%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 Genome Med %D 2013 %T Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy. %A Lupski, James R %A Gonzaga-Jauregui, Claudia %A Yang, Yaping %A Bainbridge, Matthew N %A Jhangiani, Shalini %A Buhay, Christian J %A Kovar, Christie L %A Wang, Min %A Hawes, Alicia C %A Reid, Jeffrey G %A Eng, Christine %A Muzny, Donna M %A Gibbs, Richard A %X

BACKGROUND: The debate regarding the relative merits of whole genome sequencing (WGS) versus exome sequencing (ES) centers around comparative cost, average depth of coverage for each interrogated base, and their relative efficiency in the identification of medically actionable variants from the myriad of variants identified by each approach. Nevertheless, few genomes have been subjected to both WGS and ES, using multiple next generation sequencing platforms. In addition, no personal genome has been so extensively analyzed using DNA derived from peripheral blood as opposed to DNA from transformed cell lines that may either accumulate mutations during propagation or clonally expand mosaic variants during cell transformation and propagation.

METHODS: We investigated a genome that was studied previously by SOLiD chemistry using both ES and WGS, and now perform six independent ES assays (Illumina GAII (x2), Illumina HiSeq (x2), Life Technologies' Personal Genome Machine (PGM) and Proton), and one additional WGS (Illumina HiSeq).

RESULTS: We compared the variants identified by the different methods and provide insights into the differences among variants identified between ES runs in the same technology platform and among different sequencing technologies. We resolved the true genotypes of medically actionable variants identified in the proband through orthogonal experimental approaches. Furthermore, ES identified an additional SH3TC2 variant (p.M1?) that likely contributes to the phenotype in the proband.

CONCLUSIONS: ES identified additional medically actionable variant calls and helped resolve ambiguous single nucleotide variants (SNV) documenting the power of increased depth of coverage of the captured targeted regions. Comparative analyses of WGS and ES reveal that pseudogenes and segmental duplications may explain some instances of apparent disease mutations in unaffected individuals.

%B Genome Med %V 5 %P 57 %8 2013 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/23806086?dopt=Abstract %R 10.1186/gm461 %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 Nature %D 2012 %T Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. %A Biankin, Andrew V %A Waddell, Nicola %A Kassahn, Karin S %A Gingras, Marie-Claude %A Muthuswamy, Lakshmi B %A Johns, Amber L %A Miller, David K %A Wilson, Peter J %A Patch, Ann-Marie %A Wu, Jianmin %A Chang, David K %A Cowley, Mark J %A Gardiner, Brooke B %A Song, Sarah %A Harliwong, Ivon %A Idrisoglu, Senel %A Nourse, Craig %A Nourbakhsh, Ehsan %A Manning, Suzanne %A Wani, Shivangi %A Gongora, Milena %A Pajic, Marina %A Scarlett, Christopher J %A Gill, Anthony J %A Pinho, Andreia V %A Rooman, Ilse %A Anderson, Matthew %A Holmes, Oliver %A Leonard, Conrad %A Taylor, Darrin %A Wood, Scott %A Xu, Qinying %A Nones, Katia %A Fink, J Lynn %A Christ, Angelika %A Bruxner, Tim %A Cloonan, Nicole %A Kolle, Gabriel %A Newell, Felicity %A Pinese, Mark %A Mead, R Scott %A Humphris, Jeremy L %A Kaplan, Warren %A Jones, Marc D %A Colvin, Emily K %A Nagrial, Adnan M %A Humphrey, Emily S %A Chou, Angela %A Chin, Venessa T %A Chantrill, Lorraine A %A Mawson, Amanda %A Samra, Jaswinder S %A Kench, James G %A Lovell, Jessica A %A Daly, Roger J %A Merrett, Neil D %A Toon, Christopher %A Epari, Krishna %A Nguyen, Nam Q %A Barbour, Andrew %A Zeps, Nikolajs %A Kakkar, Nipun %A Zhao, Fengmei %A Wu, Yuan Qing %A Wang, Min %A Muzny, Donna M %A Fisher, William E %A Brunicardi, F Charles %A Hodges, Sally E %A Reid, Jeffrey G %A Drummond, Jennifer %A Chang, Kyle %A Han, Yi %A Lewis, Lora R %A Dinh, Huyen %A Buhay, Christian J %A Beck, Timothy %A Timms, Lee %A Sam, Michelle %A Begley, Kimberly %A Brown, Andrew %A Pai, Deepa %A Panchal, Ami %A Buchner, Nicholas %A De Borja, Richard %A Denroche, Robert E %A Yung, Christina K %A Serra, Stefano %A Onetto, Nicole %A Mukhopadhyay, Debabrata %A Tsao, Ming-Sound %A Shaw, Patricia A %A Petersen, Gloria M %A Gallinger, Steven %A Hruban, Ralph H %A Maitra, Anirban %A Iacobuzio-Donahue, Christine A %A Schulick, Richard D %A Wolfgang, Christopher L %A Morgan, Richard A %A Lawlor, Rita T %A Capelli, Paola %A Corbo, Vincenzo %A Scardoni, Maria %A Tortora, Giampaolo %A Tempero, Margaret A %A Mann, Karen M %A Jenkins, Nancy A %A Perez-Mancera, Pedro A %A Adams, David J %A Largaespada, David A %A Wessels, Lodewyk F A %A Rust, Alistair G %A Stein, Lincoln D %A Tuveson, David A %A Copeland, Neal G %A Musgrove, Elizabeth A %A Scarpa, Aldo %A Eshleman, James R %A Hudson, Thomas J %A Sutherland, Robert L %A Wheeler, David A %A Pearson, John V %A McPherson, John D %A Gibbs, Richard A %A Grimmond, Sean M %K Animals %K Axons %K Carcinoma, Pancreatic Ductal %K Gene Dosage %K Gene Expression Regulation, Neoplastic %K Genome %K Humans %K Kaplan-Meier Estimate %K Mice %K Mutation %K Pancreatic Neoplasms %K Proteins %K Signal Transduction %X

