harris, Robert S %A Petersen, Desiree C %A Zhao, Fangqing %A Qi, Ji %A Alkan, Can %A Kidd, Jeffrey M %A Sun, Yazhou %A Drautz, Daniela I %A Bouffard, Pascal %A Muzny, Donna M %A Reid, Jeffrey G %A Nazareth, Lynne V %A Wang, Qingyu %A Burhans, Richard %A Riemer, Cathy %A Wittekindt, Nicola E %A Moorjani, Priya %A Tindall, Elizabeth A %A Danko, Charles G %A Teo, Wee Siang %A Buboltz, Anne M %A Zhang, Zhenhai %A Ma, Qianyi %A Oosthuysen, Arno %A Steenkamp, Abraham W %A Oostuisen, Hermann %A Venter, Philippus %A Gajewski, John %A Zhang, Yu %A Pugh, B Franklin %A Makova, Kateryna D %A Nekrutenko, Anton %A Mardis, Elaine R %A Patterson, Nick %A Pringle, Tom H %A Chiaromonte, Francesca %A Mullikin, James C %A Eichler, Evan E %A Hardison, Ross C %A Gibbs, Richard A %A Harkins, Timothy T %A Hayes, Vanessa M %K Asian People %K Black People %K Ethnicity %K Exons %K Genetics, Medical %K Genome, Human %K Humans %K Phylogeny %K Polymorphism, Single Nucleotide %K South Africa %K White People %X

The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.

%B Nature %V 463 %P 943-7 %8 2010 Feb 18 %G eng %N 7283 %1 https://www.ncbi.nlm.nih.gov/pubmed/20164927?dopt=Abstract %R 10.1038/nature08795 %0 Journal Article %J Atherosclerosis %D 2009 %T Carbohydrate intake modifies associations between ANGPTL4[E40K] genotype and HDL-cholesterol concentrations in White men from the Atherosclerosis Risk in Communities (ARIC) study. %A Nettleton, Jennifer A %A Volcik, Kelly A %A Hoogeveen, Ron C %A Boerwinkle, Eric %K Alleles %K Angiopoietin-Like Protein 4 %K Angiopoietins %K Atherosclerosis %K Cholesterol %K Cholesterol, HDL %K Community Health Services %K Diet %K Female %K Genetic Variation %K Genotype %K Humans %K Male %K Middle Aged %K Nutritional Sciences %K Risk %K Sex Factors %K Triglycerides %K White People %X

BACKGROUND: Common allelic variation in the angiopoietin-like 4 gene (ANGPTL4[E40K]) has been associated with low triglyceride (TG) and high HDL-C.

OBJECTIVE: We examined whether dietary macronutrient intake modified associations between ANGPTL4[E40K] variation and TG and HDL-C in White men and women from the Atherosclerosis Risk in Communities study.

DESIGN: Diet was assessed by food frequency questionnaire. Intake of fat (total fat [TF], saturated fat [SF], monounsaturated fat [MUFA], polyunsaturated fat [PUFA], and n-3 PUFA) and carbohydrate were expressed as percentage of total energy intake. ANGPTL4 A allele carriers (n=148 in men, 200 in women) were compared to non-carriers (n=3667 in men, 4496 in women). Interactions were tested separately in men and women, adjusting for study center, age, smoking, physical activity, BMI, and alcohol intake.

RESULTS: ANGPTL4 A allele carriers had significantly greater HDL-C and lower TG than non-carriers (p

CONCLUSIONS: These data suggest that ANGPTL4 variation and relative contributions of dietary fat and carbohydrate influence TG and HDL-C concentrations. In men, ANGPTL4 variation and dietary carbohydrate may interactively influence HDL-C.

%B Atherosclerosis %V 203 %P 214-20 %8 2009 Mar %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/18599063?dopt=Abstract %R 10.1016/j.atherosclerosis.2008.05.037 %0 Journal Article %J Circ Cardiovasc Genet %D 2009 %T Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium: Design of prospective meta-analyses of genome-wide association studies from 5 cohorts. %A Psaty, Bruce M %A O'Donnell, Christopher J %A Gudnason, Vilmundur %A Lunetta, Kathryn L %A Folsom, Aaron R %A Rotter, Jerome I %A Uitterlinden, André G %A Harris, Tamara B %A Witteman, Jacqueline C M %A Boerwinkle, Eric %K Adult %K Aged %K Aging %K Cohort Studies %K Female %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Genotype %K Heart Diseases %K Humans %K Male %K Meta-Analysis as Topic %K Middle Aged %K Phenotype %K Research Design %K Risk Factors %X

BACKGROUND: The primary aim of genome-wide association studies is to identify novel genetic loci associated with interindividual variation in the levels of risk factors, the degree of subclinical disease, or the risk of clinical disease. The requirement for large sample sizes and the importance of replication have served as powerful incentives for scientific collaboration. Methods- The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium was formed to facilitate genome-wide association studies meta-analyses and replication opportunities among multiple large population-based cohort studies, which collect data in a standardized fashion and represent the preferred method for estimating disease incidence. The design of the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium includes 5 prospective cohort studies from the United States and Europe: the Age, Gene/Environment Susceptibility-Reykjavik Study, the Atherosclerosis Risk in Communities Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Rotterdam Study. With genome-wide data on a total of about 38 000 individuals, these cohort studies have a large number of health-related phenotypes measured in similar ways. For each harmonized trait, within-cohort genome-wide association study analyses are combined by meta-analysis. A prospective meta-analysis of data from all 5 cohorts, with a properly selected level of genome-wide statistical significance, is a powerful approach to finding genuine phenotypic associations with novel genetic loci.

CONCLUSIONS: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium and collaborating non-member studies or consortia provide an excellent framework for the identification of the genetic determinants of risk factors, subclinical-disease measures, and clinical events.

%B Circ Cardiovasc Genet %V 2 %P 73-80 %8 2009 Feb %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/20031568?dopt=Abstract %R 10.1161/CIRCGENETICS.108.829747 %0 Journal Article %J J Bacteriol %D 2009 %T A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis Group, biotype I). %A Sillanpaa, Jouko %A Nallapareddy, Sreedhar R %A Qin, Xiang %A Singh, Kavindra V %A Muzny, Donna M %A Kovar, Christie L %A Nazareth, Lynne V %A Gibbs, Richard A %A Ferraro, Mary J %A Steckelberg, James M %A Weinstock, George M %A Murray, Barbara E %K Adhesins, Bacterial %K Fimbriae, Bacterial %K Gene Expression Profiling %K Gene Expression Regulation, Bacterial %K Genome, Bacterial %K Multigene Family %K Streptococcus %X

Members of the Streptococcus bovis group are important causes of endocarditis. However, factors associated with their pathogenicity, such as adhesins, remain uncharacterized. We recently demonstrated that endocarditis-derived Streptococcus gallolyticus subsp. gallolyticus isolates frequently adhere to extracellular matrix (ECM) proteins. Here, we generated a draft genome sequence of an ECM protein-adherent S. gallolyticus subsp. gallolyticus strain and found, by genome-wide analyses, 11 predicted LPXTG-type cell wall-anchored proteins with characteristics of MSCRAMMs, including a modular architecture of domains predicted to adopt immunoglobulin (Ig)-like folding. A recombinant segment of one of these, Acb, showed high-affinity binding to immobilized collagen, and cell surface expression of Acb correlated with the presence of acb and collagen adherence of isolates. Three of the 11 proteins have similarities to major pilus subunits and are organized in separate clusters, each including a second Ig-fold-containing MSCRAMM and a class C sortase, suggesting that the sequenced strain encodes three distinct types of pili. Reverse transcription-PCR demonstrated that all three genes of one cluster, acb-sbs7-srtC1, are cotranscribed, consistent with pilus operons of other gram-positive bacteria. Further analysis detected expression of all 11 genes in cells grown to mid to late exponential growth phases. Wide distribution of 9 of the 11 genes was observed among S. gallolyticus subsp. gallolyticus isolates with fewer genes present in other S. bovis group species/subspecies. The high prevalence of genes encoding putative MSCRAMMs and pili, including a collagen-binding MSCRAMM, among S. gallolyticus subsp. gallolyticus isolates may play an important role in the predominance of this subspecies in S. bovis endocarditis.

%B J Bacteriol %V 191 %P 6643-53 %8 2009 Nov %G eng %N 21 %1 https://www.ncbi.nlm.nih.gov/pubmed/19717590?dopt=Abstract %R 10.1128/JB.00909-09 %0 Journal Article %J Nat Genet %D 2009 %T A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. %A Khanna, Hemant %A Davis, Erica E %A Murga-Zamalloa, Carlos A %A Estrada-Cuzcano, Alejandro %A Lopez, Irma %A den Hollander, Anneke I %A Zonneveld, Marijke N %A Othman, Mohammad I %A Waseem, Naushin %A Chakarova, Christina F %A Maubaret, Cecilia %A Diaz-Font, Anna %A MacDonald, Ian %A Muzny, Donna M %A Wheeler, David A %A Morgan, Margaret %A Lewis, Lora R %A Logan, Clare V %A Tan, Perciliz L %A Beer, Michael A %A Inglehearn, Chris F %A Lewis, Richard A %A Jacobson, Samuel G %A Bergmann, Carsten %A Beales, Philip L %A Attié-Bitach, Tania %A Johnson, Colin A %A Otto, Edgar A %A Bhattacharya, Shomi S %A Hildebrandt, Friedhelm %A Gibbs, Richard A %A Koenekoop, Robert K %A Swaroop, Anand %A Katsanis, Nicholas %K Adaptor Proteins, Signal Transducing %K Alleles %K Animals %K Bardet-Biedl Syndrome %K Ciliary Body %K Europe %K Genetic Variation %K GTP Phosphohydrolases %K Humans %K Mutation %K Polymorphism, Single Nucleotide %K Retinal Degeneration %K Retinitis Pigmentosa %K RNA, Messenger %K Uveitis %K Zebrafish %X

Despite rapid advances in the identification of genes involved in disease, the predictive power of the genotype remains limited, in part owing to poorly understood effects of second-site modifiers. Here we demonstrate that a polymorphic coding variant of RPGRIP1L (retinitis pigmentosa GTPase regulator-interacting protein-1 like), a ciliary gene mutated in Meckel-Gruber (MKS) and Joubert (JBTS) syndromes, is associated with the development of retinal degeneration in individuals with ciliopathies caused by mutations in other genes. As part of our resequencing efforts of the ciliary proteome, we identified several putative loss-of-function RPGRIP1L mutations, including one common variant, A229T. Multiple genetic lines of evidence showed this allele to be associated with photoreceptor loss in ciliopathies. Moreover, we show that RPGRIP1L interacts biochemically with RPGR, loss of which causes retinal degeneration, and that the Thr229-encoded protein significantly compromises this interaction. Our data represent an example of modification of a discrete phenotype of syndromic disease and highlight the importance of a multifaceted approach for the discovery of modifier alleles of intermediate frequency and effect.

%B Nat Genet %V 41 %P 739-45 %8 2009 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/19430481?dopt=Abstract %R 10.1038/ng.366 %0 Journal Article %J Am J Med Genet B Neuropsychiatr Genet %D 2009 %T Common and rare variants of DAOA in bipolar disorder. %A Maheshwari, Manjula %A Shi, Jiajun %A Badner, Judith A %A Skol, Andrew %A Willour, Virginia L %A Muzny, Donna M %A Wheeler, David A %A Gerald, Fowler R %A Detera-Wadleigh, Sevilla %A McMahon, Francis J %A Potash, James B %A Gershon, Elliot S %A Liu, Chunyu %A Gibbs, Richard A %K Bipolar Disorder %K Carrier Proteins %K Cloning, Molecular %K Exons %K Female %K Genetic Predisposition to Disease %K Humans %K Intracellular Signaling Peptides and Proteins %K Male %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %X

The D-amino acid oxidase activator (DAOA, previously known as G72) gene, mapped on 13q33, has been reported to be genetically associated with bipolar disorder (BP) in several populations. The consistency of associated variants is unclear and rare variants in exons of the DAOA gene have not been investigated in psychiatric diseases. We employed a conditional linkage method-STatistical Explanation for Positional Cloning (STEPC) to evaluate whether any associated single nucleotide polymorphisms (SNPs) account for the evidence of linkage in a pedigree series that previously has been linked to marker D13S779 at 13q33. We also performed an association study in a sample of 376 Caucasian BP parent-proband trios by genotyping 38 common SNPs in the gene region. Besides, we resequenced coding regions and flanking intronic sequences of DAOA in 555 Caucasian unrelated BP patients and 564 mentally healthy controls, to identify putative functional rare variants that may contribute to disease. One SNP rs1935058 could "explain" the linkage signal in the family sample set (P = 0.055) using STEPC analysis. No significant allelic association was detected in an association study by genotyping 38 common SNPs in 376 Caucasian BP trios. Resequencing identified 53 SNPs, of which 46 were novel SNPs. There was no significant excess of rare variants in cases relative to controls. Our results suggest that DAOA does not have a major effect on BP susceptibility. However, DAOA may contribute to bipolar susceptibility in some specific families as evidenced by the STEPC analysis.

%B Am J Med Genet B Neuropsychiatr Genet %V 150B %P 960-6 %8 2009 Oct 05 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/19194963?dopt=Abstract %R 10.1002/ajmg.b.30925 %0 Journal Article %J Evol Biol %D 2009 %T Comparison of Mandibular Phenotypic and Genetic Integration between Baboon and Mouse. %A Willmore, Katherine E %A Roseman, Charles C %A Rogers, Jeffrey %A Cheverud, James M %A Richtsmeier, Joan T %X

In this study we compare patterns of mandibular integration between mice and baboons using both phenotypic and quantitative genetic data. Specifically, we test how well each species fits with the mosaic model of mandibular integration suggested by Atchley and Hall (Biol Rev Camb Philos Soc 66:101-157, 1991) based on developmental modules. We hypothesize that patterns of integration will be similar for mice and baboons and that both species will show strong integration within developmental modules and weaker integration between modules. Corresponding landmark data were collected from the hemi-mandibles of an advanced intercross mouse sample (N = 1239) and mandibles from a baboon sample of known pedigree from the Southwest Foundation for Biomedical Research (N = 430). We used four methods of analysis to quantify and compare the degree of mandibular integration between species including two methods based on a priori assumptions, and two a posteriori analyses. We found that patterns of integration are broadly similar for baboon and mouse mandibles, with both species displaying a modular pattern of integration. While there is a general trend of similarity in integration patterns between species, there were some marked differences. Mice are strongly correlated among distances within the coronoid process and the incisive alveolar region, whereas baboons are strongly integrated within the condylar process. We discuss the potential evolutionary implications of the similar patterns of integration between these species with an emphasis on the role of modularity.

