Publications

Filters: Keyword is DNA Copy Number Variations  [Clear All Filters]
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Ritter DI, Haines K, Cheung H, Davis CF, Lau CC, Berg JS, Brown CW, Thompson PA, Gibbs RA, Wheeler DA, Plon SE. Identifying gene disruptions in novel balanced de novo constitutional translocations in childhood cancer patients by whole-genome sequencing. Genet Med. 2015 ;17(10):831-5.
Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao H-T, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang S-HL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SWai, Lupski JR, Patel A, Shaw CA, Stankiewicz P. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med. 2017 ;9(1):83.
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Gambin T, Akdemir ZC, Yuan B, Gu S, Chiang T, Carvalho CMB, Shaw C, Jhangiani S, Boone PM, Eldomery MK, Karaca E, Bayram Y, Stray-Pedersen A, Muzny DM, Charng W-L, Bahrambeigi V, Belmont JW, Boerwinkle E, Beaudet AL, Gibbs RA, Lupski JR. Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort. Nucleic Acids Res. 2017 ;45(4):1633-1648.
Du H, Dardas Z, Jolly A, Grochowski CM, Jhangiani SN, Li H, Muzny DM, Fatih JM, Yesil G, Elcioglu NH, Gezdirici A, Marafi D, Pehlivan D, Calame DG, Carvalho CMB, Posey JE, Gambin T, Coban-Akdemir Z, Lupski JR. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. Nucleic Acids Res. 2024 ;52(4):e18.
Daines B, Wang H, Li Y, Han Y, Gibbs RA, Chen R. High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics. 2009 ;182(4):935-41.
Baslan T, Kovaka S, Sedlazeck FJ, Zhang Y, Wappel R, Tian S, Lowe SW, Goodwin S, Schatz MC. High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Res. 2021 ;49(21):e124.
Zhang J, Gambin T, Yuan B, Szafranski P, Rosenfeld JA, Balwi MAl, Alswaid A, Al-Gazali L, Shamsi AMAl, Komara M, Ali BR, Roeder E, McAuley L, Roy DS, Manchester DK, Magoulas P, King LE, Hannig V, Bonneau D, Denommé-Pichon A-S, Charif M, Besnard T, Bézieau S, Cogné B, Andrieux J, Zhu W, He W, Vetrini F, Ward PA, Cheung SWai, Bi W, Eng CM, Lupski JR, Yang Y, Patel A, Lalani SR, Xia F, Stankiewicz P. Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. Hum Genet. 2017 ;136(4):377-386.
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Lodish MB, Yuan B, Levy I, Braunstein GD, Lyssikatos C, Salpea P, Szarek E, Karageorgiadis AS, Belyavskaya E, Raygada M, Faucz FRueda, Izzat L, Brain C, Gardner J, Quezado M, J Carney A, Lupski JR, Stratakis CA. Germline PRKACA amplification causes variable phenotypes that may depend on the extent of the genomic defect: molecular mechanisms and clinical presentations. Eur J Endocrinol. 2015 ;172(6):803-11.
Pehlivan D, Bayram Y, Gunes N, Akdemir ZCoban, Shukla A, Bierhals T, Tabakci B, Sahin Y, Gezdirici A, Fatih JM, Gulec EYilmaz, Yesil G, Punetha J, Ocak Z, Grochowski CM, Karaca E, Albayrak HMutlu, Radhakrishnan P, Erdem HBagis, Sahin I, Yildirim T, Bayhan IA, Bursali A, Elmas M, Yuksel Z, Ozdemir O, Silan F, Yildiz O, Yesilbas O, Isikay S, Balta B, Gu S, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Boerwinkle E, Gibbs RA, Tsiakas K, Hempel M, Girisha KMohan, Gul D, Posey JE, Elcioglu NH, Tuysuz B, Lupski JR. The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance. Am J Hum Genet. 2019 ;105(1):132-150.
Farrar JE, Schuback HL, Ries RE, Wai D, Hampton OA, Treviño LR, Alonzo TA, Auvil JMGuidry, Davidsen TM, Gesuwan P, Hermida L, Muzny DM, Dewal N, Rustagi N, Lewis LR, Gamis AS, Wheeler DA, Smith MA, Gerhard DS, Meshinchi S. Genomic Profiling of Pediatric Acute Myeloid Leukemia Reveals a Changing Mutational Landscape from Disease Diagnosis to Relapse. Cancer Res. 2016 ;76(8):2197-205.
Harel T, Lupski JR. Genomic disorders 20 years on-mechanisms for clinical manifestations. Clin Genet. 2018 ;93(3):439-449.
Ikeda Y, Oda K, Nakagawa S, Murayama-Hosokawa S, Yamamoto S, Ishikawa S, Wang L, Takazawa Y, Maeda D, Wada-Hiraike O, Kawana K, Fukayama M, Aburatani H, Yano T, Kozuma S, Taketani Y. Genome-wide single nucleotide polymorphism arrays as a diagnostic tool in patients with synchronous endometrial and ovarian cancer. Int J Gynecol Cancer. 2012 ;22(5):725-31.
Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW. Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol. 2019 ;28(6):1491-1505.