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

%B Nature %V 491 %P 399-405 %8 2012 Nov 15 %G eng %N 7424 %1 https://www.ncbi.nlm.nih.gov/pubmed/23103869?dopt=Abstract %R 10.1038/nature11547 %0 Journal Article %J Nature %D 2012 %T Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. %A Hughes, Jennifer F %A Skaletsky, Helen %A Brown, Laura G %A Pyntikova, Tatyana %A Graves, Tina %A Fulton, Robert S %A Dugan, Shannon %A Ding, Yan %A Buhay, Christian J %A Kremitzki, Colin %A Wang, Qiaoyan %A Shen, Hua %A Holder, Michael %A Villasana, Donna %A Nazareth, Lynne V %A Cree, Andrew %A Courtney, Laura %A Veizer, Joelle %A Kotkiewicz, Holland %A Cho, Ting-Jan %A Koutseva, Natalia %A Rozen, Steve %A Muzny, Donna M %A Warren, Wesley C %A Gibbs, Richard A %A Wilson, Richard K %A Page, David C %K Animals %K Chromosomes, Human, Y %K Conserved Sequence %K Crossing Over, Genetic %K Evolution, Molecular %K Gene Amplification %K Gene Deletion %K Humans %K In Situ Hybridization, Fluorescence %K Macaca mulatta %K Male %K Models, Genetic %K Molecular Sequence Data %K Pan troglodytes %K Radiation Hybrid Mapping %K Selection, Genetic %K Time Factors %K Y Chromosome %X

The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200-300 million years. The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes' genes owing to genetic decay. This evolutionary decay was driven by a series of five 'stratification' events. Each event suppressed X-Y crossing over within a chromosome segment or 'stratum', incorporated that segment into the MSY and subjected its genes to the erosive forces that attend the absence of crossing over. The last of these events occurred 30 million years ago, 5 million years before the human and Old World monkey lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome, remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage. To investigate this question, we sequenced the MSY of the rhesus macaque, an Old World monkey, and compared it to the human MSY. We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. In the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 million years ago. Likewise, the rhesus MSY has not lost any older genes (from strata 1-4) during the past 25 million years, despite its major structural differences to the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection.