%B Evol Biol %V 36 %P 19-36 %8 2009 Mar %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/22212926?dopt=Abstract %R 10.1007/s11692-009-9056-9 %0 Journal Article %J Mol Plant Microbe Interact %D 2009 %T Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics. %A Duan, Yongping %A Zhou, Lijuan %A Hall, David G %A Li, Wenbin %A Harshavardhan Doddapaneni %A Lin, Hong %A Liu, Li %A Vahling, Cheryl M %A Gabriel, Dean W %A Williams, Kelly P %A Dickerman, Allan %A Sun, Yijun %A Gottwald, Tim %K Animals %K Bacterial Proteins %K Carrier Proteins %K Citrus %K Genome, Bacterial %K Genomics %K Hemiptera %K Molecular Sequence Data %K Phylogeny %K Rhizobiaceae %K Sequence Analysis, DNA %K Symbiosis %X

Citrus huanglongbing is the most destructive disease of citrus worldwide. It is spread by citrus psyllids and is associated with a low-titer, phloem-limited infection by any of three uncultured species of alpha-Proteobacteria, 'Candidatus Liberibacter asiaticus', 'Ca. L. americanus', and 'Ca. L. africanus'. A complete circular 'Ca. L. asiaticus' genome has been obtained by metagenomics, using the DNA extracted from a single 'Ca. L. asiaticus'-infected psyllid. The 1.23-Mb genome has an average 36.5% GC content. Annotation revealed a high percentage of genes involved in both cell motility (4.5%) and active transport in general (8.0%), which may contribute to its virulence. 'Ca. L. asiaticus' appears to have a limited ability for aerobic respiration and is likely auxotrophic for at least five amino acids. Consistent with its intracellular nature, 'Ca. L. asiaticus' lacks type III and type IV secretion systems as well as typical free-living or plant-colonizing extracellular degradative enzymes. 'Ca. L. asiaticus' appears to have all type I secretion system genes needed for both multidrug efflux and toxin effector secretion. Multi-protein phylogenetic analysis confirmed 'Ca. L. asiaticus' as an early-branching and highly divergent member of the family Rhizobiaceae. This is the first genome sequence of an uncultured alpha-proteobacteria that is both an intracellular plant pathogen and insect symbiont.

%B Mol Plant Microbe Interact %V 22 %P 1011-20 %8 2009 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/19589076?dopt=Abstract %R 10.1094/MPMI-22-8-1011 %0 Journal Article %J Genome Res %D 2009 %T The completion of the Mammalian Gene Collection (MGC). %A Temple, Gary %A Gerhard, Daniela S %A Rasooly, Rebekah %A Feingold, Elise A %A Good, Peter J %A Robinson, Cristen %A Mandich, Allison %A Derge, Jeffrey G %A Lewis, Jeanne %A Shoaf, Debonny %A Collins, Francis S %A Jang, Wonhee %A Wagner, Lukas %A Shenmen, Carolyn M %A Misquitta, Leonie %A Schaefer, Carl F %A Buetow, Kenneth H %A Bonner, Tom I %A Yankie, Linda %A Ward, Ming %A Phan, Lon %A Astashyn, Alex %A Brown, Garth %A Farrell, Catherine %A Hart, Jennifer %A Landrum, Melissa %A Maidak, Bonnie L %A Murphy, Michael %A Murphy, Terence %A Rajput, Bhanu %A Riddick, Lillian %A Webb, David %A Weber, Janet %A Wu, Wendy %A Pruitt, Kim D %A Maglott, Donna %A Siepel, Adam %A Brejova, Brona %A Diekhans, Mark %A Harte, Rachel %A Baertsch, Robert %A Kent, Jim %A Haussler, David %A Brent, Michael %A Langton, Laura %A Comstock, Charles L G %A Stevens, Michael %A Wei, Chaochun %A van Baren, Marijke J %A Salehi-Ashtiani, Kourosh %A Murray, Ryan R %A Ghamsari, Lila %A Mello, Elizabeth %A Lin, Chenwei %A Pennacchio, Christa %A Schreiber, Kirsten %A Shapiro, Nicole %A Marsh, Amber %A Pardes, Elizabeth %A Moore, Troy %A Lebeau, Anita %A Muratet, Mike %A Simmons, Blake %A Kloske, David %A Sieja, Stephanie %A Hudson, James %A Sethupathy, Praveen %A Brownstein, Michael %A Bhat, Narayan %A Lazar, Joseph %A Jacob, Howard %A Gruber, Chris E %A Smith, Mark R %A McPherson, John %A Garcia, Angela M %A Gunaratne, Preethi H %A Wu, Jiaqian %A Muzny, Donna %A Gibbs, Richard A %A Young, Alice C %A Bouffard, Gerard G %A Blakesley, Robert W %A Mullikin, Jim %A Green, Eric D %A Dickson, Mark C %A Rodriguez, Alex C %A Grimwood, Jane %A Schmutz, Jeremy %A Myers, Richard M %A Hirst, Martin %A Zeng, Thomas %A Tse, Kane %A Moksa, Michelle %A Deng, Merinda %A Ma, Kevin %A Mah, Diana %A Pang, Johnson %A Taylor, Greg %A Chuah, Eric %A Deng, Athena %A Fichter, Keith %A Go, Anne %A Lee, Stephanie %A Wang, Jing %A Griffith, Malachi %A Morin, Ryan %A Moore, Richard A %A Mayo, Michael %A Munro, Sarah %A Wagner, Susan %A Jones, Steven J M %A Holt, Robert A %A Marra, Marco A %A Lu, Sun %A Yang, Shuwei %A Hartigan, James %A Graf, Marcus %A Wagner, Ralf %A Letovksy, Stanley %A Pulido, Jacqueline C %A Robison, Keith %A Esposito, Dominic %A Hartley, James %A Wall, Vanessa E %A Hopkins, Ralph F %A Ohara, Osamu %A Wiemann, Stefan %K Animals %K Cloning, Molecular %K Computational Biology %K DNA %K DNA, Complementary %K Gene Library %K Genes %K Humans %K Mammals %K Mice %K National Institutes of Health (U.S.) %K Rats %K Reverse Transcriptase Polymerase Chain Reaction %K United States %X

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.

%B Genome Res %V 19 %P 2324-33 %8 2009 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/19767417?dopt=Abstract %R 10.1101/gr.095976.109 %0 Journal Article %J PLoS Genet %D 2009 %T Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). %A Degenhardt, Jeremiah D %A de Candia, Paola %A Chabot, Adrien %A Schwartz, Stuart %A Henderson, Les %A Ling, Binhua %A Hunter, Meredith %A Jiang, Zhaoshi %A Palermo, Robert E %A Katze, Michael %A Eichler, Evan E %A Ventura, Mario %A Rogers, Jeffrey %A Marx, Preston %A Gilad, Yoav %A Bustamante, Carlos D %K Animals %K Calibration %K Chemokine CCL3 %K Disease Progression %K DNA Primers %K Gene Dosage %K Genetics, Population %K Immune System %K Likelihood Functions %K Macaca mulatta %K Microsatellite Repeats %K Models, Statistical %K Proportional Hazards Models %K Reverse Transcriptase Polymerase Chain Reaction %K Simian Acquired Immunodeficiency Syndrome %X

Variation in genes underlying host immunity can lead to marked differences in susceptibility to HIV infection among humans. Despite heavy reliance on non-human primates as models for HIV/AIDS, little is known about which host factors are shared and which are unique to a given primate lineage. Here, we investigate whether copy number variation (CNV) at CCL3-like genes (CCL3L), a key genetic host factor for HIV/AIDS susceptibility and cell-mediated immune response in humans, is also a determinant of time until onset of simian-AIDS in rhesus macaques. Using a retrospective study of 57 rhesus macaques experimentally infected with SIVmac, we find that CCL3L CNV explains approximately 18% of the variance in time to simian-AIDS (p<0.001) with lower CCL3L copy number associating with more rapid disease course. We also find that CCL3L copy number varies significantly (p<10(-6)) among rhesus subpopulations, with Indian-origin macaques having, on average, half as many CCL3L gene copies as Chinese-origin macaques. Lastly, we confirm that CCL3L shows variable copy number in humans and chimpanzees and report on CCL3L CNV within and among three additional primate species. On the basis of our findings we suggest that (1) the difference in population level copy number may explain previously reported observations of longer post-infection survivorship of Chinese-origin rhesus macaques, (2) stratification by CCL3L copy number in rhesus SIV vaccine trials will increase power and reduce noise due to non-vaccine-related differences in survival, and (3) CCL3L CNV is an ancestral component of the primate immune response and, therefore, copy number variation has not been driven by HIV or SIV per se.

%B PLoS Genet %V 5 %P e1000346 %8 2009 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/19165326?dopt=Abstract %R 10.1371/journal.pgen.1000346 %0 Journal Article %J Bioinformatics %D 2008 %T cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation. %A Persampieri, Jason %A Ritter, Deborah I %A Lees, Daniel %A Lehoczky, Jessica %A Li, Qiang %A Guo, Su %A Chuang, Jeffrey H %K Animals %K Base Sequence %K Computational Biology %K Conserved Sequence %K Databases, Genetic %K DNA %K Gene Expression Regulation %K Humans %K Internet %K Molecular Sequence Data %K Regulatory Sequences, Nucleic Acid %K Software %K Zebrafish %X

There are thousands of strongly conserved non-coding elements (CNEs) in vertebrate genomes, and their functions remain largely unknown. However, without biologically relevant criteria for prioritizing them, selecting a particular CNE sequences to study can be haphazard. To address this problem, we present cneViewer-a database and webtool that systematizes information on conserved non-coding DNA elements in zebrafish. A key feature here is the ability to search for CNEs that may be relevant to tissue-specific gene regulation, based on known developmental expression patterns of nearby genes. cneViewer provides this and other organizing features that significantly facilitate experimental design and CNE analysis.

%B Bioinformatics %V 24 %P 2418-9 %8 2008 Oct 15 %G eng %N 20 %1 https://www.ncbi.nlm.nih.gov/pubmed/18718943?dopt=Abstract %R 10.1093/bioinformatics/btn443 %0 Journal Article %J BMC Res Notes %D 2008 %T Comparative phylogenomics and multi-gene cluster analyses of the Citrus Huanglongbing (HLB)-associated bacterium Candidatus Liberibacter. %A Doddapaneni, Harshavardhan %A Liao, Huihong %A Lin, Hong %A Bai, Xianjin %A Zhao, Xiaolong %A Civerolo, Edwin L %A Irey, Michael %A Coletta-Filho, Helvecio %A Pietersen, Gerhard %X

BACKGROUND: Huanglongbing (HLB, previously known as citrus greening), is associated with Candidatus Liberibacter species and is a serious threat to citrus production world-wide. The pathogen is a Gram negative, unculturable, phloem-limited bacterium with limited known genomic information. Expanding the genetic knowledge of this organism may provide better understanding of the pathogen and possibly develop effective strategies for control and management of HLB.

RESULTS: Here, we report cloning and characterization of an additional 14.7 Kb of new genomic sequences from three different genomic regions of the Candidatus Liberibacter asiaticus (Las). Sequence variation analyses among the available Ca. Liberibacter species sequences as well as the newly cloned 1.5 Kb of rpoB gene from different Ca. Liberibacter strains have identified INDELs and SNPs. Phylogenetic analysis of the deduced protein sequences from the cloned regions characterizes the HLB-associated Candidatus Liberibacter as a new clade in the sub-division of the alpha-proteobacteria.

CONCLUSION: Comparative analyses of the cloned gene regions of Candidatus Liberibacter with members of the order Rhizobiales suggest overall gene structure and order conservation, albeit with minor variations including gene decay due to the identified pseudogenes. The newly cloned gene regions contribute to our understanding of the molecular aspects of genomic evolution of Ca. Liberibacter.

%B BMC Res Notes %V 1 %P 72 %8 2008 Aug 28 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/18755041?dopt=Abstract %R 10.1186/1756-0500-1-72 %0 Journal Article %J Nature %D 2008 %T The complete genome of an individual by massively parallel DNA sequencing. %A Wheeler, David A %A Srinivasan, Maithreyan %A Egholm, Michael %A Shen, Yufeng %A Chen, Lei %A McGuire, Amy %A He, Wen %A Chen, Yi-Ju %A Makhijani, Vinod %A Roth, G Thomas %A Gomes, Xavier %A Tartaro, Karrie %A Niazi, Faheem %A Turcotte, Cynthia L %A Irzyk, Gerard P %A Lupski, James R %A Chinault, Craig %A Song, Xing-Zhi %A Liu, Yue %A Yuan, Ye %A Nazareth, Lynne %A Xiang Qin %A Donna M Muzny %A Margulies, Marcel %A Weinstock, George M %A Richard A Gibbs %A Rothberg, Jonathan M %K Alleles %K Computational Biology %K Genetic Predisposition to Disease %K Genetic Variation %K Genome, Human %K Genomics %K Genotype %K Humans %K Individuality %K Male %K Oligonucleotide Array Sequence Analysis %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Sensitivity and Specificity %K Sequence Alignment %K Sequence Analysis, DNA %K Software %X

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.

%B Nature %V 452 %P 872-6 %8 2008 Apr 17 %G eng %N 7189 %1 https://www.ncbi.nlm.nih.gov/pubmed/18421352?dopt=Abstract %R 10.1038/nature06884 %0 Journal Article %J J Bacteriol %D 2008 %T The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. %A Durfee, Tim %A Nelson, Richard %A Baldwin, Schuyler %A Plunkett, Guy %A Burland, Valerie %A Mau, Bob %A Petrosino, Joseph F %A Qin, Xiang %A Muzny, Donna M %A Ayele, Mulu %A Gibbs, Richard A %A Csörgo, Bálint %A Pósfai, György %A Weinstock, George M %A Blattner, Frederick R %K Escherichia coli %K Genes, Bacterial %K Genome, Bacterial %K Models, Genetic %K Mutation %K Sequence Analysis, DNA %X

Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and maintenance of large plasmids. The strain was constructed by serial genetic recombination steps, but the underlying sequence changes remained unverified. We report the complete genomic sequence of DH10B by using reads accumulated from the bovine sequencing project at Baylor College of Medicine and assembled with DNAStar's SeqMan genome assembler. The DH10B genome is largely colinear with that of the wild-type K-12 strain MG1655, although it is substantially more complex than previously appreciated, allowing DH10B biology to be further explored. The 226 mutated genes in DH10B relative to MG1655 are mostly attributable to the extensive genetic manipulations the strain has undergone. However, we demonstrate that DH10B has a 13.5-fold higher mutation rate than MG1655, resulting from a dramatic increase in insertion sequence (IS) transposition, especially IS150. IS elements appear to have remodeled genome architecture, providing homologous recombination sites for a 113,260-bp tandem duplication and an inversion. DH10B requires leucine for growth on minimal medium due to the deletion of leuLABCD and harbors both the relA1 and spoT1 alleles causing both sensitivity to nutritional downshifts and slightly lower growth rates relative to the wild type. Finally, while the sequence confirms most of the reported alleles, the sequence of deoR is wild type, necessitating reexamination of the assumed basis for the high transformability of DH10B.