Longchamps RJ, Yang SY, Castellani CA, Shi W, Lane J, Grove ML, Bartz TM, Sarnowski C, Liu C, Burrows K, Guyatt AL, Gaunt TR, Kacprowski T, Yang J, De Jager PL, Yu L, Bergman A, Xia R, Fornage M, Feitosa MF, Wojczynski MK, Kraja AT, Province MA, Amin N, Rivadeneira F, Tiemeier H, Uitterlinden AG, Broer L, Van Meurs JBJ, van Duijn CM, Raffield LM, Lange L, Rich SS, Lemaitre RN, Goodarzi MO, Sitlani CM, C Y Mak A, Bennett DA, Rodriguez S, Murabito JM, Lunetta KL, Sotoodehnia N, Atzmon G, Ye K, Barzilai N, Brody JA, Psaty BM, Taylor KD, Rotter JI, Boerwinkle E, Pankratz N, Arking DE. Genome-wide analysis of mitochondrial DNA copy number reveals loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation. Hum Genet. 2022 ;141(1):127-146.
Guo D-chuan, Grove ML, Prakash SK, Eriksson P, Hostetler EM, LeMaire SA, Body SC, Shalhub S, Estrera AL, Safi HJ, Regalado ES, Zhou W, Mathis MR, Eagle KA, Yang B, Willer CJ, Boerwinkle E, Milewicz DM. Genetic Variants in LRP1 and ULK4 Are Associated with Acute Aortic Dissections. Am J Hum Genet. 2016 ;99(3):762-769.
Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJasmine, Quist M, Nowak JA, Nishihara R, Qian ZRong, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJoo, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DSanghoon, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U. Genetic Mechanisms of Immune Evasion in Colorectal Cancer. Cancer Discov. 2018 ;8(6):730-749.
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Okamoto Y, Goksungur MTuba, Pehlivan D, Beck CR, Gonzaga-Jauregui C, Muzny DM, Atik MM, Carvalho CMB, Matur Z, Bayraktar S, Boone PM, Akyuz K, Gibbs RA, Battaloglu E, Parman Y, Lupski JR. Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D. Genet Med. 2014 ;16(5):386-394.
Fan X, Zhao S, Yu C, Wu D, Yan Z, Fan L, Song Y, Wang Y, Li C, Ming Y, Gui B, Niu Y, Li X, Yang X, Luo S, Zhang Q, Zhao X, Pan H, Li M, Xia W, Qiu G, Liu P, Zhang S, Zhang J, Wu Z, Lupski JR, Posey JE, Chen S, Gong C, Wu N. Exome sequencing reveals genetic architecture in patients with isolated or syndromic short stature. J Genet Genomics. 2021 ;48(5):396-402.
Charng W-L, Karaca E, Akdemir ZCoban, Gambin T, Atik MM, Gu S, Posey JE, Jhangiani SN, Muzny DM, Doddapaneni H, Hu J, Boerwinkle E, Gibbs RA, Rosenfeld JA, Cui H, Xia F, Manickam K, Yang Y, Faqeih EA, Asmari AAl, Saleh MAM, El-Hattab AW, Lupski JR. Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate. BMC Med Genomics. 2016 ;9(1):42.
Wang P, Castellani CA, Yao J, Huan T, Bielak LF, Zhao W, Haessler J, Joehanes R, Sun X, Guo X, Longchamps RJ, Manson JAE, Grove ML, Bressler J, Taylor KD, Lappalainen T, Kasela S, Van Den Berg DJ, Hou L, Reiner A, Liu Y, Boerwinkle E, Smith JA, Peyser PA, Fornage M, Rich SS, Rotter JI, Kooperberg C, Arking DE, Levy D, Liu C. Epigenome-wide association study of mitochondrial genome copy number. Hum Mol Genet. 2021 ;31(2):309-319.
Sajan SA, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Glaze DG, Kaufmann WE, Skinner SA, Annese F, Friez MJ, Lane J, Percy AK, Neul JL. Enrichment of mutations in chromatin regulators in people with Rett syndrome lacking mutations in MECP2. Genet Med. 2017 ;19(1):13-19.
Jacobs DI, Fukumura K, Bainbridge MN, Armstrong GN, Tsavachidis S, Gu X, Doddapaneni HV, Hu J, Jayaseelan JC, Muzny DM, Huse JT, Bondy ML. Elucidating the molecular pathogenesis of glioma: integrated germline and somatic profiling of a familial glioma case series. Neuro Oncol. 2018 ;20(12):1625-1633.
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Bahrambeigi V, Song X, Sperle K, Beck CR, Hijazi H, Grochowski CM, Gu S, Seeman P, Woodward KJ, Carvalho CMB, Hobson GM, Lupski JR. Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants. Genome Med. 2019 ;11(1):80.
Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat. 2020 ;41(2):487-501.
de Ligt J, Boone PM, Pfundt R, Vissers LELM, Richmond T, Geoghegan J, O'Moore K, de Leeuw N, Shaw C, Brunner HG, Lupski JR, Veltman JA, Hehir-Kwa JY. Detection of clinically relevant copy number variants with whole-exome sequencing. Hum Mutat. 2013 ;34(10):1439-48.