%B Nature %V 483 %P 82-6 %8 2012 Feb 22 %G eng %N 7387 %1 https://www.ncbi.nlm.nih.gov/pubmed/22367542?dopt=Abstract %R 10.1038/nature10843 %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 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 2008 %T The genome of the model beetle and pest Tribolium castaneum. %A Stephen Richards %A Richard A Gibbs %A Weinstock, George M %A Brown, Susan J %A Denell, Robin %A Beeman, Richard W %A Richard A Gibbs %A Beeman, Richard W %A Brown, Susan J %A Bucher, Gregor %A Friedrich, Markus %A Grimmelikhuijzen, Cornelis J P %A Klingler, Martin %A Lorenzen, Marce %A Stephen Richards %A Roth, Siegfried %A Schröder, Reinhard %A Tautz, Diethard %A Zdobnov, Evgeny M %A Donna M Muzny %A Richard A Gibbs %A Weinstock, George M %A Attaway, Tony %A Bell, Stephanie %A Buhay, Christian J %A Chandrabose, Mimi N %A Chavez, Dean %A Clerk-Blankenburg, Kerstin P %A Cree, Andrew %A Dao, Marvin %A Davis, Clay %A Chacko, Joseph %A Dinh, Huyen %A Dugan-Rocha, Shannon %A Fowler, Gerald %A Garner, Toni T %A Garnes, Jeffrey %A Gnirke, Andreas %A Hawes, Alica %A Hernandez, Judith %A Hines, Sandra %A Holder, Michael %A Hume, Jennifer %A Jhangiani, Shalini N %A Joshi, Vandita %A Ziad Khan %A Jackson, Laronda %A Kovar, Christie %A Kowis, Andrea %A Lee, Sandra %A Lewis, Lora R %A Margolis, Jon %A Morgan, Margaret %A Nazareth, Lynne V %A Nguyen, Ngoc %A Okwuonu, Geoffrey %A Parker, David %A Stephen Richards %A Ruiz, San-Juana %A Santibanez, Jireh %A Savard, Joël %A Steven E Scherer %A Schneider, Brian %A Sodergren, Erica %A Tautz, Diethard %A Vattahil, Selina %A Villasana, Donna %A White, Courtney S %A Wright, Rita %A Park, Yoonseong %A Beeman, Richard W %A Lord, Jeff %A Oppert, Brenda %A Lorenzen, Marce %A Brown, Susan %A Wang, Liangjiang %A Savard, Joël %A Tautz, Diethard %A Stephen Richards %A Weinstock, George %A Richard A Gibbs %A Liu, Yue %A Kim C Worley %A Weinstock, George %A Elsik, Christine G %A Reese, Justin T %A Elhaik, Eran %A Landan, Giddy %A Graur, Dan %A Arensburger, Peter %A Atkinson, Peter %A Beeman, Richard W %A Beidler, Jim %A Brown, Susan J %A Demuth, Jeffery P %A Drury, Douglas W %A Du, Yu-Zhou %A Fujiwara, Haruhiko %A Lorenzen, Marce %A Maselli, Vincenza %A Osanai, Mizuko %A Park, Yoonseong %A Robertson, Hugh M %A Tu, Zhijian %A Wang, Jian-jun %A Wang, Suzhi %A Stephen Richards %A Song, Henry %A Zhang, Lan %A Sodergren, Erica %A Werner, Doreen %A Stanke, Mario %A Morgenstern, Burkhard %A Solovyev, Victor %A Kosarev, Peter %A Brown, Garth %A Chen, Hsiu-Chuan %A Ermolaeva, Olga %A Hlavina, Wratko %A Kapustin, Yuri %A Kiryutin, Boris %A Kitts, Paul %A Maglott, Donna %A Pruitt, Kim %A