%B J Bacteriol %V 190 %P 2597-606 %8 2008 Apr %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/18245285?dopt=Abstract %R 10.1128/JB.01695-07 %0 Journal Article %J BMC Microbiol %D 2008 %T Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. %A Matejková, Petra %A Strouhal, Michal %A Smajs, David %A Norris, Steven J %A Palzkill, Timothy %A Petrosino, Joseph F %A Sodergren, Erica %A Norton, Jason E %A Singh, Jaz %A Richmond, Todd A %A Molla, Michael N %A Albert, Thomas J %A Weinstock, George M %K Animals %K Chromosome Mapping %K DNA Fingerprinting %K Genome, Bacterial %K Humans %K Molecular Sequence Data %K Oligonucleotide Array Sequence Analysis %K Open Reading Frames %K Polymorphism, Single Nucleotide %K Rabbits %K Reproducibility of Results %K Sequence Analysis, DNA %K Syphilis %K Treponema pallidum %X

BACKGROUND: Syphilis spirochete Treponema pallidum ssp. pallidum remains the enigmatic pathogen, since no virulence factors have been identified and the pathogenesis of the disease is poorly understood. Increasing rates of new syphilis cases per year have been observed recently.

RESULTS: The genome of the SS14 strain was sequenced to high accuracy by an oligonucleotide array strategy requiring hybridization to only three arrays (Comparative Genome Sequencing, CGS). Gaps in the resulting sequence were filled with targeted dideoxy-terminators (DDT) sequencing and the sequence was confirmed by whole genome fingerprinting (WGF). When compared to the Nichols strain, 327 single nucleotide substitutions (224 transitions, 103 transversions), 14 deletions, and 18 insertions were found. On the proteome level, the highest frequency of amino acid-altering substitution polymorphisms was in novel genes, while the lowest was in housekeeping genes, as expected by their evolutionary conservation. Evidence was also found for hypervariable regions and multiple regions showing intrastrain heterogeneity in the T. pallidum chromosome.

CONCLUSION: The observed genetic changes do not have influence on the ability of Treponema pallidum to cause syphilitic infection, since both SS14 and Nichols are virulent in rabbit. However, this is the first assessment of the degree of variation between the two syphilis pathogens and paves the way for phylogenetic studies of this fascinating organism.

%B BMC Microbiol %V 8 %P 76 %8 2008 May 15 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/18482458?dopt=Abstract %R 10.1186/1471-2180-8-76 %0 Journal Article %J J Lipid Res %D 2008 %T Comprehensive evaluation of apolipoprotein H gene (APOH) variation identifies novel associations with measures of lipid metabolism in GENOA. %A Leduc, Magalie S %A Shimmin, Lawrence C %A Klos, Kathy L E %A Hanis, Craig %A Boerwinkle, Eric %A Hixson, James E %K beta 2-Glycoprotein I %K Black People %K Genetic Variation %K Genotype %K Haplotypes %K Humans %K Lipid Metabolism %K Multicenter Studies as Topic %K Polymorphism, Single Nucleotide %K White People %X

Apolipoprotein H (apoH, also named beta-2 glycoprotein I) is found on several classes of lipoproteins, and is involved in the activation of lipoprotein lipase in lipid metabolism. We have comprehensively investigated the association of variation in the apoH gene (APOH) with lipid traits in hepatic cholesterol transport, dietary cholesterol transport (DCT), and reverse cholesterol transport (RCT). Our study population consisted of families from the Genetic Epidemiology Network of Arteriopathy multicenter study that include African Americans, Mexican Americans, and European Americans. We individually tested 36 single-nucleotide polymorphisms (SNPs) that span the APOH locus, including nonsynonymous variants that result in known apoH charge isoforms. In addition, we constructed haplotypes from SNPs in the 5' promoter region that comprise cis-acting regulatory elements, as well as haplotypes for multiple amino acid substitutions. We found point-wise significant associations of APOH variants with various lipid measures in the three racial groups. The strongest associations were found for DCT traits (triglyceride and apoE levels) in Mexican Americans with a nonsynonymous variant (SNP 14917, Cys306Gly) that may alter apoH protein folding in a region involved in phospholipid binding. In conclusion, family-based analyses of APOH variants have identified associations with measures of lipid metabolism in three American racial groups.

%B J Lipid Res %V 49 %P 2648-56 %8 2008 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/18676959?dopt=Abstract %R 10.1194/jlr.M800155-JLR200 %0 Journal Article %J Nature %D 2008 %T Comprehensive genomic characterization defines human glioblastoma genes and core pathways. %K Adolescent %K Adult %K Aged %K Aged, 80 and over %K Brain Neoplasms %K DNA Methylation %K DNA Modification Methylases %K DNA Repair %K DNA Repair Enzymes %K Female %K Gene Dosage %K Gene Expression Regulation, Neoplastic %K Genes, erbB-1 %K Genes, Tumor Suppressor %K Genome, Human %K Genomics %K Glioblastoma %K Humans %K Male %K Middle Aged %K Models, Molecular %K Mutation %K Neurofibromin 1 %K Phosphatidylinositol 3-Kinases %K Protein Structure, Tertiary %K Retrospective Studies %K Signal Transduction %K Tumor Suppressor Proteins %X

Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas--the most common type of adult brain cancer--and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.

%B Nature %V 455 %P 1061-8 %8 2008 Oct 23 %G eng %N 7216 %1 https://www.ncbi.nlm.nih.gov/pubmed/18772890?dopt=Abstract %R 10.1038/nature07385 %0 Journal Article %J Nature %D 2007 %T Characterizing the cancer genome in lung adenocarcinoma. %A Weir, Barbara A %A Woo, Michele S %A Getz, Gad %A Perner, Sven %A Ding, Li %A Beroukhim, Rameen %A Lin, William M %A Province, Michael A %A Kraja, Aldi %A Johnson, Laura A %A Shah, Kinjal %A Sato, Mitsuo %A Thomas, Roman K %A Barletta, Justine A %A Borecki, Ingrid B %A Broderick, Stephen %A Chang, Andrew C %A Chiang, Derek Y %A Chirieac, Lucian R %A Cho, Jeonghee %A Fujii, Yoshitaka %A Gazdar, Adi F %A Giordano, Thomas %A Greulich, Heidi %A Hanna, Megan %A Johnson, Bruce E %A Kris, Mark G %A Lash, Alex %A Lin, Ling %A Lindeman, Neal %A Mardis, Elaine R %A McPherson, John D %A Minna, John D %A Morgan, Margaret B %A Nadel, Mark %A Orringer, Mark B %A Osborne, John R %A Ozenberger, Brad %A Ramos, Alex H %A Robinson, James %A Roth, Jack A %A Rusch, Valerie %A Sasaki, Hidefumi %A Shepherd, Frances %A Sougnez, Carrie %A Spitz, Margaret R %A Tsao, Ming-Sound %A Twomey, David %A Verhaak, Roel G W %A Weinstock, George M %A Wheeler, David A %A Winckler, Wendy %A Yoshizawa, Akihiko %A Yu, Soyoung %A Zakowski, Maureen F %A Zhang, Qunyuan %A Beer, David G %A Wistuba, Ignacio I %A Watson, Mark A %A Garraway, Levi A %A Ladanyi, Marc %A Travis, William D %A Pao, William %A Rubin, Mark A %A Gabriel, Stacey B %A Gibbs, Richard A %A Varmus, Harold E %A Wilson, Richard K %A Lander, Eric S %A Meyerson, Matthew %K Adenocarcinoma %K Cell Line, Tumor %K Chromosome Deletion %K Chromosomes, Human, Pair 14 %K Gene Amplification %K Genome, Human %K Genomics %K Genotype %K Humans %K Intracellular Signaling Peptides and Proteins %K Loss of Heterozygosity %K Lung Neoplasms %K Neoplasms %K Nuclear Proteins %K Polymorphism, Single Nucleotide %K Proto-Oncogene Mas %K RNA Interference %K Thyroid Nuclear Factor 1 %K Transcription Factors %X

Somatic alterations in cellular DNA underlie almost all human cancers. The prospect of targeted therapies and the development of high-resolution, genome-wide approaches are now spurring systematic efforts to characterize cancer genomes. Here we report a large-scale project to characterize copy-number alterations in primary lung adenocarcinomas. By analysis of a large collection of tumours (n = 371) using dense single nucleotide polymorphism arrays, we identify a total of 57 significantly recurrent events. We find that 26 of 39 autosomal chromosome arms show consistent large-scale copy-number gain or loss, of which only a handful have been linked to a specific gene. We also identify 31 recurrent focal events, including 24 amplifications and 7 homozygous deletions. Only six of these focal events are currently associated with known mutations in lung carcinomas. The most common event, amplification of chromosome 14q13.3, is found in approximately 12% of samples. On the basis of genomic and functional analyses, we identify NKX2-1 (NK2 homeobox 1, also called TITF1), which lies in the minimal 14q13.3 amplification interval and encodes a lineage-specific transcription factor, as a novel candidate proto-oncogene involved in a significant fraction of lung adenocarcinomas. More generally, our results indicate that many of the genes that are involved in lung adenocarcinoma remain to be discovered.

%B Nature %V 450 %P 893-8 %8 2007 Dec 06 %G eng %N 7171 %1 https://www.ncbi.nlm.nih.gov/pubmed/17982442?dopt=Abstract %R 10.1038/nature06358 %0 Journal Article %J Science %D 2007 %T Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens". %A Fuli Yu %A Hill, R Sean %A Schaffner, Stephen F %A Sabeti, Pardis C %A Wang, Eric T %A Mignault, Andre A %A Ferland, Russell J %A Moyzis, Robert K %A Walsh, Christopher A %A Reich, David %K Adaptation, Biological %K Asian People %K Biological Evolution %K Black People %K Brain %K Gene Frequency %K Haplotypes %K Humans %K Nerve Tissue Proteins %K Polymorphism, Single Nucleotide %K Recombination, Genetic %K Selection, Genetic %K Sequence Analysis, DNA %K Time %K White People %X

Mekel-Bobrov et al. (Reports, 9 September 2005, p. 1720) suggested that ASPM, a gene associated with microcephaly, underwent natural selection within the last 500 to 14,100 years. Their analyses based on comparison with computer simulations indicated that ASPM had an unusual pattern of variation. However, when we compare ASPM empirically to a large number of other loci, its variation is not unusual and does not support selection.

%B Science %V 316 %P 370 %8 2007 Apr 20 %G eng %N 5823 %1 https://www.ncbi.nlm.nih.gov/pubmed/17446375?dopt=Abstract %R 10.1126/science.316.5823.370a %0 Journal Article %J BMC Plant Biol %D 2007 %T Comparative analysis of ESTs involved in grape responses to Xylella fastidiosa infection. %A Lin, Hong %A Doddapaneni, Harshavardhan %A Takahashi, Yuri %A Walker, M Andrew %K Cluster Analysis %K DNA, Complementary %K Expressed Sequence Tags %K Gene Expression Regulation, Plant %K Gene Library %K Molecular Sequence Data %K Nucleic Acid Hybridization %K Plant Diseases %K Plant Leaves %K Plant Shoots %K Plant Stems %K Reverse Transcriptase Polymerase Chain Reaction %K Sequence Analysis, DNA %K Time Factors %K Vitis %K Xylella %X

BACKGROUND: The gram-negative bacterium Xylella fastidiosa (Xf) is the causal agent of Pierce's disease (PD) in grape as well as diseases of many fruit and ornamental plants. The current molecular breeding efforts have identified genetic basis of PD resistance in grapes. However, the transcriptome level characterization of the host response to this pathogen is lacking.

RESULTS: Twelve tissue specific subtractive suppression hybridization (SSH) cDNA libraries derived from a time course sampling scheme were constructed from stems, leaves and shoots of PD resistant and susceptible sibling genotypes (V. rupestris x V. arizonica) in response to Xf infection. A total of 5,794 sequences were obtained from these cDNA libraries from which 993 contigs and 949 singletons were derived. Using Gene Ontology (GO) hierarchy, the non-redundant sequences were classified into the three principal categories: molecular function (30%), cellular components (9%) and biological processes (7%). Comparative analysis found variations in EST expression pattern between infected and non-infected PD resistant and PD susceptible grape genotypes. Among the three tissues, libraries from stem tissues showed significant differences in transcript quality suggesting their important role in grape-Xylella interaction.

CONCLUSION: This study constitutes the first attempt to characterize the Vitis differential transcriptome associated with host-pathogen interactions from different explants and genotypes. All the generated ESTs have been submitted to GenBank and are also available through our website for further functional studies.

%B BMC Plant Biol %V 7 %P 8 %8 2007 Feb 22 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/17316447?dopt=Abstract %R 10.1186/1471-2229-7-8 %0 Journal Article %J J Infect Dis %D 2007 %T Conservation of virally encoded microRNAs in Kaposi sarcoma--associated herpesvirus in primary effusion lymphoma cell lines and in patients with Kaposi sarcoma or multicentric Castleman disease. %A Marshall, Vickie %A Parks, Thomas %A Bagni, Rachel %A Wang, Cheng Dian %A Samols, Mark A %A Jianhong Hu %A Wyvil, Kathleen M %A Aleman, Karen %A Little, Richard F %A Yarchoan, Robert %A Renne, Rolf %A Whitby, Denise %K Acquired Immunodeficiency Syndrome %K Base Sequence %K Castleman Disease %K Cell Line, Tumor %K Conserved Sequence %K Genetic Variation %K Herpesvirus 8, Human %K Humans %K Lymphoma %K MicroRNAs %K Molecular Sequence Data %K Nucleic Acid Conformation %K Phylogeny %K Sarcoma, Kaposi %X

BACKGROUND: MicroRNAs are small noncoding RNAs that posttranscriptionally regulate gene expression. Kaposi sarcoma (KS)-associated herpesvirus (KSHV) encodes 12 distinct microRNA genes, all of which are located within the latency-associated region that is highly expressed in all KSHV-associated malignancies.

METHODS: We amplified, cloned, and sequenced a 2.8-kbp-long region containing a cluster of 10 microRNAs plus a 646-bp fragment of K12/T0.7 containing the remaining 2 microRNAs from 5 primary effusion lymphoma-derived cell lines and from 17 patient samples. The patients included 2 with classic KS, 12 with AIDS-KS (8 from the United States, 1 from Europe, 3 from Africa, and 4 from Central/South America), and 2 with multicentric Castleman disease (MCD). Additionally, we analyzed the K1, open reading frame 75, and K15 genes to determine KSHV subtypes, and we performed a phylogenetic analysis.

RESULTS: Phylogenetic analysis of the 2.8-kbp microRNA region revealed 2 distinct clusters of sequences: a major (A/C) and a variant (B/Q) cluster. The variant cluster included sequences from 3 patients of African origin and both patients with MCD. Some microRNAs were highly conserved, whereas others had changes that could affect processing and, therefore, biological activity.

CONCLUSIONS: These data demonstrate that KSHV microRNA genes are under tight selection in vivo and suggest that they contribute to the biological activity and possibly the pathogenesis of KSHV-associated malignancies.