Sapojnikov, Victor %A Souvorov, Alexandre %A Mackey, Aaron J %A Waterhouse, Robert M %A Wyder, Stefan %A Zdobnov, Evgeny M %A Zdobnov, Evgeny M %A Wyder, Stefan %A Kriventseva, Evgenia V %A Kadowaki, Tatsuhiko %A Bork, Peer %A Aranda, Manuel %A Bao, Riyue %A Beermann, Anke %A Berns, Nicola %A Bolognesi, Renata %A Bonneton, François %A Bopp, Daniel %A Brown, Susan J %A Bucher, Gregor %A Butts, Thomas %A Chaumot, Arnaud %A Denell, Robin E %A Ferrier, David E K %A Friedrich, Markus %A Gordon, Cassondra M %A Jindra, Marek %A Klingler, Martin %A Lan, Que %A Lattorff, H Michael G %A Laudet, Vincent %A von Levetsow, Cornelia %A Liu, Zhenyi %A Lutz, Rebekka %A Lynch, Jeremy A %A da Fonseca, Rodrigo Nunes %A Posnien, Nico %A Reuter, Rolf %A Roth, Siegfried %A Savard, Joël %A Schinko, Johannes B %A Schmitt, Christian %A Schoppmeier, Michael %A Schröder, Reinhard %A Shippy, Teresa D %A Simonnet, Franck %A Marques-Souza, Henrique %A Tautz, Diethard %A Tomoyasu, Yoshinori %A Trauner, Jochen %A Van der Zee, Maurijn %A Vervoort, Michel %A Wittkopp, Nadine %A Wimmer, Ernst A %A Yang, Xiaoyun %A Jones, Andrew K %A Sattelle, David B %A Ebert, Paul R %A Nelson, David %A Scott, Jeffrey G %A Beeman, Richard W %A Muthukrishnan, Subbaratnam %A Kramer, Karl J %A Arakane, Yasuyuki %A Beeman, Richard W %A Zhu, Qingsong %A Hogenkamp, David %A Dixit, Radhika %A Oppert, Brenda %A Jiang, Haobo %A Zou, Zhen %A Marshall, Jeremy %A Elpidina, Elena %A Vinokurov, Konstantin %A Oppert, Cris %A Zou, Zhen %A Evans, Jay %A Lu, Zhiqiang %A Zhao, Picheng %A Sumathipala, Niranji %A Altincicek, Boran %A Vilcinskas, Andreas %A Williams, Michael %A Hultmark, Dan %A Hetru, Charles %A Jiang, Haobo %A Grimmelikhuijzen, Cornelis J P %A Hauser, Frank %A Cazzamali, Giuseppe %A Williamson, Michael %A Park, Yoonseong %A Li, Bin %A Tanaka, Yoshiaki %A Predel, Reinhard %A Neupert, Susanne %A Schachtner, Joachim %A Verleyen, Peter %A Raible, Florian %A Bork, Peer %A Friedrich, Markus %A Walden, Kimberly K O %A Robertson, Hugh M %A Angeli, Sergio %A Forêt, Sylvain %A Bucher, Gregor %A Schuetz, Stefan %A Maleszka, Ryszard %A Wimmer, Ernst A %A Beeman, Richard W %A Lorenzen, Marce %A Tomoyasu, Yoshinori %A Miller, Sherry C %A Grossmann, Daniela %A Bucher, Gregor %K Animals %K Base Composition %K Body Patterning %K Cytochrome P-450 Enzyme System %K DNA Transposable Elements %K Genes, Insect %K Genome, Insect %K Growth and Development %K Humans %K Insecticides %K Neurotransmitter Agents %K Oogenesis %K Phylogeny %K Proteome %K Receptors, G-Protein-Coupled %K Receptors, Odorant %K Repetitive Sequences, Nucleic Acid %K RNA Interference %K Taste %K Telomere %K Tribolium %K Vision, Ocular %X

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

%B Nature %V 452 %P 949-55 %8 2008 Apr 24 %G eng %N 7190 %1 https://www.ncbi.nlm.nih.gov/pubmed/18362917?dopt=Abstract %R 10.1038/nature06784 %0 Journal Article %J Science %D 2007 %T Evolutionary and biomedical insights from the rhesus macaque genome. %A Richard A Gibbs %A Jeffrey Rogers %A Katze, Michael G %A Bumgarner, Roger %A Weinstock, George M %A Mardis, Elaine R %A Remington, Karin A %A Strausberg, Robert L %A Venter, J Craig %A Wilson, Richard K %A Batzer, Mark A %A Bustamante, Carlos D %A Eichler, Evan E %A Hahn, Matthew W %A Hardison, Ross C %A Makova, Kateryna D %A Miller, Webb %A Milosavljevic, Aleksandar %A Palermo, Robert E %A Siepel, Adam %A Sikela, James M %A Attaway, Tony %A Bell, Stephanie %A Bernard, Kelly E %A Buhay, Christian J %A Chandrabose, Mimi N %A Dao, Marvin %A Davis, Clay %A Delehaunty, Kimberly D %A Ding, Yan %A Dinh, Huyen H %A Dugan-Rocha, Shannon %A Fulton, Lucinda A %A Gabisi, Ramatu Ayiesha %A Garner, Toni T %A Godfrey, Jennifer %A Hawes, Alicia C %A Hernandez, Judith %A Hines, Sandra %A Holder, Michael %A Hume, Jennifer %A Jhangiani, Shalini N %A Joshi, Vandita %A Ziad Khan %A Kirkness, Ewen F %A Cree, Andrew %A Fowler, R Gerald %A Lee, Sandra %A Lewis, Lora R %A Li, Zhangwan %A Liu, Yih-Shin %A Moore, Stephanie M %A Donna M Muzny %A Nazareth, Lynne V %A Ngo, Dinh Ngoc %A Okwuonu, Geoffrey O %A Pai, Grace %A Parker, David %A Paul, Heidie A %A Pfannkoch, Cynthia %A Pohl, Craig S %A Rogers, Yu-Hui %A Ruiz, San Juana %A Aniko Sabo %A Santibanez, Jireh %A Schneider, Brian W %A Smith, Scott M %A Sodergren, Erica %A Svatek, Amanda F %A Utterback, Teresa R %A Vattathil, Selina %A Warren, Wesley %A White, Courtney Sherell %A Chinwalla, Asif T %A Feng, Yucheng %A Halpern, Aaron L %A Hillier, LaDeana W %A Huang, Xiaoqiu %A Minx, Pat %A Nelson, Joanne O %A Pepin, Kymberlie H %A Xiang Qin %A Sutton, Granger G %A Venter, Eli %A Walenz, Brian P %A Wallis, John W %A Kim C Worley %A Yang, Shiaw-Pyng %A Jones, Steven M %A Marra, Marco A %A Rocchi, Mariano %A Schein, Jacqueline E %A Baertsch, Robert %A Clarke, Laura %A Csuros, Miklos %A Glasscock, Jarret %A R. Alan Harris %A Havlak, Paul %A Jackson, Andrew R %A Jiang, Huaiyang %A Liu, Yue %A Messina, David N %A Shen, Yufeng %A Song, Henry Xing-Zhi %A Wylie, Todd %A Zhang, Lan %A Birney, Ewan %A Han, Kyudong %A Konkel, Miriam K %A Lee, Jungnam %A Smit, Arian F A %A Ullmer, Brygg %A Wang, Hui %A Xing, Jinchuan %A Burhans, Richard %A Cheng, Ze %A Karro, John E %A Ma, Jian %A Raney, Brian %A She, Xinwei %A