%B J Infect Dis %V 195 %P 645-59 %8 2007 Mar 01 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/17262705?dopt=Abstract %R 10.1086/511434 %0 Journal Article %J DNA Seq %D 2007 %T Corticotropin releasing hormone (CRH) gene variation: comprehensive resequencing for variant and molecular haplotype discovery in monosomic hybrid cell lines. %A Shimmin, Lawrence C %A Natarajan, Sivamani %A Ibarguen, Heladio %A Montasser, May %A Kim, Do-Kyun %A Hanis, Craig L %A Eric Boerwinkle %A Wadhwa, Pathik D %A Hixson, James E %K Animals %K Base Sequence %K Cell Line %K Corticotropin-Releasing Hormone %K Ethnicity %K Female %K Haplotypes %K Humans %K Hybrid Cells %K Linkage Disequilibrium %K Male %K Mice %K Molecular Sequence Data %K Monosomy %K Phylogeny %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %X

Candidate gene association studies have met with mixed success due to many reasons including incomplete surveys of genetic variation and differences in patterns of genetic variation among study populations. We present the results of comprehensive variant discovery for the corticotropin releasing hormone gene (CRH on chromosome 8) encoding a neuropeptide that is central to many physiologic pathways. Mouse-human hybrid cell lines were constructed that are monosomic for human chromosome 8 for resequencing of separated CRH alleles to identify variants and directly determine their chromosomal phase for three major ethnic groups including African Americans (AA), Mexican Americans (MA) and European Americans (EA). We also resequenced diploid individuals to evaluate single nucleotide polymorphism (SNP) discovery in the limited numbers of monosomic hybrid cell lines. Our results show that CRH variation is very different in AA, yielding larger numbers of variants and haplotypes compared to MA and EA. Analysis of LD structure found three haplotype blocks in AA and two blocks in EA. Comparisons between AA and EA groups yielded extremely high measures of genetic differentiation (Wright's F(ST)>0.6), likely reflecting disruptive selection in CRH evolution. Network analysis showed that AA have retained an ancestral CRH haplotype, while the most common EA haplotype is derived from a single recombination event.

%B DNA Seq %V 18 %P 434-44 %8 2007 Dec %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/17676473?dopt=Abstract %R 10.1080/10425170701388719 %0 Journal Article %J J Bacteriol %D 2006 %T Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence. %A Petrosino, Joseph F %A Xiang, Qin %A Karpathy, Sandor E %A Jiang, Huaiyang %A Yerrapragada, Shailaja %A Liu, Yamei %A Gioia, Jason %A Hemphill, Lisa %A Gonzalez, Arely %A Raghavan, T M %A Uzman, Akif %A Fox, George E %A Highlander, Sarah %A Reichard, Mason %A Morton, Rebecca J %A Clinkenbeard, Kenneth D %A Weinstock, George M %K Chromosomes, Bacterial %K DNA Transposable Elements %K DNA, Bacterial %K Evolution, Molecular %K Francisella tularensis %K Gene Rearrangement %K Genome, Bacterial %K Molecular Sequence Data %K Polymorphism, Genetic %K Pseudogenes %K Recombination, Genetic %K Sequence Analysis, DNA %K Sequence Homology %K Virulence %X

The gamma-proteobacterium Francisella tularensis is one of the most infectious human pathogens, and the highly virulent organism F. tularensis subsp. tularensis (type A) and less virulent organism F. tularensis subsp. holarctica (type B) are most commonly associated with significant disease in humans and animals. Here we report the complete genome sequence and annotation for a low-passage type B strain (OSU18) isolated from a dead beaver found near Red Rock, Okla., in 1978. A comparison of the F. tularensis subsp. holarctica sequence with that of F. tularensis subsp. tularensis strain Schu4 (P. Larsson et al., Nat. Genet. 37:153-159, 2005) highlighted genetic differences that may underlie different pathogenicity phenotypes and the evolutionary relationship between type A and type B strains. Despite extensive DNA sequence identity, the most significant difference between type A and type B isolates is the striking amount of genomic rearrangement that exists between the strains. All but two rearrangements can be attributed to homologous recombination occurring between two prominent insertion elements, ISFtu1 and ISFtu2. Numerous pseudogenes have been found in the genomes and are likely contributors to the difference in virulence between the strains. In contrast, no rearrangements have been observed between the OSU18 genome and the genome of the type B live vaccine strain (LVS), and only 448 polymorphisms have been found within non-transposase-coding sequences whose homologs are intact in OSU18. Nonconservative differences between the two strains likely include the LVS attenuating mutation(s).

%B J Bacteriol %V 188 %P 6977-85 %8 2006 Oct %G eng %N 19 %1 https://www.ncbi.nlm.nih.gov/pubmed/16980500?dopt=Abstract %R 10.1128/JB.00506-06 %0 Journal Article %J Genome Res %D 2006 %T Community annotation: procedures, protocols, and supporting tools. %A Elsik, Christine G %A Worley, Kim C %A Zhang, Lan %A Milshina, Natalia V %A Jiang, Huaiyang %A Reese, Justin T %A Childs, Kevin L %A Venkatraman, Anand %A Dickens, C Michael %A Weinstock, George M %A Richard A Gibbs %K Animals %K Bees %K Databases, Genetic %K Genome, Human %K Genomics %K Humans %K Models, Genetic %K Molecular Sequence Data %K Sequence Analysis %X

Investigators at the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) and BeeBase organized a community-wide effort to manually annotate the honey bee (Apis mellifera) genome. Although various strategies for manual annotation have been used in the past, the value of dispersed community annotation has not yet been demonstrated. Here we make a case for the merit of dispersed community annotation. We present annotation procedures, standard protocols, and tools used for sequence analysis, data submission, and data management. We also report lessons learned from this dispersed community annotation effort for a metazoan genome.

%B Genome Res %V 16 %P 1329-33 %8 2006 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/17065605?dopt=Abstract %R 10.1101/gr.5580606 %0 Journal Article %J Anim Genet %D 2006 %T Comparative analysis of the bovine MHC class IIb sequence identifies inversion breakpoints and three unexpected genes. %A Childers, C P %A Newkirk, H L %A Honeycutt, D A %A Ramlachan, N %A Donna M Muzny %A Sodergren, E %A Richard A Gibbs %A Weinstock, G M %A Womack, J E %A Skow, L C %K Animals %K Cattle %K Chromosome Inversion %K Chromosomes, Mammalian %K Contig Mapping %K Evolution, Molecular %K Genes, MHC Class II %K Histones %K Humans %K Molecular Sequence Data %K Sequence Analysis, DNA %X

The bovine major histocompatibility complex (MHC) or BoLA is organized differently from typical mammalian MHCs in that a large portion of the class II region, called class IIb, has been transposed to a position near the centromere on bovine chromosome 23. Gene mapping indicated that the rearrangement resulted from a single inversion, but the boundaries and gene content of the inverted segment have not been fully determined. Here, we report the genomic sequence of BoLA IIb. Comparative sequence analysis with the human MHC revealed that the proximal inversion breakpoint occurred approximately 2.5 kb from the 3' end of the glutamate-cysteine ligase, catalytic subunit (GCLC) locus and that the distal breakpoint occurred about 2 kb from the 5' end from a divergent class IIDRbeta-like sequence designated DSB. Gene content, order and orientation of BoLA IIb are consistent with the single inversion hypothesis when compared with the corresponding region of the human class II MHC (HLA class II). Differences with HLA include the presence of a single histone H2B gene located between the proteasome subunit, beta type, 9 (PSMB9) and DMB loci and a duplicated TAP2 with a variant splice site. BoLA IIb spans approximately 450 kb DNA, with 20 apparently intact genes and no obvious pseudogenes. The region contains 227 simple sequence repeats (SSRs) and approximately 167 kb of retroviral-related repetitive DNA. Nineteen of the 20 genes identified in silico are supported by bovine EST data indicating that the functional gene content of BoLA IIb has not been diminished because it has been transposed from the remainder of BoLA genes.

%B Anim Genet %V 37 %P 121-9 %8 2006 Apr %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/16573526?dopt=Abstract %R 10.1111/j.1365-2052.2005.01395.x %0 Journal Article %J Virology %D 2006 %T Complete nucleotide sequence of a P2 family lysogenic bacteriophage, varphiMhaA1-PHL101, from Mannheimia haemolytica serotype A1. %A Highlander, Sarah K %A Weissenberger, Sarah %A Alvarez, Laura E %A Weinstock, George M %A Berget, Peter B %K Bacteriophages %K Base Composition %K Base Sequence %K DNA Replication %K DNA Viruses %K DNA, Viral %K Gene Expression Regulation, Viral %K Mannheimia haemolytica %K Transcription, Genetic %K Viral Proteins %X

The 34,525 nucleotide sequence of a double-stranded DNA bacteriophage (phiMhaA1-PHL101) from Mannheimia haemolytica serotype A1 has been determined. The phage encodes 50 open reading frames. Twenty-three of the proteins are similar to proteins of the P2 family of phages. Other protein sequences are most similar to possible prophage sequences from the draft genome of Histophilus somni 2336. Fourteen open reading frames encode proteins with no known homolog. The P2 orthologues are collinear in phiMhaA1-PHL101, with the exception of the phage tail protein gene T, which maps in a unique location between the S and V genes. The phage ORFs can be arranged into 17 possible transcriptional units and many of the genes are predicted to be translationally coupled. Southern blot analysis revealed phiMhaA1-PHL101 sequences in other A1 isolates as well as in serotype A5, A6, A9, and A12 strains of M. haemolytica, but not in the related organisms, Mannheimia glucosida or Pasteurella trehalosi.

%B Virology %V 350 %P 79-89 %8 2006 Jun 20 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/16631219?dopt=Abstract %R 10.1016/j.virol.2006.03.024 %0 Journal Article %J Arterioscler Thromb Vasc Biol %D 2006 %T Consistent effects of genes involved in reverse cholesterol transport on plasma lipid and apolipoprotein levels in CARDIA participants. %A Klos, Kathy L E %A Sing, Charles F %A Eric Boerwinkle %A Hamon, Sara C %A Rea, Thomas J %A Clark, Andrew %A Fornage, Myriam %A Hixson, James E %K Adult %K Apolipoproteins %K Apolipoproteins A %K Apolipoproteins C %K Apolipoproteins E %K ATP Binding Cassette Transporter 1 %K ATP-Binding Cassette Transporters %K Biological Transport, Active %K Black People %K Carrier Proteins %K Cholesterol %K Cholesterol Ester Transfer Proteins %K Coronary Artery Disease %K Female %K Genetic Predisposition to Disease %K Genotype %K Glycoproteins %K Haplotypes %K Humans %K Lipids %K Male %K Polymorphism, Single Nucleotide %K White People %X

OBJECTIVE: To identify common variations in genes in the reverse cholesterol transport pathway with nongender-specific influence on plasma lipid and apolipoprotein levels.

METHODS AND RESULTS: An average of 5 single nucleotide polymorphisms (SNPs) were genotyped within each of 45 genomic regions (54 genes) in blacks (1131 females and 812 males) and whites (1102 females and 954 males) from the Coronary Artery Risk Development in Young Adults (CARDIA) study. SNPs and gene-based 3-SNP haplotypes were evaluated for their ability to predict variation in plasma apolipoproteins (apo) A-I and apoB, total cholesterol (TC), high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides (TG). We identified 14 SNPs in 6 candidate gene regions that explained statistically significant variation in the same trait in both genders of at least one race and with evidence of consistent genotype mean trend across gender within race. Haplotype analyses identified 9 candidate gene regions that explained statistically significant variation in one or both races.

CONCLUSIONS: Four gene regions, ABCA1, APOA1/C3/A4/A5, APOE/C1/C4/C2, and CETP, explained plasma lipoprotein variation most consistently across strata. Other gene regions that influence plasma lipid and apolipoprotein levels within race include CYP7A1, LPL, PPARA, SOAT1, and SREBF2.

%B Arterioscler Thromb Vasc Biol %V 26 %P 1828-36 %8 2006 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/16763159?dopt=Abstract %R 10.1161/01.ATV.0000231523.19199.45 %0 Journal Article %J J Virol %D 2005 %T Characterization of the minimal replicator of Kaposi's sarcoma-associated herpesvirus latent origin. %A Hu, Jianhong %A Renne, Rolf %K Antigens, Viral %K DNA Replication %K DNA, Viral %K Enhancer Elements, Genetic %K Herpesvirus 8, Human %K Humans %K Nuclear Proteins %K Replication Origin %K Sarcoma, Kaposi %K Terminal Repeat Sequences %K Virus Latency %X

The latency-associated nuclear antigen (LANA) of Kaposi's sarcoma-associated herpesvirus (KSHV) binds to two sites within the 801-bp-long terminal repeat (TR) and is the only viral protein required for episomal maintenance. While two or more copies of TR are required for long-term maintenance, a single TR confers LANA-dependent origin activity on plasmid DNA. Deletion mapping revealed a 71-bp-long minimal replicator containing two distinctive sequence elements: LANA binding sites (LBS1/2) and an adjacent 29- to 32-bp-long GC-rich sequence which we termed the replication element. Furthermore, the transcription factor Sp1 can bind to TR outside the minimal replicator and contributes to TR's previously reported enhancer activity.

%B J Virol %V 79 %P 2637-42 %8 2005 Feb %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/15681465?dopt=Abstract %R 10.1128/JVI.79.4.2637-2642.2005 %0 Journal Article %J J Virol %D 2005 %T Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. %A Samols, Mark A %A Hu, Jianhong %A Skalsky, Rebecca L %A Renne, Rolf %K Cloning, Molecular %K Herpesvirus 8, Human %K Humans %K MicroRNAs %K Virus Latency %X

MicroRNAs (miRNAs) are small, noncoding regulatory RNA molecules that bind to 3' untranslated regions (UTRs) of mRNAs to either prevent their translation or induce their degradation. Previously identified in a variety of organisms ranging from plants to mammals, miRNAs are also now known to be produced by viruses. The human gammaherpesvirus Epstein-Barr virus has been shown to encode miRNAs, which potentially regulate both viral and cellular genes. To determine whether Kaposi's sarcoma-associated herpesvirus (KSHV) encodes miRNAs, we cloned small RNAs from KSHV-positive primary effusion lymphoma-derived cells and endothelial cells. Sequence analysis revealed 11 isolated RNAs of 19 to 23 bases in length that perfectly align with KSHV. Surprisingly, all candidate miRNAs mapped to a single genomic locale within the latency-associated region of KSHV. These data suggest that viral and host cellular gene expression may be regulated by miRNAs during both latent and lytic KSHV replication.

%B J Virol %V 79 %P 9301-5 %8 2005 Jul %G eng %N 14 %1 https://www.ncbi.nlm.nih.gov/pubmed/15994824?dopt=Abstract %R 10.1128/JVI.79.14.9301-9305.2005 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2005 %T Color-blind fluorescence detection for four-color DNA sequencing. %A Lewis, Ernest K %A Haaland, Wade C %A Nguyen, Freddy %A Heller, Daniel A %A Allen, Matthew J %A MacGregor, Robert R %A Berger, C Scott %A Willingham, Britain %A Burns, Lori A %A Scott, Graham B I %A Kittrell, Carter %A Johnson, Bruce R %A Curl, Robert F %A Metzker, Michael L %K Base Sequence %K Color %K Fluorescence %K Fluorescent Dyes %K Reproducibility of Results %K Sensitivity and Specificity %K Sequence Analysis, DNA %X

We present an approach called pulsed multiline excitation (PME) for measurements of multicomponent, fluorescence species and demonstrate its application in capillary electrophoresis for DNA sequencing. To fully demonstrate the advantages of PME, a fluorescent dye set has been developed whose absorption maxima span virtually the entire visible spectrum. Unlike emission wavelength-dependent approaches for identifying fluorescent species, the removal of the spectral component in PME confers a number of advantages including higher and normalized signals from all dyes present in the assay, the elimination of spectral cross-talk between dyes, and higher signal collection efficiency. Base-calling is unambiguously determined once dye mobility corrections are made. These advantages translate into significantly enhanced signal quality as illustrated in the primary DNA sequencing data and provide a means for achieving accurate base-calling at lower reagent concentrations.