Cox, Michael J %A Demuth, Jeffery P %A Dumas, Laura J %A Han, Sang-Gook %A Hopkins, Janet %A Karimpour-Fard, Anis %A Kim, Young H %A Pollack, Jonathan R %A Vinar, Tomas %A Addo-Quaye, Charles %A Degenhardt, Jeremiah %A Denby, Alexandra %A Hubisz, Melissa J %A Indap, Amit %A Kosiol, Carolin %A Lahn, Bruce T %A Lawson, Heather A %A Marklein, Alison %A Nielsen, Rasmus %A Vallender, Eric J %A Clark, Andrew G %A Ferguson, Betsy %A Hernandez, Ryan D %A Hirani, Kashif %A Kehrer-Sawatzki, Hildegard %A Kolb, Jessica %A Patil, Shobha %A Pu, Ling-Ling %A Ren, Yanru %A Smith, David Glenn %A David A Wheeler %A Schenck, Ian %A Ball, Edward V %A Rui Chen %A Cooper, David N %A Giardine, Belinda %A Hsu, Fan %A Kent, W James %A Lesk, Arthur %A Nelson, David L %A O'brien, William E %A Prüfer, Kay %A Stenson, Peter D %A Wallace, James C %A Ke, Hui %A Liu, Xiao-Ming %A Wang, Peng %A Xiang, Andy Peng %A Yang, Fan %A Barber, Galt P %A Haussler, David %A Karolchik, Donna %A Kern, Andy D %A Kuhn, Robert M %A Smith, Kayla E %A Zwieg, Ann S %K Animals %K Biomedical Research %K Evolution, Molecular %K Female %K Gene Duplication %K Gene Rearrangement %K Genetic Diseases, Inborn %K Genetic Variation %K Genome %K Humans %K Macaca mulatta %K Male %K Multigene Family %K Mutation %K Pan troglodytes %K Sequence Analysis, DNA %K Species Specificity %X

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

%B Science %V 316 %P 222-34 %8 2007 Apr 13 %G eng %N 5822 %1 https://www.ncbi.nlm.nih.gov/pubmed/17431167?dopt=Abstract %R 10.1126/science.1139247 %0 Journal Article %J BMC Microbiol %D 2007 %T Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. %A Highlander, Sarah K %A Hultén, Kristina G %A Qin, Xiang %A Jiang, Huaiyang %A Yerrapragada, Shailaja %A Mason, Edward O %A Shang, Yue %A Williams, Tiffany M %A Fortunov, Régine M %A Liu, Yamei %A Igboeli, Okezie %A Petrosino, Joseph %A Tirumalai, Madhan %A Uzman, Akif %A Fox, George E %A Cardenas, Ana Maria %A Muzny, Donna M %A Hemphill, Lisa %A Ding, Yan %A Dugan, Shannon %A Blyth, Peter R %A Buhay, Christian J %A Dinh, Huyen H %A Hawes, Alicia C %A Holder, Michael %A Kovar, Christie L %A Lee, Sandra L %A Liu, Wen %A Nazareth, Lynne V %A Wang, Qiaoyan %A Zhou, Jianling %A Kaplan, Sheldon L %A Weinstock, George M %K Adolescent %K Anti-Bacterial Agents %K Base Sequence %K Genomic Islands %K Humans %K Hydrolases %K Methicillin Resistance %K Molecular Epidemiology %K Molecular Sequence Data %K Open Reading Frames %K Plasmids %K Polymorphism, Genetic %K Staphylococcal Infections %K Staphylococcus aureus %K United States %X