%B Proc Natl Acad Sci U S A %V 102 %P 5346-51 %8 2005 Apr 12 %G eng %N 15 %1 https://www.ncbi.nlm.nih.gov/pubmed/15800037?dopt=Abstract %R 10.1073/pnas.0501606102 %0 Journal Article %J Hypertension %D 2005 %T Combined genealogical, mapping, and expression approaches to identify spontaneously hypertensive rat hypertension candidate genes. %A Hinojos, Cruz A %A Eric Boerwinkle %A Fornage, Myriam %A Doris, Peter A %K Animals %K Blood Pressure %K Chromosome Mapping %K Expressed Sequence Tags %K Gene Expression %K Genome %K Hypertension %K Kidney %K Oligonucleotide Array Sequence Analysis %K Pedigree %K Quantitative Trait Loci %K Rats %K Rats, Inbred SHR %K Rats, Inbred WKY %K Regression Analysis %K Species Specificity %X

Allelic expression in genes has become recognized as a heritable trait by which phenotypes are generated. We have examined gene expression in the rat kidney using genome-wide microarray technology (Affymetrix). Gene expression was determined across 4 rat strains, 3 hypertensive spontaneously hypertensive rat (SHR) substrains (SHR-A3, SHR-B2, and SHR-C), and a normotensive strain (Wistar-Kyoto [WKY]). Expression measurements were made in multiple animals from all strains at 4 time points (4 weeks, 8 weeks, 12 weeks, and 18 weeks of age), covering the prehypertensive period in SHR (4 weeks), and the period of rapidly rising blood pressure (8 and 12 weeks) and of sustained hypertension (18 weeks). Regression analysis revealed a close relationship across all strains during the first 3 time points, after which SHR-A3 became a substantial outlier. SHR-B2 and SHR-C demonstrated a very close relationship in gene expression at all times but also showed increased differences compared with the other strains at 18 weeks of age. We identified genes that were consistently different in expression, comparing all SHR substrains at each time point with WKY. The resulting list of genes was compared with blood pressure quantitative trait loci reported for SHR to refine a number of genes consistently differentially expressed between SHR substrains and WKY, persistently differentially expressed across multiple time points, and located in SHR blood pressure-determinative regions of the genome. Genealogical relationships and SHR substrain intercrosses suggest that genes responsible for heritable hypertension in SHR are shared across SHR substrains. The present approach identifies a number of genes that may influence blood pressure in SHR by virtue of allelic effects on gene expression.

%B Hypertension %V 45 %P 698-704 %8 2005 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/15710778?dopt=Abstract %R 10.1161/01.HYP.0000156498.78896.37 %0 Journal Article %J Genome Res %D 2005 %T Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. %A Richards, Stephen %A Liu, Yue %A Bettencourt, Brian R %A Hradecky, Pavel %A Letovsky, Stan %A Nielsen, Rasmus %A Thornton, Kevin %A Hubisz, Melissa J %A Chen, Rui %A Meisel, Richard P %A Couronne, Olivier %A Hua, Sujun %A Smith, Mark A %A Zhang, Peili %A Liu, Jing %A Bussemaker, Harmen J %A van Batenburg, Marinus F %A Howells, Sally L %A Scherer, Steven E %A Sodergren, Erica %A Matthews, Beverly B %A Crosby, Madeline A %A Schroeder, Andrew J %A Ortiz-Barrientos, Daniel %A Rives, Catharine M %A Metzker, Michael L %A Muzny, Donna M %A Scott, Graham %A Steffen, David %A Wheeler, David A %A Worley, Kim C %A Havlak, Paul %A Durbin, K James %A Egan, Amy %A Gill, Rachel %A Hume, Jennifer %A Morgan, Margaret B %A Miner, George %A Hamilton, Cerissa %A Huang, Yanmei %A Waldron, Lenée %A Verduzco, Daniel %A Clerc-Blankenburg, Kerstin P %A Dubchak, Inna %A Noor, Mohamed A F %A Anderson, Wyatt %A White, Kevin P %A Clark, Andrew G %A Schaeffer, Stephen W %A Gelbart, William %A Weinstock, George M %A Gibbs, Richard A %K Animals %K Chromosome Breakage %K Chromosome Inversion %K Chromosome Mapping %K Chromosomes %K Conserved Sequence %K Drosophila %K Drosophila melanogaster %K Enhancer Elements, Genetic %K Evolution, Molecular %K Gene Rearrangement %K Genes, Insect %K Genetic Variation %K Genome %K Molecular Sequence Data %K Predictive Value of Tests %K Repetitive Sequences, Nucleic Acid %K Sequence Analysis, DNA %X

We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species--but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

%B Genome Res %V 15 %P 1-18 %8 2005 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/15632085?dopt=Abstract %R 10.1101/gr.3059305 %0 Journal Article %J Nat Genet %D 2004 %T Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. %A McClelland, Michael %A Sanderson, Kenneth E %A Clifton, Sandra W %A Latreille, Phil %A Porwollik, Steffen %A Aniko Sabo %A Meyer, Rekha %A Bieri, Tamberlyn %A Ozersky, Phil %A McLellan, Michael %A Harkins, C Richard %A Wang, Chunyan %A Nguyen, Christine %A Berghoff, Amy %A Elliott, Glendoria %A Kohlberg, Sara %A Strong, Cindy %A Du, Feiyu %A Carter, Jason %A Kremizki, Colin %A Layman, Dan %A Leonard, Shawn %A Sun, Hui %A Fulton, Lucinda %A Nash, William %A Miner, Tracie %A Minx, Patrick %A Delehaunty, Kim %A Fronick, Catrina %A Magrini, Vincent %A Nhan, Michael %A Warren, Wesley %A Florea, Liliana %A Spieth, John %A Wilson, Richard K %K Base Sequence %K Evolution, Molecular %K Gene Library %K Genetic Variation %K Genome Components %K Genome, Bacterial %K Humans %K Microarray Analysis %K Molecular Sequence Data %K Mutation %K Pseudogenes %K Salmonella paratyphi A %K Salmonella typhi %K Sequence Analysis, DNA %K Species Specificity %X

Salmonella enterica serovars often have a broad host range, and some cause both gastrointestinal and systemic disease. But the serovars Paratyphi A and Typhi are restricted to humans and cause only systemic disease. It has been estimated that Typhi arose in the last few thousand years. The sequence and microarray analysis of the Paratyphi A genome indicates that it is similar to the Typhi genome but suggests that it has a more recent evolutionary origin. Both genomes have independently accumulated many pseudogenes among their approximately 4,400 protein coding sequences: 173 in Paratyphi A and approximately 210 in Typhi. The recent convergence of these two similar genomes on a similar phenotype is subtly reflected in their genotypes: only 30 genes are degraded in both serovars. Nevertheless, these 30 genes include three known to be important in gastroenteritis, which does not occur in these serovars, and four for Salmonella-translocated effectors, which are normally secreted into host cells to subvert host functions. Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae).

%B Nat Genet %V 36 %P 1268-74 %8 2004 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/15531882?dopt=Abstract %R 10.1038/ng1470 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2004 %T Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. %A Seshadri, Rekha %A Myers, Garry S A %A Tettelin, Hervé %A Eisen, Jonathan A %A Heidelberg, John F %A Dodson, Robert J %A Davidsen, Tanja M %A DeBoy, Robert T %A Fouts, Derrick E %A Haft, Dan H %A Selengut, Jeremy %A Ren, Qinghu %A Brinkac, Lauren M %A Madupu, Ramana %A Kolonay, Jamie %A Durkin, Scott A %A Daugherty, Sean C %A Shetty, Jyoti %A Shvartsbeyn, Alla %A Gebregeorgis, Elizabeth %A Geer, Keita %A Tsegaye, Getahun %A Malek, Joel %A Ayodeji, Bola %A Shatsman, Sofiya %A McLeod, Michael P %A Smajs, David %A Howell, Jerrilyn K %A Pal, Sangita %A Amin, Anita %A Vashisth, Pankaj %A McNeill, Thomas Z %A Xiang, Qin %A Sodergren, Erica %A Baca, Ernesto %A Weinstock, George M %A Norris, Steven J %A Fraser, Claire M %A Paulsen, Ian T %K ATP-Binding Cassette Transporters %K Bacterial Proteins %K Base Sequence %K Borrelia burgdorferi %K Genes, Bacterial %K Genome, Bacterial %K Leptospira interrogans %K Models, Genetic %K Molecular Sequence Data %K Mouth %K Sequence Homology, Amino Acid %K Treponema %K Treponema pallidum %X

We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.

%B Proc Natl Acad Sci U S A %V 101 %P 5646-51 %8 2004 Apr 13 %G eng %N 15 %1 https://www.ncbi.nlm.nih.gov/pubmed/15064399?dopt=Abstract %R 10.1073/pnas.0307639101 %0 Journal Article %J J Bacteriol %D 2004 %T Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. %A McLeod, Michael P %A Qin, Xiang %A Karpathy, Sandor E %A Gioia, Jason %A Highlander, Sarah K %A Fox, George E %A McNeill, Thomas Z %A Jiang, Huaiyang %A Muzny, Donna %A Jacob, Leni S %A Hawes, Alicia C %A Sodergren, Erica %A Gill, Rachel %A Hume, Jennifer %A Morgan, Maggie %A Fan, Guangwei %A Amin, Anita G %A Gibbs, Richard A %A Hong, Chao %A Yu, Xue-Jie %A Walker, David H %A Weinstock, George M %K Chromosome Inversion %K DNA, Bacterial %K Electron Transport Complex IV %K Frameshifting, Ribosomal %K Gene Expression Regulation, Bacterial %K Gene Rearrangement %K Genes, Bacterial %K Genes, rRNA %K Genome, Bacterial %K Genomics %K Molecular Sequence Data %K Pseudogenes %K Rickettsia %K Rickettsia conorii %K Rickettsia typhi %K RNA, Transfer %K RNA, Untranslated %K Sequence Analysis, DNA %K Sequence Homology %K Synteny %X

Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome sequence of R. typhi (1,111,496 bp) and compare it to the two published rickettsial genome sequences: R. prowazekii and R. conorii. We identified 877 genes in R. typhi encoding 3 rRNAs, 33 tRNAs, 3 noncoding RNAs, and 838 proteins, 3 of which are frameshifts. In addition, we discovered more than 40 pseudogenes, including the entire cytochrome c oxidase system. The three rickettsial genomes share 775 genes: 23 are found only in R. prowazekii and R. typhi, 15 are found only in R. conorii and R. typhi, and 24 are unique to R. typhi. Although most of the genes are colinear, there is a 35-kb inversion in gene order, which is close to the replication terminus, in R. typhi, compared to R. prowazekii and R. conorii. In addition, we found a 124-kb R. typhi-specific inversion, starting 19 kb from the origin of replication, compared to R. prowazekii and R. conorii. Inversions in this region are also seen in the unpublished genome sequences of R. sibirica and R. rickettsii, indicating that this region is a hot spot for rearrangements. Genome comparisons also revealed a 12-kb insertion in the R. prowazekii genome, relative to R. typhi and R. conorii, which appears to have occurred after the typhus (R. prowazekii and R. typhi) and spotted fever (R. conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae.

%B J Bacteriol %V 186 %P 5842-55 %8 2004 Sep %G eng %N 17 %1 https://www.ncbi.nlm.nih.gov/pubmed/15317790?dopt=Abstract %R 10.1128/JB.186.17.5842-5855.2004 %0 Journal Article %J Methods Mol Biol %D 2004 %T Construction of small genome BAC library for functional and genomic applications. %A Smajs, David %A Norris, Steven J %A Weinstock, George M %K Base Sequence %K Chromosomes, Artificial, Bacterial %K DNA Primers %K DNA, Bacterial %K Electrophoresis, Gel, Pulsed-Field %K Escherichia coli %K Genetic Vectors %K Genome, Bacterial %K Genomic Library %K Genomics %K Restriction Mapping %K Treponema pallidum %B Methods Mol Biol %V 255 %P 47-56 %8 2004 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/15020814?dopt=Abstract %R 10.1385/1-59259-752-1:047 %0 Journal Article %J Mol Microbiol %D 2003 %T Clinical isolates of Enterococcus faecium exhibit strain-specific collagen binding mediated by Acm, a new member of the MSCRAMM family. %A Nallapareddy, Sreedhar R %A Weinstock, George M %A Murray, Barbara E %K Adhesins, Bacterial %K Amino Acid Sequence %K Animals %K Bacterial Adhesion %K Cell Membrane %K Collagen %K Collagen Type I %K Enterococcus faecium %K Genetic Complementation Test %K Gram-Positive Bacteria %K Humans %K Molecular Sequence Data %K Mutation %K Protein Structure, Tertiary %K Pseudogenes %K Rabbits %K Recombinant Proteins %K Sequence Homology, Amino Acid %K Species Specificity %X

A collagen-binding adhesin of Enterococcus faecium, Acm, was identified. Acm shows 62% similarity to the Staphylococcus aureus collagen adhesin Cna over the entire protein and is more similar to Cna (60% and 75% similarity with Cna A and B domains respectively) than to the Enterococcus faecalis collagen-binding adhesin, Ace, which shares homology with Acm only in the A domain. Despite the detection of acm in 32 out of 32 E. faecium isolates, only 11 of these (all clinical isolates, including four vancomycin-resistant endocarditis isolates and seven other isolates) exhibited binding to collagen type I (CI). Although acm from three CI-binding vancomycin-resistant E. faecium clinical isolates showed 100% identity, analysis of acm genes and their promoter regions from six non-CI-binding strains identified deletions or mutations that introduced stop codons and/or IS elements within the gene or the promoter region in five out of six strains, suggesting that the presence of an intact functional acm gene is necessary for binding of E. faecium strains to CI. Recombinant Acm A domain showed specific and concentration-dependent binding to collagen, and this protein competed with E. faecium binding to immobilized CI. Consistent with the adherence phenotype and sequence data, probing with Acm-specific IgGs purified from anti-recombinant Acm A polyclonal rabbit serum confirmed the surface expression of Acm in three out of three collagen-binding clinical isolates of E. faecium tested, but in none of the strains with a non-functional pseudo acm gene. Introduction of a functional acm gene into two non-CI-binding natural acm mutant strains conferred a CI-binding phenotype, further confirming that native Acm is sufficient for the binding of E. faecium to CI. These results demonstrate that acm, which encodes a potential virulence factor, is functional only in certain infection-derived clinical isolates of E. faecium, and suggest that Acm is the primary adhesin responsible for the ability of E. faecium to bind collagen.

%B Mol Microbiol %V 47 %P 1733-47 %8 2003 Mar %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/12622825?dopt=Abstract %R 10.1046/j.1365-2958.2003.03417.x %0 Journal Article %J Genome Inform %D 2003 %T Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments. %A Csuros, Miklos %A Li, Bingshan %A Milosavljevic, Aleksandar %K Animals %K Chromosomes, Artificial, Bacterial %K Computational Biology %K Computer Simulation %K Drosophila melanogaster %K Genome %K Reproducibility of Results %K Research Design %K Sequence Alignment %X

This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a BAC-linked assembly of a whole genome sequence. Secondly, we introduce a novel physical mapping method, called Clone-Array Pooled Shotgun Mapping (CAPS-MAP), which computes the physical ordering of BACs in a random library. Both CAPSS and CAPS-MAP construct subclone libraries from pooled genomic BAC clones.

%B Genome Inform %V 14 %P 186-95 %8 2003 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/15706533?dopt=Abstract %0 Journal Article %J Hum Genet %D 2003 %T Comparison of strategies for selecting single nucleotide polymorphisms for case/control association studies. %A Huang, Qiqing %A Fu, Yun-Xin %A Eric Boerwinkle %K Case-Control Studies %K Haplotypes %K Humans %K Linkage Disequilibrium %K Patient Selection %K Phenotype %K Polymorphism, Single Nucleotide %K Regression Analysis %K Sample Size %X

It is widely believed that a subset of single nucleotide polymorphisms (SNPs) is able to capture the majority of the information for genotype-phenotype association studies that is contained in the complete compliment of genetic variations. The question remains, how does one select that particular subset of SNPs in order to maximize the power of detecting a significant association? In this study, we have used a simulation approach to compare three competing methods of site selection: random selection, selection based on pair-wise linkage disequilibrium, and selection based on maximizing haplotype diversity. The results indicate that site selection based on maximizing haplotype diversity is preferred over random selection and selection based on pair-wise linkage disequilibrium. The results also indicate that it is more prudent to increase the sample size to improve a study's power than to continuously increase the number of SNPs. These results have direct implications for designing gene-based and genome-wide association studies.

%B Hum Genet %V 113 %P 253-7 %8 2003 Aug %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/12811538?dopt=Abstract %R 10.1007/s00439-003-0965-x %0 Journal Article %J C R Biol %D 2003 %T Concatenation cDNA sequencing for transcriptome analysis. %A Gunaratne, Preethi H %A Wu, Jia Qian %A Garcia, Angela M %A Hulyk, Steven %A Kim C Worley %A Margolin, Judith F %A Richard A Gibbs %K Cloning, Molecular %K DNA, Complementary %K DNA, Concatenated %K Genetic Techniques %K Humans %K Sequence Analysis, DNA %K Transcription, Genetic %X

We describe a high-throughput cDNA sequencing pipeline (http://www.hgsc.bcm.tmc.edu/projects/cdna) built in response to the emerging need for rapid sequencing of large cDNA collections. Using this strategy cDNA inserts are purified and joined through concatenation into large molecules. These 'pseudo-BACs' are subjected to random shotgun sequencing whereby the majority of cDNA inserts in the pool are sequenced. Using this concatenation cDNA sequencing platform, we have contributed more than 13000 full-length cDNA sequences from human and mouse to the Mammalian Gene Collection (MGC).

%B C R Biol %V 326 %P 971-7 %8 2003 Oct-Nov %G eng %N 10-11 %1 https://www.ncbi.nlm.nih.gov/pubmed/14744103?dopt=Abstract %R 10.1016/j.crvi.2003.09.032 %0 Journal Article %J Photosynth Res %D 2003 %T Cyanobacterial signature genes. %A Martin, Kirt A %A Siefert, Janet L %A Yerrapragada, Sailaja %A Lu, Yue %A McNeill, Thomas Z %A Moreno, Pedro A %A Weinstock, George M %A Widger, William R %A Fox, George E %X

A comparison of 8 cyanobacterial genomes reveals that there are 181 shared genes that do not have obvious orthologs in other bacteria. These signature genes define aspects of the genotype that are uniquely cyanobacterial. Approximately 25% of these genes have been associated with some function. These signature genes may or may not be involved in photosynthesis but likely they will be in many cases. In addition, several examples of widely conserved gene order involving two or more signature genes were observed. This suggests there may be regulatory processes that have been preserved throughout the long history of the cyanobacterial phenotype. The results presented here will be especially useful because they identify which of the many genes of unassigned function are likely to be of the greatest interest.

%B Photosynth Res %V 75 %P 211-21 %8 2003 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/16228602?dopt=Abstract %R 10.1023/A:1023990402346 %0 Journal Article %J BMC Genomics %D 2002 %T The cloning, genomic organization and tissue expression profile of the human DLG5 gene. %A Shah, Gopi %A Brugada, Ramon %A Gonzalez, Oscar %A Czernuszewicz, Grazyna %A Gibbs, Richard A %A Bachinski, Linda %A Roberts, Robert %X

BACKGROUND: Familial atrial fibrillation, an autosomal dominant disease, was previously mapped to chromosome 10q22. One of the genes mapped to the 10q22 region is DLG5, a member of the MAGUKs (Membrane Associated Gyanylate Kinase) family which mediates intracellular signaling. Only a partial cDNA was available for DLG5. To exclude potential disease inducing mutations, it was necessary to obtain a complete cDNA and genomic sequence of the gene.

METHODS: The Northern Blot analysis performed using 3' UTR of this gene indicated the transcript size to be about 7.2 KB. Using race technique and library screening the entire cDNA was cloned. This gene was evaluated by sequencing the coding region and splice functions in normal and affected family members with familial atrial fibrillation. Furthermore, haploid cell lines from affected patients were generated and analyzed for deletions that may have been missed by PCR.

RESULTS: We identified two distinct alternately spliced transcripts of this gene. The genomic sequence of the DLG5 gene spanned 79 KB with 32 exons and was shown to have ubiquitous human tissue expression including placenta, heart, skeletal muscle, liver and pancreas.

CONCLUSIONS: The entire cDNA of DLG5 was identified, sequenced and its genomic organization determined.

%B BMC Genomics %V 3 %P 6 %8 2002 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/11876824?dopt=Abstract %R 10.1186/1471-2164-3-6 %0 Journal Article %J BMC Genomics %D 2002 %T The cloning, genomic organization and tissue expression profile of the human DLG5 gene: Correction. %A Shah, Gopi %A Brugada, Ramon %A Gonzalez, Oscar %A Czernuszewicz, Grazyna %A Gibbs, Richard A %A Bachinski, Linda %A Roberts, Robert %B BMC Genomics %V 3 %P 14 %8 2002 Jun 11 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/12060488?dopt=Abstract %R 10.1186/1471-2164-3-14 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2002 %T A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. %A Katsanis, Nicholas %A Worley, Kim C %A Gonzalez, Guillermo %A Ansley, Stephen J %A Lupski, James R %K Databases, Nucleic Acid %K Electronic Data Processing %K Expressed Sequence Tags %K Genome %K Humans %K Retina %K Retinal Diseases %K Transcription, Genetic %X

Grouping genes by virtue of their sequence similarity, functional association, or spatiotemporal distribution is an important first step in investigating function. Given the recent identification of >30,000 human genes either by analyses of genomic sequence or by derivation/assembly of ESTs, automated means of discerning gene function and association with disease are critical for the efficient processing of this large volume of data. We have designed a series of computational tools to manipulate the EST sequence database (dbEST) to predict EST clusters likely representing genes expressed exclusively or preferentially in a specific tissue. We implemented this tool by extracting 40,000 human retinal ESTs and performing in silico subtraction against 1.4 million human ESTs. This process yielded 925 ESTs likely to be specifically or preferentially expressed in the retina. We mapped all retinal-specific/predominant sequences in the human genome and produced a web-based searchable map of the retina transcriptome, onto which we overlaid the positions of all mapped but uncloned retinopathy genes. This resource has provided positional candidates for 42 of 51 uncloned retinopathies and may expedite substantially the identification of disease-associated genes. More importantly, the ability to systematically group ESTs according to their predicted expression profile is likely to be an important resource for studying gene function in a wide range of tissues and physiological systems and to identify positional candidate genes for human disorders whose phenotypic manifestations are restricted to specific tissues/organs/cell types.

%B Proc Natl Acad Sci U S A %V 99 %P 14326-31 %8 2002 Oct 29 %G eng %N 22 %1 https://www.ncbi.nlm.nih.gov/pubmed/12391299?dopt=Abstract %R 10.1073/pnas.222409099 %0 Journal Article %J Immunogenetics %D 2001 %T CFFM4: a new member of the CD20/FcepsilonRIbeta family. %A Marie-Claude Gingras %A Lapillonne, H %A Margolin, J F %K Acute Disease %K Amino Acid Sequence %K Antigens, CD %K Antigens, CD20 %K Base Sequence %K Cell Differentiation %K Cells, Cultured %K Cloning, Molecular %K Hematopoietic Stem Cells %K Humans %K Leukemia, Myeloid %K Membrane Proteins %K Molecular Sequence Data %K Monocytes %K Receptors, IgE %K RNA, Messenger %K Sequence Homology, Amino Acid %K Tissue Distribution %K Tumor Cells, Cultured %K U937 Cells %X

Proteins with transmembrane domains are classified in different families based on their structure, amino acid homology, and function. In this study, we report the identification, sequence, and expression profile of a new member of the CD20/FcepsilonRIbeta family, CD20/FcepsilonRIbeta family member 4 (CFFM4). The CFFM4 gene contains seven exons and six introns and is transcribed into an mRNA encoding a 240-amino acid protein with four hydrophobic regions. The CFFM4 protein shares a high degree of homology with the other members of the family, especially in the hydrophobic regions where several amino acids are conserved. However, the CFFM4 protein can be distinguished from the other members of the family based on the length of the second extracellular loop and the absence of an immunoreceptor tyrosine-based activation motif signal. Another distinct characteristic is that CFFM4 mRNA expression is not limited to the hematopoietic lineage. CFFM4 was detected by Northern dot blot in a variety of normal and cancerous tissues. CFFM4 expression was also compared in developmentally early hematopoietic human bone marrow CD34+ stem cells versus peripheral blood-derived CD14+ mature monocytes, in the undifferentiated versus differentiated myelomonocytic U937 cell line, and in acute myelogenous leukemia FAB1 versus FAB5. In each of these systems, cellular myelomonocytic differentiation correlated with an increase in CFFM4 mRNA expression. Such results indicate that CFFM4 is associated with mature cellular function in the monocytic lineage and like CD20 and FcepsilonRIbeta, it may be a component of a receptor complex involved in signal transduction.

%B Immunogenetics %V 53 %P 468-76 %8 2001 Aug %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/11685457?dopt=Abstract %R 10.1007/s002510100345 %0 Journal Article %J Genes Genet Syst %D 2001 %T Characterization of cryptic flagellin genes in Shigella boydii and Shigella dysenteriae. %A Tominaga, A %A Mahmoud, M A %A al Mamun, A A %A Mukaihara, T %K Alleles %K Amino Acid Sequence %K Blotting, Southern %K Cloning, Molecular %K Electrophoresis, Polyacrylamide Gel %K Evolution, Molecular %K Flagellin %K Genetic Variation %K Immunoblotting %K Models, Genetic %K Molecular Sequence Data %K Plasmids %K Sequence Analysis, DNA %K Shigella boydii %K Shigella dysenteriae %K Species Specificity %X

Flagellin (fliC) genes of 12 Shigella boydii and five Shigella dysenteriae strains were characterized. Though these strains are nonmotile, the cryptic fliCSB gene, cloned from S. boydii strain C3, is functional for expression of flagellin. It consists of 1,704 bp, and encodes 568 amino acid residues (57,918 Da). The fliCSD gene from S. dysenteriae strain 16 consists of 1,650 bp encoding 549 amino acid residues (57,591 Da) and contains an IS1 element inserted in its 3' end. The two genes are composed of the 5'-constant, central variable and 3'-constant sequences, like other known fliC genes. The two genes share high homology in nucleotide and amino acid sequences with each other and also with the Escherichia coli fliCE gene, indicating that both genes are closely related to the fliCE gene. Comparison of the central variable sequences of six different fliC genes showed that the fliCSB and fliCSD genes share low homology in amino acid sequence with the other fliC genes, suggesting that they encode antigenic determinants intrinsic to respective subgroups. However, Southern blotting using as probes the central variable sequences of several fliC genes showed that four of 12 S. boydii strains have a fliC gene similar to that of Shigella flexneri, and that among five fliC genes from S. dysenteriae strains, one is similar to that of S. flexneri, two are similar to that of S. boydii, and only one is unique to S. dysenteriae. Some of these variant alleles were verified by immunoblotting with flagellins produced from cloned fliC genes. The presence of variant fliC alleles in S. boydii and S. dysenteriae indicates that subdivision into subgroups does not reflect the ancestral flagella H antigenic relationships. These data will be useful in considering the evolutionary divergence of the Shigella spp..

%B Genes Genet Syst %V 76 %P 111-20 %8 2001 Apr %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/11434456?dopt=Abstract %R 10.1266/ggs.76.111 %0 Journal Article %J J Bacteriol %D 2001 %T Characterization of fsr, a regulator controlling expression of gelatinase and serine protease in Enterococcus faecalis OG1RF. %A Qin, X %A Singh, K V %A Weinstock, G M %A Murray, B E %K Amino Acid Sequence %K Bacterial Proteins %K Base Sequence %K Enterococcus faecalis %K Gelatinases %K Gene Deletion %K Gene Expression Regulation, Bacterial %K Gene Expression Regulation, Enzymologic %K Gram-Positive Bacterial Infections %K Humans %K Molecular Sequence Data %K Plasmids %K Promoter Regions, Genetic %K Reverse Transcriptase Polymerase Chain Reaction %K Sequence Analysis, DNA %K Serine Endopeptidases %X

We have previously identified a locus, fsr, a homologue of staphylococcal agr loci, which positively regulates the expression of gelatinase and serine protease (encoded by gelE and sprE, respectively) in Enterococcus faecalis OG1RF. The expression of the three genes in the fsr locus, fsrA, fsrB, and fsrC, appears to be autoregulated, and we have shown that mutants with insertion disruptions in each of these three genes were significantly attenuated in a mouse peritonitis model compared to the parent strain. In the present study, we showed that fsrB and fsrC are highly expressed in the postexponential growth phase and that their expression is cell density dependent. Reverse transcriptase PCR using primers covering the intergenic regions in the fsr/gelE loci confirmed that fsrB and fsrC, as well as gelE and sprE, are cotranscribed. We also showed, using a nonpolar fsrB deletion mutant, that fsrB, the homologue of agrB of staphylococci with unknown function, is required for the regulatory function of fsr. Primer extension and analysis of transcriptional fusions indicated the presence of promoters immediately upstream of fsrA, of fsrB, and of gelE and that the fsrB and gelE promoters are fsr dependent, while the fsrA promoter is an fsr-independent weak constitutive promoter. Two conserved 7-bp direct repeats were found immediately upstream of the fsrB and gelE promoters, similar to the repeats found upstream of P2 and P3 promoters of the agr locus; deletions and mutations in the repeated sequences completely abolished the fsrB and gelE promoter activities, suggesting that the repeats are important for the regulatory function in the fsrB and gelE promoter regions.