BACKGROUND: Community acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) increasingly causes disease worldwide. USA300 has emerged as the predominant clone causing superficial and invasive infections in children and adults in the USA. Epidemiological studies suggest that USA300 is more virulent than other CA-MRSA. The genetic determinants that render virulence and dominance to USA300 remain unclear.

RESULTS: We sequenced the genomes of two pediatric USA300 isolates: one CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at Texas Children's Hospital in Houston. DNA sequencing was performed by Sanger dideoxy whole genome shotgun (WGS) and 454 Life Sciences pyrosequencing strategies. The sequence of the USA300 MRSA strain was rigorously annotated. In USA300-MRSA 2658 chromosomal open reading frames were predicted and 3.1 and 27 kilobase (kb) plasmids were identified. USA300-MSSA contained a 20 kb plasmid with some homology to the 27 kb plasmid found in USA300-MRSA. Two regions found in US300-MRSA were absent in USA300-MSSA. One of these carried the arginine deiminase operon that appears to have been acquired from S. epidermidis. The USA300 sequence was aligned with other sequenced S. aureus genomes and regions unique to USA300 MRSA were identified.

CONCLUSION: USA300-MRSA is highly similar to other MRSA strains based on whole genome alignments and gene content, indicating that the differences in pathogenesis are due to subtle changes rather than to large-scale acquisition of virulence factor genes. The USA300 Houston isolate differs from another sequenced USA300 strain isolate, derived from a patient in San Francisco, in plasmid content and a number of sequence polymorphisms. Such differences will provide new insights into the evolution of pathogens.

%B BMC Microbiol %V 7 %P 99 %8 2007 Nov 06 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/17986343?dopt=Abstract %R 10.1186/1471-2180-7-99 %0 Journal Article %J Nature %D 2006 %T The DNA sequence, annotation and analysis of human chromosome 3. %A Donna M Muzny %A Steven E Scherer %A Kaul, Rajinder %A Wang, Jing %A Yu, Jun %A Sudbrak, Ralf %A Buhay, Christian J %A Rui Chen %A Cree, Andrew %A Ding, Yan %A Dugan-Rocha, Shannon %A Gill, Rachel %A Gunaratne, Preethi %A R. Alan Harris %A Hawes, Alicia C %A Hernandez, Judith %A Hodgson, Anne V %A Hume, Jennifer %A Jackson, Andrew %A Ziad Khan %A Kovar-Smith, Christie %A Lewis, Lora R %A Lozado, Ryan J %A Metzker, Michael L %A Milosavljevic, Aleksandar %A Miner, George R %A Morgan, Margaret B %A Nazareth, Lynne V %A Scott, Graham %A Sodergren, Erica %A Song, Xing-Zhi %A Steffen, David %A Wei, Sharon %A David A Wheeler %A Wright, Mathew W %A Kim C Worley %A Yuan, Ye %A Zhang, Zhengdong %A Adams, Charles Q %A Ansari-Lari, M Ali %A Ayele, Mulu %A Brown, Mary J %A Chen, Guan %A Chen, Zhijian %A Clendenning, James %A Clerc-Blankenburg, Kerstin P %A Chen, Runsheng %A Chen, Zhu %A Davis, Clay %A Delgado, Oliver %A Dinh, Huyen H %A Dong, Wei %A Draper, Heather %A Ernst, Stephen %A Fu, Gang %A Gonzalez-Garay, Manuel L %A Garcia, Dawn K %A Gillett, Will %A Gu, Jun %A Hao, Bailin %A Haugen, Eric %A Havlak, Paul %A He, Xin %A Hennig, Steffen %A Hu, Songnian %A Huang, Wei %A Jackson, Laronda R %A Jacob, Leni S %A Kelly, Susan H %A Kube, Michael %A Levy, Ruth %A Li, Zhangwan %A Liu, Bin %A Liu, Jing %A Liu, Wen %A Lu, Jing %A Maheshwari, Manjula %A Nguyen, Bao-Viet %A Okwuonu, Geoffrey O %A Palmeiri, Anthony %A Pasternak, Shiran %A Perez, Lesette M %A Phelps, Karen A %A Plopper, Farah J H %A Qiang, Boqin %A Raymond, Christopher %A Rodriguez, Ruben %A Saenphimmachak, Channakhone %A Santibanez, Jireh %A Shen, Hua %A Shen, Yan %A Subramanian, Sandhya %A Tabor, Paul E %A Verduzco, Daniel %A Waldron, Lenée %A Wang, Jian %A Wang, Jun %A Wang, Qiaoyan %A Williams, Gabrielle A %A Wong, Gane K-S %A Yao, Zhijian %A Zhang, Jingkun %A Zhang, Xiuqing %A Zhao, Guoping %A Zhou, Jianling %A Zhou, Yang %A Nelson, David %A Lehrach, Hans %A Reinhardt, Richard %A Naylor, Susan L %A Yang, Huanming %A Olson, Maynard %A Weinstock, George %A Richard A Gibbs %K Animals %K Base Sequence %K Chromosome Breakage %K Chromosome Inversion %K Chromosomes, Human, Pair 3 %K Contig Mapping %K CpG Islands %K DNA, Complementary %K Evolution, Molecular %K Expressed Sequence Tags %K Human Genome Project %K Humans %K Macaca mulatta %K Molecular Sequence Data %K Pan troglodytes %K Sequence Analysis, DNA %K Synteny %X