%B J Bacteriol %V 183 %P 3372-82 %8 2001 Jun %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/11344145?dopt=Abstract %R 10.1128/JB.183.11.3372-3382.2001 %0 Journal Article %J J Biol Chem %D 2001 %T Characterization of the rat GRIK5 kainate receptor subunit gene promoter and its intragenic regions involved in neural cell specificity. %A Chew, L J %A Yuan, X %A Steven E Scherer %A Qie, L %A Huang, F %A Hayes, W P %A Gallo, V %K 5' Flanking Region %K Animals %K Base Sequence %K Cells, Cultured %K Deoxyribonuclease I %K Humans %K Mice %K Mice, Transgenic %K Molecular Sequence Data %K Neurons %K Organ Specificity %K Promoter Regions, Genetic %K Protein Subunits %K Rats %K Receptors, Kainic Acid %K Sp1 Transcription Factor %X

The GRIK5 (glutamate receptor ionotropic kainate-5) gene encodes the kainate-preferring glutamate receptor subunit KA2. The GRIK5 promoter is TATA-less and GC-rich, with multiple consensus initiator sequences. Transgenic mouse lines carrying 4 kilobases of the GRIK5 5'-flanking sequence showed lacZ reporter expression predominantly in the nervous system. Reporter assays in central glial (CG-4) and non-neural cells indicated that a 1200-base pair (bp) 5'-flanking region could sustain neural cell-specific promoter activity. Transcriptional activity was associated with the formation of a transcription factor IID-containing complex on an initiator sequence located 1100 bp upstream of the first intron. In transfection studies, deletion of exonic sequences downstream of the promoter resulted in reporter gene activity that was no longer neural cell-specific. When placed downstream of the GRIK5 promoter, a 77-bp sequence from the deleted fragment completely silenced reporter expression in NIH3T3 fibroblasts while attenuating activity in CG-4 cells. Analysis of the 77-bp sequence revealed a functional SP1-binding site and a sequence resembling a neuron-restrictive silencer element. The latter sequence, however, did not display cell-specific binding of REST-like proteins. Our studies thus provide evidence for intragenic control of GRIK5 promoter activity and suggest that elements contributing to tissue-specific expression are contained within the first exon.

%B J Biol Chem %V 276 %P 42162-71 %8 2001 Nov 09 %G eng %N 45 %1 https://www.ncbi.nlm.nih.gov/pubmed/11533047?dopt=Abstract %R 10.1074/jbc.M101895200 %0 Journal Article %J Genome Res %D 2001 %T A clone-array pooled shotgun strategy for sequencing large genomes. %A Cai, W W %A Chen, R %A Richard A Gibbs %A Bradley, A %K Animals %K Computer Simulation %K Genome %K Humans %K Mice %K Oligonucleotide Array Sequence Analysis %K Software %X

A simplified strategy for sequencing large genomes is proposed. Clone-Array Pooled Shotgun Sequencing (CAPSS) is based on pooling rows and columns of arrayed genomic clones, for shotgun library construction. Random sequences are accumulated, and the data are processed by sequential comparison of rows and columns to assemble the sequence of clones at points of intersection. Compared with either a clone-by-clone approach or whole-genome shotgun sequencing, CAPSS requires relatively few library constructions and only minimal computational power for a complete genome assembly. The strategy is suitable for sequencing large genomes for which there are no sequence-ready maps, but for which relatively high resolution STS maps and highly redundant BAC libraries are available. It is immediately applicable to the sequencing of mouse, rat, zebrafish, and other important genomes, and can be managed in a cooperative fashion to take advantage of a distributed international DNA sequencing capacity.

%B Genome Res %V 11 %P 1619-23 %8 2001 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/11591638?dopt=Abstract %R 10.1101/gr.198101 %0 Journal Article %J Genome Res %D 2001 %T Comparing vertebrate whole-genome shotgun reads to the human genome. %A Chen, R %A Bouck, J B %A Weinstock, G M %A Gibbs, R A %K Animals %K Base Sequence %K Computational Biology %K Conserved Sequence %K Databases, Genetic %K Expressed Sequence Tags %K Genome %K Genome, Human %K Heterochromatin %K Humans %K Mice %K Molecular Sequence Data %K Rats %K Sequence Analysis, DNA %K Sequence Homology, Nucleic Acid %K Species Specificity %K Transcription, Genetic %X

Multi-species sequence comparisons are a very efficient way to reveal conserved genes. Because sequence finishing is expensive and time consuming, many genome sequences are likely to stay incomplete. A challenge is to use these fragmented data for understanding the human genome. Methods for using cross-species whole-genome shotgun sequence (WGS) for genome annotation are described in this paper. About one-half million high-quality rat WGS reads (covering 7.5% of the rat genome) generated at the Baylor College of Medicine Human Genome Sequencing Center were compared with the human genome. Using computer-generated random reads as a negative control, a set of parameters was determined for reliable interpretation of BLAST search results. About 10% of the rat reads contain regions that are conserved in the human genomic sequence and about one-third of these include known gene-coding regions. Mapping the conserved regions to human chromosomes showed a 23-fold enrichment for coding regions compared with noncoding regions. This approach can also be applied to other mammalian genomes for gene finding. These data predicted approximately 42,500 genes in the human, slightly more than reported previously.

%B Genome Res %V 11 %P 1807-16 %8 2001 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/11691844?dopt=Abstract %R 10.1101/gr.203601 %0 Journal Article %J Can J Physiol Pharmacol %D 2000 %T Cloning and functional expression of the hNPY Y5 receptor in human endometrial cancer (HEC-1B) cells. %A Moser, C %A Bernhardt, G %A Michel, J %A Schwarz, H %A Buschauer, A %K Cloning, Molecular %K Cyclic AMP %K Endometrial Neoplasms %K Female %K Humans %K Polymerase Chain Reaction %K Radioligand Assay %K Receptors, Neuropeptide Y %K Transfection %K Tumor Cells, Cultured %X

Aiming to develop a functional assay for the human NPY Y5 receptor based on adenylyl cyclase activity, HEC-1B cells, in which cAMP synthesis can be efficiently stimulated with forskolin, were selected for the transfection with the pcDNA3-Y5-FLAG and the pcDEF3-Y5 vectors. After optimization of the transfection procedure, the binding of [3H]propionyl-NPY to transiently and stably expressed Y5 receptors was determined. The affinities of NPY, NPY derivatives, and rPP (pNPY > or = p(Leu31Pro34)NPY = p(2-36)NPY > or = p(D-Trp32)NPY > p(13-36)NPY > rPP) were in accordance with the NPY Y5 receptor subtype. For [3H]propionyl-pNPY approximately 1.7 x 10(5) and 1 x 10(6) binding sites per transiently and stably transfected cell, respectively, were determined. The KD values were 2.4 +/- 0.4 and 1.7 +/-0.2 nM, respectively. Due to the high expression of the receptor protein, both stably and transiently transfected cells can be conveniently used in routine radioligand binding studies. By contrast, functional assays were only feasible with HEC-1B cells stably expressing the Y5 receptor. In these cells, 10 nM pNPY inhibited the forskolin-stimulated cAMP synthesis by 75%. This effect was partially antagonized by the Y5 antagonist N-¿trans-[4-(2-naphthylmethylamino)-methyl]cyclohexylmethyl) naphthalene-2-sulfonamide. Although the genetic variability of cancer cells is in principle incompatible with a stable phenotype, both ligand binding characteristics and functionality of the Y5 receptor remained unchanged for more than 30 passages.

%B Can J Physiol Pharmacol %V 78 %P 134-42 %8 2000 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/10737676?dopt=Abstract %0 Journal Article %J Genomics %D 2000 %T Construction of a high-resolution physical map of the chromosome 10q22-q23 dilated cardiomyopathy locus and analysis of candidate genes. %A Bowles, K R %A Abraham, S E %A Brugada, R %A Zintz, C %A Comeaux, J %A Sorajja, D %A Tsubata, S %A Li, H %A Brandon, L %A Richard A Gibbs %A Steven E Scherer %A Bowles, N E %A Towbin, J A %K Cardiomyopathy, Dilated %K Chromosomes, Bacterial %K Chromosomes, Human, Pair 10 %K DNA Mutational Analysis %K Expressed Sequence Tags %K Family Health %K Female %K Genetic Predisposition to Disease %K Genomic Library %K Humans %K Male %K Pedigree %K Phenotype %K Physical Chromosome Mapping %K Sequence Analysis, DNA %X

Dilated cardiomyopathy (DCM) is a major cause of morbidity and mortality and a leading cause of cardiac transplantation worldwide. Multiple loci and three genes encoding cardiac actin, desmin, and lamin A/C have been described for autosomal dominant DCM. Using recombination analysis, we have narrowed the 10q21-q23 locus to a region of approximately 4.1 cM. In addition, we have constructed a BAC contig, composed of 199 clones, which was used to develop a high-resolution physical map that contains the DCM critical region (approximately 3.9 Mb long). Seven genes, including ANX11, PPIF, DLG5, RPC155, RPS24, SFTPA1, and KCNMA1, have been mapped to the region of interest. RPC155, RPS24, SFTPA1, and KCNMA1 were excluded from further analysis based on their known functions and tissue-specific expression patterns. Mutational analysis of ANX11, DLG5, and PPIF revealed no disease-associated mutations. Multiple ESTs have also been mapped to the critical region.

%B Genomics %V 67 %P 109-27 %8 2000 Jul 15 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/10903836?dopt=Abstract %R 10.1006/geno.2000.6242 %0 Journal Article %J Trends Genet %D 1999 %T Comparison of gene indexing databases. %A Bouck, J %A Yu, W %A Richard A Gibbs %A Kim C Worley %K Abstracting and Indexing %K Alternative Splicing %K Cluster Analysis %K Databases, Factual %K DNA, Complementary %K Expressed Sequence Tags %K Genome, Human %K Humans %B Trends Genet %V 15 %P 159-62 %8 1999 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/10203827?dopt=Abstract %R 10.1016/s0168-9525(99)01709-6 %0 Journal Article %J Genome Res %D 1998 %T Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. %A Ansari-Lari, M A %A Oeltjen, J C %A Schwartz, S %A Zhang, Z %A Donna M Muzny %A Lu, J %A Gorrell, J H %A Chinault, A C %A Belmont, J W %A Miller, W %A Richard A Gibbs %K Amino Acid Sequence %K Animals %K Chromosome Mapping %K Chromosomes %K Chromosomes, Human, Pair 12 %K Conserved Sequence %K Humans %K Mice %K Molecular Sequence Data %K Multigene Family %K Repetitive Sequences, Nucleic Acid %K Sequence Alignment %K Sequence Analysis, DNA %X

The Human Genome Project has created a formidable challenge: the extraction of biological information from extensive amounts of raw sequence. With the increasing availability of genomic sequence from other species, one approach to extracting coding and regulatory element information is through cross-species sequence comparison. To assess the strengths and weaknesses of this methodology for large-scale sequence analysis, 227 kb of mouse sequence syntenic to a gene-rich cluster on human chromosome 12p13 was obtained. Primarily through percent identity plots (PIPs) of SIM comparative sequence alignments, the sequence of coding regions, putative alternative exons, conserved noncoding regions, and correlation in repetitive element insertions were easily determined. The analysis demonstrated that the number, order, and orientation of all 17 genes are conserved between the two species, whereas two human pseudogenes are absent in mouse. In addition, apart from MIRs, no direct correlation of distribution or position of the majority of repetitive elements between the two species is seen. Finally, in examining the synonymous and nonsynonymous substitution rates in the conserved genes, a large variation in nonsynonymous rates is observed indicating that the genes in this region are diverging at different rates. This study indicates the utility and strength of large-scale cross-species sequence comparisons in the extraction of biological information from raw sequence, especially when combined with other computational tools such as GRAIL and BLAST.

%B Genome Res %V 8 %P 29-40 %8 1998 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/9445485?dopt=Abstract %0 Journal Article %J J Bacteriol %D 1997 %T Cloning and characterization of the region III flagellar operons of the four Shigella subgroups: genetic defects that cause loss of flagella of Shigella boydii and Shigella sonnei. %A al Mamun, A A %A Tominaga, A %A Enomoto, M %K Bacterial Proteins %K Chromosome Mapping %K Cloning, Molecular %K DNA Transposable Elements %K Escherichia coli Proteins %K Flagella %K Gene Deletion %K Membrane Proteins %K Molecular Sequence Data %K Movement %K Operon %K Sequence Analysis, DNA %K Shigella %K Shigella boydii %K Shigella sonnei %X

To detect genetic defects that might have caused loss of flagella in Shigella boydii and Shigella sonnei, the region III flagellar (fli) operons were cloned from certain strains and analyzed with reference to the restriction maps and genetic maps of Escherichia coli fli operons. S. boydii NCTC9733 (strain C5 in this paper) had the 988-bp internal deletion in the fliF gene that encodes a large substructural protein of the basal body. Two strains (C1 and C8) had deletions of the entire fliF operon, and the remaining three (C3, C4, and C9) differed in the size of the restriction fragments carrying the fliF and fliL operons. Loss of flagella in S. boydii appears to originate in some defect in the fliF operon. S. sonnei IID969 lacked the fliD gene and, in place of it, carried two IS600 elements as inverted repeats. Genes downstream from fliD were not detected in the cloned fragment despite its large size but did appear elsewhere in the chromosome. The fliD gene encodes a cap protein of the flagellar filament, and its deletion results in overexpression of class 3 operons by the increased amount of FliA (sigmaF) caused by the excess export of the anti-sigma factor FlgM. Three other strains also had the fliD deletion, and two of them had another deletion in the fliF-fliG-fliH region. The fliD deletion might be the primary cause of loss of flagella in S. sonnei. The lack of FliF or FliD in each subgroup is discussed in connection with the maintenance of virulence and bacterial growth. We also discuss the process of loss of flagella in relation to transposition of IS elements and alterations of the noncoding region, which were found to be common to at least three subgroups.