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

%B Nature %V 440 %P 1194-8 %8 2006 Apr 27 %G eng %N 7088 %1 https://www.ncbi.nlm.nih.gov/pubmed/16641997?dopt=Abstract %R 10.1038/nature04728 %0 Journal Article %J Nature %D 2006 %T The finished DNA sequence of human chromosome 12. %A Scherer, Steven E %A Donna M Muzny %A Buhay, Christian J %A Rui Chen %A Cree, Andrew %A Ding, Yan %A Dugan-Rocha, Shannon %A Gill, Rachel %A Gunaratne, Preethi %A R. Alan Harris %A Hawes, Alicia C %A Hernandez, Judith %A Hodgson, Anne V %A Hume, Jennifer %A Jackson, Andrew %A Ziad Khan %A Kovar-Smith, Christie %A Lewis, Lora R %A Lozado, Ryan J %A Metzker, Michael L %A Milosavljevic, Aleksandar %A Miner, George R %A Montgomery, Kate T %A Morgan, Margaret B %A Nazareth, Lynne V %A Scott, Graham %A Sodergren, Erica %A Song, Xing-Zhi %A Steffen, David %A Lovering, Ruth C %A Wheeler, David A %A Worley, Kim C %A Yuan, Yi %A Zhang, Zhengdong %A Adams, Charles Q %A Ansari-Lari, M Ali %A Ayele, Mulu %A Brown, Mary J %A Chen, Guan %A Chen, Zhijian %A Clerc-Blankenburg, Kerstin P %A Davis, Clay %A Delgado, Oliver %A Dinh, Huyen H %A Draper, Heather %A Gonzalez-Garay, Manuel L %A Havlak, Paul %A Jackson, Laronda R %A Jacob, Leni S %A Kelly, Susan H %A Li, Li %A Li, Zhangwan %A Liu, Jing %A Liu, Wen %A Lu, Jing %A Maheshwari, Manjula %A Nguyen, Bao-Viet %A Okwuonu, Geoffrey O %A Pasternak, Shiran %A Perez, Lesette M %A Plopper, Farah J H %A Santibanez, Jireh %A Shen, Hua %A Tabor, Paul E %A Verduzco, Daniel %A Waldron, Lenée %A Wang, Qiaoyan %A Williams, Gabrielle A %A Zhang, Jingkun %A Zhou, Jianling %A Allen, Carlana C %A Amin, Anita G %A Anyalebechi, Vivian %A Bailey, Michael %A Barbaria, Joseph A %A Bimage, Kesha E %A Bryant, Nathaniel P %A Burch, Paula E %A Burkett, Carrie E %A Burrell, Kevin L %A Calderon, Eliana %A Cardenas, Veronica %A Carter, Kelvin %A Casias, Kristal %A Cavazos, Iracema %A Cavazos, Sandra R %A Ceasar, Heather %A Chacko, Joseph %A Chan, Sheryl N %A Chavez, Dean %A Christopoulos, Constantine %A Chu, Joseph %A Cockrell, Raynard %A Cox, Caroline D %A Dang, Michelle %A Dathorne, Stephanie R %A David, Robert %A Davis, Candi Mon'Et %A Davy-Carroll, Latarsha %A Deshazo, Denise R %A Donlin, Jeremy E %A D'Souza, Lisa %A Eaves, Kristy A %A Simons, Rain %A Emery-Cohen, Alexandra J %A Escotto, Michael %A Flagg, Nicole %A Forbes, Lisa D %A Gabisi, Abdul M %A Garza, Melissa %A Hamilton, Cerissa %A Henderson, Nicholas %A Hernandez, Omar %A Hines, Sandra %A Hogues, Marilyn E %A Huang, Mei %A Idlebird, DeVincent G %A Johnson, Rudy %A Jolivet, Angela %A Jones, Sally %A Kagan, Ryan %A King, Laquisha M %A Leal, Belita %A Lebow, Heather %A Lee, Sandra %A LeVan, Jaclyn M %A Lewis, Lakeshia C %A London, Pamela %A Lorensuhewa, Lorna M %A Loulseged, Hermela %A Lovett, Demetria A %A Lucier, Alice %A Lucier, Raymond L %A Ma, Jie %A Madu, Renita C %A Mapua, Patricia %A Martindale, Ashley D %A Martinez, Evangelina %A Massey, Elizabeth %A Mawhiney, Samantha %A Meador, Michael G %A Mendez, Sylvia %A Mercado, Christian %A Mercado, Iracema C %A Merritt, Christina E %A Miner, Zachary L %A Minja, Emmanuel %A Mitchell, Teresa %A Mohabbat, Farida %A Mohabbat, Khatera %A Montgomery, Baize %A Moore, Niki %A Morris, Sidney %A Munidasa, Mala %A Ngo, Robin N %A Nguyen, Ngoc B %A Nickerson, Elizabeth %A Nwaokelemeh, Ogechi O %A Nwokenkwo, Stanley %A Obregon, Melissa %A Oguh, Maryann %A Oragunye, Njideka %A Oviedo, Rodolfo J %A Parish, Bridgette J %A Parker, David N %A Parrish, Julia %A Parks, Kenya L %A Paul, Heidie A %A Payton, Brett A %A Perez, Agapito %A Perrin, William %A Pickens, Adam %A Primus, Eltrick L %A Pu, Ling-Ling %A Puazo, Maria %A Quiles, Miyo M %A Quiroz, Juana B %A Rabata, Dina %A Reeves, Kacy %A Ruiz, San Juana %A Shao, Hongmei %A Sisson, Ida %A Sonaike, Titilola %A Sorelle, Richard P %A Sutton, Angelica E %A Svatek, Amanda F %A Svetz, Leah Anne %A Tamerisa, Kavitha S %A Taylor, Tineace R %A Teague, Brian %A Thomas, Nicole %A Thorn, Rachel D %A Trejos, Zulma Y %A Trevino, Brenda K %A Ukegbu, Ogechi N %A Urban, Jeremy B %A Vasquez, Lydia I %A Vera, Virginia A %A Villasana, Donna M %A Wang, Ling %A Ward-Moore, Stephanie %A Warren, James T %A Wei, Xuehong %A White, Flower %A Williamson, Angela L %A Wleczyk, Regina %A Wooden, Hailey S %A Wooden, Steven H %A Yen, Jennifer %A Yoon, Lillienne %A Yoon, Vivienne %A Zorrilla, Sara E %A Nelson, David %A Kucherlapati, Raju %A Weinstock, George %A Richard A Gibbs %K Animals %K Base Composition %K Chromosomes, Human, Pair 12 %K CpG Islands %K Evolution, Molecular %K Expressed Sequence Tags %K Genes %K Humans %K Linkage Disequilibrium %K Microsatellite Repeats %K Molecular Sequence Data %K Mutagenesis, Insertional %K Pan troglodytes %K Sequence Analysis, DNA %K Sequence Deletion %K Short Interspersed Nucleotide Elements %K Synteny %X

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

%B Nature %V 440 %P 346-51 %8 2006 Mar 16 %G eng %N 7082 %1 https://www.ncbi.nlm.nih.gov/pubmed/16541075?dopt=Abstract %R 10.1038/nature04569