%B J Bacteriol %V 179 %P 4493-500 %8 1997 Jul %G eng %N 14 %1 https://www.ncbi.nlm.nih.gov/pubmed/9226258?dopt=Abstract %R 10.1128/jb.179.14.4493-4500.1997 %0 Journal Article %J Genome Res %D 1996 %T A comparative transcription map of the murine bare patches (Bpa) and striated (Str) critical regions and human Xq28. %A Levin, M L %A Chatterjee, A %A Pragliola, A %A Kim C Worley %A Wehnert, M %A Zhuchenko, O %A Smith, R F %A Lee, C C %A Herman, G E %K Amino Acid Sequence %K Animals %K Base Sequence %K Blotting, Northern %K Blotting, Southern %K Chondrodysplasia Punctata %K Chromosome Mapping %K Cloning, Molecular %K DNA, Complementary %K Exons %K Genetic Markers %K Humans %K Incontinentia Pigmenti %K Mice %K Molecular Sequence Data %K Restriction Mapping %K Sequence Analysis %K Sequence Homology, Amino Acid %K X Chromosome %K Zinc Fingers %X

The X-linked developmental mouse mutations bare patches (Bpa) and striated (Str) may be homologous to human X-linked dominant chondrodysplasia punctata (CDPX2) and incontinentia pigmenti (IP2), respectively, based on their genetic mapping and clinical phenotypes. Bpa and Str have been localized to an overlapping critical region of 600 kb that demonstrates conserved gene order with loci in human Xq28 between DXS1104 and DXS52. As part of efforts to isolate the genes involved in these disorders, we have begun to develop a comparative transcription map spanning this region in both species. Using techniques of cross-species conservation and hybridization, exon trapping, and cDNA selection we have identified four known genes or members of gene families--caltractin, a member of the gamma-aminobutyric acid (GABAA) receptor gene family, a member of the melanoma antigen gene (MAGE) family, and several members of the murine-specific, X-linked lymphocyte regulated gene (Xlr3) family. Trapped exons and, in some cases, longer cDNAs have been isolated for potentially 7-9 additional genes. One cDNA demonstrates highly significant homology with members of the Krüppel family of zinc finger transcription factors. A second novel cDNA demonstrates homology at the 3' end of the predicted amino acid sequence to a LIM domain consensus. Gene order appears conserved among those cDNAs determined to be present in both human and mouse. Three of the murine transcripts appear to be present in multiple copies within the Bpa/Str critical region and could be associated with a predisposition to genomic rearrangements. Reverse transcriptase PCR (RT-PCR) and Northern analysis demonstrate that several of the transcripts are expressed in mid-gestation murine embryos and neonatal skin, making them candidates for the Bpa and Str mutations and their respective homologous human disorders.

%B Genome Res %V 6 %P 465-77 %8 1996 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/8828036?dopt=Abstract %R 10.1101/gr.6.6.465 %0 Journal Article %J Cytogenet Cell Genet %D 1996 %T Conservation of human chromosome 18 in baboons (Papio hamadryas): a linkage map of eight human microsatellites. %A Perelygin, A A %A Kammerer, C M %A Stowell, N C %A Rogers, J %K Animals %K Chromosomes, Human, Pair 18 %K Evolution, Molecular %K Female %K Hominidae %K Humans %K Lod Score %K Male %K Microsatellite Repeats %K Papio %K Pedigree %K Phylogeny %K Polymerase Chain Reaction %K Recombination, Genetic %K Species Specificity %X

A panel of 25 microsatellite loci known to map to human chromosome 18 was screened for length polymorphisms in a multigenerational pedigree of baboons (Papio hamadryas). Eight of these loci were polymorphic in the baboon pedigrees, with observed heterozygosity values ranging from 0.16 to 0.88. All eight loci show strong evidence of linkage. The most likely map order among the microsatellite loci for Papio is completely compatible with the locus order found in the human genome, and sex differences in recombination rates are also similar in the two species. We conclude that the organization of the chromosomal region defined by these loci is largely conserved between baboons and humans.

%B Cytogenet Cell Genet %V 75 %P 207-9 %8 1996 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/9067425?dopt=Abstract %R 10.1159/000134484 %0 Journal Article %J Medinfo %D 1995 %T Collaborative social and medical service application. %A Petermann, C A %A Buffone, G J %A Bobroff, R B %A Moore, D M %A Dargahi, R %A Moreau, D R %A Gilson, H S %A Li, Y %A Fowler, J %A Beck, J R %K Adolescent %K Adolescent Health Services %K Adult %K Ambulatory Care Information Systems %K Female %K Humans %K Male %K Medical Records Systems, Computerized %K Social Work %K Systems Integration %K Texas %X

Baylor College of Medicine has five Teen Health Clinics (THC) dispersed throughout Harris county. The population served by the clinics includes inner-city adolescent boys and girls 19 years of age and under. Patients receive services such as family planning, sexually transmitted disease screening and treatment, perinatal care, counseling, and support services. Adolescents may receive services at any one of the clinics at no cost to the adolescent or their dependents. Given the geographical distribution of the clinics and the reliance on paper-based records, client services cannot be provided efficiently or expeditiously. According to the statistics developed by Clinic staff, ineffective coordination of service needs and client schedules undermine the follow-up needed for effective care. For example, a counselor will often need to balance a school schedule, clinic visits, well baby follow-up, and the Best Friends Program for a new mother. In addition, the lack of ready access to patient information impairs the ability of clinical and social service staff to provide continuity of care. In fact, some cases of client dropout are attributable to these difficulties. We have developed the Collaborative Social and Medical Service Application (CSMSA) to facilitate the provision of social and medical services to this population. The CSMSA is a domain-specific application based on a robust infrastructure known as the Ambulatory Services Architecture (ASA). This system is designed to support integrated social and ambulatory care. The ASA is a Baylor developed application framework and architecture for the computerization of the patient medical record in the ambulatory care setting. The working environment for the CSMSA user is an integrated desktop which provides an operating environment for both third-party applications and the CSMSA, as well as a fundamental set of services. The integrated desktop services include a mechanism for object organization or grouping, a facility for the management of desktop objects including disposal and storage, and an embedded search utility to assist in the location of desktop objects as well as other application objects. The access control mechanism will provide the security for the desktop environment by requiring the user to log into and out of the environment. This security mechanism will also enable/disable CSMSA tools based on the user's role at the clinic. The CSMSA is designed to provide work process, functionality and data access appropriate to the responsibilities of the user, e.g., a THC clerk may have permission to view a patient's orders but does not have the facility to create an order. Patient context is defined through a patient browser containing the master patient index or a user defined patient list. Patient encounters are managed using forms based on the process for each encounter type (e.g., initial visit). Forms are used for data entry and for queries. Data entry forms are only committed to the patient database (i.e., making the patient data available to other users who have permission to access the data) when the user approves the data. The CSMSA provides a means to suspend an entry into a chart by saving incomplete or non-committed data entry forms as part of the desktop state which is restored when the user logs into the system. CSMSA was designed to provide a robust, expandable application capable of accommodating the changes in health care and social services delivery while encompassing evolving software standards and new technology. This goal was achieved using object-oriented methodologies and technologies, combined with an object-oriented database management system as the foundation of our server to facilitate the evolution of our data model.

%B Medinfo %V 8 Pt 2 %P 1671 %8 1995 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/8591539?dopt=Abstract %0 Journal Article %J J Neuroimmunol %D 1995 %T Comparison of cell adhesion molecule expression between glioblastoma multiforme and autologous normal brain tissue. %A Marie-Claude Gingras %A Roussel, E %A Bruner, J M %A Branch, C D %A Moser, R P %K Antigens, CD %K Antigens, Tumor-Associated, Carbohydrate %K Brain Chemistry %K Brain Neoplasms %K Carrier Proteins %K CD58 Antigens %K Cell Adhesion Molecules %K Endothelium, Vascular %K Glioblastoma %K Humans %K Hyaluronan Receptors %K Immunohistochemistry %K Integrins %K Intercellular Adhesion Molecule-1 %K Membrane Glycoproteins %K Receptors, Cell Surface %K Receptors, Lymphocyte Homing %X

We investigated glioblastoma multiforme (GBM) for a pattern of consistent alterations in cell adhesion molecules (CAM) expression that might distinguish tumor from normal autologous brain tissue. We used frozen section immunohistochemistry with anti-CAM and computerized image analysis to quantify staining intensity which we expressed as relative intensity units (RIU). Our results showed that normal brain tissue generally did not express alpha 1 beta 1, intercellular CAM-1 (ICAM-1), and sialylated Lewisx, slightly expressed alpha 2, alpha 4, alpha 5, alpha 6 beta 1, alpha v beta 3, lymphocyte function-associated antigen-3 (LFA-3), Lewisx, sialylated LewisLewisx, had a good expression of alpha 3 beta 1 and CD44, and strongly expressed neural CAM (NCAM). GBM expressed alpha 2, alpha 3, alpha 5, alpha 6 beta 1, alpha v beta 3, ICAM-1, LFA-3, CD44, Lewisx, sialylated Lewisx, and sialylated LewisLewisx significantly higher (2-11-fold RIU) than normal brain tissue. ICAM-1 and LFA-3 were the most distinctive markers of GBM. The small blood vessel endothelial cells of the normal brain and the GBM showed a few differences. The tumor endothelium expression of alpha 2 beta 1, alpha 4 beta 1, and LFA-3 RIU appeared twice higher than in normal endothelium and alpha 6 beta 1 showed an average of 40% RIU decrease in comparison to normal. These results show that the expression of several CAM is consistently altered in GBM and its microvasculature when compared with autologous normal brain tissue.

%B J Neuroimmunol %V 57 %P 143-53 %8 1995 Mar %G eng %N 1-2 %1 https://www.ncbi.nlm.nih.gov/pubmed/7535788?dopt=Abstract %R 10.1016/0165-5728(94)00178-q %0 Journal Article %J DNA Seq %D 1995 %T Complete sequence of a 38.4-kb human cosmid insert containing the polymorphic marker DXS455 from Xq28. %A Andersson, B %A Lu, F %A Donna M Muzny %A Warren, S T %A Richard A Gibbs %K Bacteriophage M13 %K Base Sequence %K Cosmids %K DNA %K Gene Library %K Genetic Markers %K Humans %K Minisatellite Repeats %K Molecular Sequence Data %K Repetitive Sequences, Nucleic Acid %K X Chromosome %X

The complete DNA sequence of a cosmid mapping to human Xq28 (DXS455) has been determined using a shotgun approach (genbank accession number: L31948). The cosmid insert is 38.4 kb in length, and contains several repetitive sequences, including a highly repetitive region located in a fragment previously shown to contain a polymorphic VNTR locus, as well as short di- and tri-nucleotide repeats. In addition to the previously known VNTR locus, a CA-repeat and an unusual 800-bp repetitive region have been found to be polymorphic. The repeated sequence mapping to the site of the VNTR locus spans 480 bp in the cosmid. In addition to several AT-dinucleotide stretches, this repeat has four copies of a 25 bp repeat unit and flanking sequences similar to this 25-mer. No expressed sequences have so far been identified in this cosmid.

%B DNA Seq %V 5 %P 219-23 %8 1995 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/7626781?dopt=Abstract %R 10.3109/10425179509030969 %0 Journal Article %J Proc Annu Symp Comput Appl Med Care %D 1994 %T Collaborative Social and Medical Service System. %A Petermann, C A %A Bobroff, R B %A Moore, D M %A Gilson, H S %A Li, Y %A Dargahi, R %A Classen, D W %A Fowler, J %A Moreau, D R %A Beck, J R %K Adolescent %K Adolescent Health Services %K Ambulatory Care Information Systems %K Computer Communication Networks %K Computer Security %K Computer Systems %K Female %K Humans %K Male %K Medical Records Systems, Computerized %K Social Work %K Software %K Texas %K User-Computer Interface %X

This paper describes the Collaborative Social and Medical Services System, a robust information infrastructure for integrated social and medical care. The Collaborative Social and Medical Services System design and architecture address the primary goals of creating a readily extensible social and ambulatory care system. Our initial step toward reaching this goal is the delivery of an application supporting the operations of the Baylor Teen Health Clinics. This paper discusses our prototype experiences, system architecture, components, and the standards we are addressing.

%B Proc Annu Symp Comput Appl Med Care %P 614-8 %8 1994 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/7950001?dopt=Abstract %0 Journal Article %J Biochem Med Metab Biol %D 1992 %T Characterization of human genomic yeast artificial chromosome inserts containing hexokinase 1 coding information on chromosome 10. %A Gelb, B D %A Kim C Worley %A Griffin, L D %A Adams, V %A Chinault, A C %A McCabe, E R %K Animals %K Base Sequence %K Chromosome Mapping %K Chromosomes, Fungal %K Chromosomes, Human, Pair 10 %K Cricetinae %K DNA %K Genome, Human %K Hexokinase %K Humans %K Isoenzymes %K Molecular Sequence Data %K Polymerase Chain Reaction %K Yeasts %X

Hexokinase 1 (HK1) is one of four mammalian HK isoenzymes and maps to human chromosome 10. Two yeast artificial chromosomes (YACs) were identified in the Washington University human YAC library using polymerase chain reaction (PCR) primers designed with knowledge of the human HK1 cDNA sequence. YAC B129B12 is 120 kb in length and maps entirely to chromosome 10. YAC A159D5 is 400 kb in length and appears to have resulted from a recombination of chromosome 10 with non-chromosome 10 material. We report these YACs as potential resources for those interested in HK1 gene organization and mapping, as well as those desiring additional genomic information and markers on chromosome 10.

%B Biochem Med Metab Biol %V 47 %P 265-9 %8 1992 Jun %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/1627358?dopt=Abstract %R 10.1016/0885-4505(92)90035-w %0 Journal Article %J Am J Hum Genet %D 1991 %T Carrier detection and prenatal diagnosis in Duchenne and Becker muscular dystrophy families, using dinucleotide repeat polymorphisms. %A Clemens, P R %A Fenwick, R G %A Chamberlain, J S %A Gibbs, R A %A de Andrade, M %A Chakraborty, R %A Caskey, C T %K Alleles %K Base Sequence %K Cells, Cultured %K Dystrophin %K Female %K Gene Frequency %K Genetic Carrier Screening %K Genetic Markers %K Humans %K Male %K Molecular Sequence Data %K Muscular Dystrophies %K Pedigree %K Polydeoxyribonucleotides %K Polymerase Chain Reaction %K Polymorphism, Genetic %K Pregnancy %K Prenatal Diagnosis %K Repetitive Sequences, Nucleic Acid %X

To improve carrier detection and prenatal diagnosis for Duchenne and Becker muscular dystrophy families, we determined allele frequencies and measures of variation for four (dC-dA)n.(dG-dT)n loci identified within a deletion-prone region of the human dystrophin gene. The loci are highly polymorphic, with predicted heterozygosities of 71.6%-93.3%. Direct DNA sequence analysis of the (dC-dA)n.(dG-dT)n locus in intron 49 revealed an additional length polymorphism which varies by single-basepair increments, is adjacent to the dinucleotide repeat block, and enhances the polymorphic content of this marker. The four (dC-dA)n.(dG-dT)n loci are each easily amplified by PCR in two diplex reactions. The variability of allele lengths at these loci makes them ideal for carrier detection and prenatal diagnosis, often providing diagnostic information when RFLP analysis is uninformative. These markers have aided in identification of deletion mutations, exclusion of maternal cell contamination of chorionic villus samples, confirmation of paternity, and mapping of gene recombinations. The allele identification of these loci can be performed either with a radiolabel or with an automated, nonradioactive, fluorescent gel detection system.

%B Am J Hum Genet %V 49 %P 951-60 %8 1991 Nov %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/1928100?dopt=Abstract