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Yuan B, Neira J, Gu S, Harel T, Liu P, Briceño I, Elsea SH, Gómez A, Potocki L, Lupski JR. Nonrecurrent PMP22-RAI1 contiguous gene deletions arise from replication-based mechanisms and result in Smith-Magenis syndrome with evident peripheral neuropathy. Hum Genet. 2016 ;135(10):1161-74.
Duan R, Saadi NWaill, Grochowski CM, Bhadila G, Faridoun A, Mitani T, Du H, Fatih JM, Jhangiani SN, Akdemir ZC, Gibbs RA, Pehlivan D, Posey JE, Marafi D, Lupski JR. A novel homozygous SLC13A5 whole-gene deletion generated by Alu/Alu-mediated rearrangement in an Iraqi family with epileptic encephalopathy. Am J Med Genet A. 2021 ;185(7):1972-1980.
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Liu P, Yuan B, Carvalho CMB, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Akdemir ZCoban, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SWai, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell. 2017 ;168(5):830-842.e7.
Thomas GWC, Wang RJ, Nguyen J, Harris RA, Raveendran M, Rogers J, Hahn MW. Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques. Mol Biol Evol. 2021 ;38(4):1460-1471.
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Zhang Y, Yang L, Kucherlapati M, Chen F, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Li W, Park PJ, Kucherlapati R, Creighton CJ. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Rep. 2018 ;24(2):515-527.
Campbell IM, Stewart JR, James RA, Lupski JR, Stankiewicz P, Olofsson P, Shaw CA. Parent of origin, mosaicism, and recurrence risk: probabilistic modeling explains the broken symmetry of transmission genetics. Am J Hum Genet. 2014 ;95(4):345-59.
Liu Q, Karolak JA, Grochowski CM, Wilson TA, Rosenfeld JA, Bacino CA, Lalani SR, Patel A, Breman A, Smith JL, Cheung SWai, Lupski JR, Bi W, Stankiewicz P. Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings. Genomics. 2020 ;112(5):2937-2941.
Campbell IM, Yuan B, Robberecht C, Pfundt R, Szafranski P, McEntagart ME, Nagamani SCS, Erez A, Bartnik M, Wiśniowiecka-Kowalnik B, Plunkett KS, Pursley AN, Kang S-HL, Bi W, Lalani SR, Bacino CA, Vast M, Marks K, Patton M, Olofsson P, Patel A, Veltman JA, Cheung SWai, Shaw CA, Vissers LELM, Vermeesch JR, Lupski JR, Stankiewicz P. Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders. Am J Hum Genet. 2014 ;95(2):173-82.
Liu P, Kaplan A, Yuan B, Hanna JH, Lupski JR, Reiner O. Passage number is a major contributor to genomic structural variations in mouse iPSCs. Stem Cells. 2014 ;32(10):2657-67.
Szafranski P, Coban-Akdemir ZH, Rupps R, Grazioli S, Wensley D, Jhangiani SN, Popek E, Lee AF, Lupski JR, Boerkoel CF, Stankiewicz P. Phenotypic expansion of TBX4 mutations to include acinar dysplasia of the lungs. Am J Med Genet A. 2016 ;170(9):2440-4.
Song X, Beck CR, Du R, Campbell IM, Coban-Akdemir Z, Gu S, Breman AM, Stankiewicz P, Ira G, Shaw CA, Lupski JR. Predicting human genes susceptible to genomic instability associated with /-mediated rearrangements. Genome Res. 2018 ;28(8):1228-1242.
Stray-Pedersen A, Sorte HSørmo, Samarakoon P, Gambin T, Chinn IK, Akdemir ZHCoban, Erichsen HChristian, Forbes LR, Gu S, Yuan B, Jhangiani SN, Muzny DM, Rødningen OKristin, Sheng Y, Nicholas SK, Noroski LM, Seeborg FO, Davis CM, Canter DL, Mace EM, Vece TJ, Allen CE, Abhyankar HA, Boone PM, Beck CR, Wiszniewski W, Fevang B, Aukrust P, Tjønnfjord GE, Gedde-Dahl T, Hjorth-Hansen H, Dybedal I, Nordøy I, Jørgensen SF, Abrahamsen TG, Øverland T, Bechensteen AGrete, Skogen V, Osnes LTN, Kulseth MAnn, Prescott TE, Rustad CF, Heimdal KR, Belmont JW, Rider NL, Chinen J, Cao TN, Smith EA, Caldirola MSoledad, Bezrodnik L, Reyes SOswaldo Lu, Rosales FJEspinosa, Guerrero-Cursaru NDenisse, Pedroza LAlberto, Poli CM, Franco JL, Vargas CMTrujillo, Becerra JCarlos Ald, Wright N, Issekutz TB, Issekutz AC, Abbott J, Caldwell JW, Bayer DK, Chan AY, Aiuti A, Cancrini C, Holmberg E, West C, Burstedt M, Karaca E, Yesil G, Artac H, Bayram Y, Atik MMusa, Eldomery MK, Ehlayel MS, Jolles S, Flatø B, Bertuch AA, I Hanson C, Zhang VW, Wong L-J, Hu J, Walkiewicz M, Yang Y, Eng CM, Boerwinkle E, Gibbs RA, Shearer WT, Lyle R, Orange JS, Lupski JR. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol. 2017 ;139(1):232-245.
Wang J, Chen L, Zhou C, Wang L, Xie H, Xiao Y, Zhu H, Hu T, Zhang Z, Zhu Q, Liu Z, Liu S, Wang H, Xu M, Ren Z, Yu F, Cram DS, Liu H. Prospective chromosome analysis of 3429 amniocentesis samples in China using copy number variation sequencing. Am J Obstet Gynecol. 2018 ;219(3):287.e1-287.e18.
Zhang Y, Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. Nat Commun. 2022 ;13(1):2669.
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Liu Q, Grochowski CM, Bi W, Lupski JR, Stankiewicz P. Quantitative Assessment of Parental Somatic Mosaicism for Copy-Number Variant (CNV) Deletions. Curr Protoc Hum Genet. 2020 ;106(1):e99.
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Brownstein CA, Smith RS, Rodan LH, Gorman MP, Hojlo MA, Garvey EA, Li J, Cabral K, Bowen JJ, Rao AS, Genetti CA, Carroll D, Deaso EA, Agrawal PB, Rosenfeld JA, Bi W, Howe J, Stavropoulos DJ, Hansen AW, Hamoda HM, Pinard F, Caracansi A, Walsh CA, D'Angelo EJ, Beggs AH, Zarrei M, Gibbs RA, Scherer SW, Glahn DC, Gonzalez-Heydrich J. RCL1 copy number variants are associated with a range of neuropsychiatric phenotypes. Mol Psychiatry. 2021 ;26(5):1706-1718.
Lindstrand A, Davis EE, Carvalho CMB, Pehlivan D, Willer JR, Tsai I-C, Ramanathan S, Zuppan C, Sabo A, Muzny DM, Gibbs RA, Liu P, Lewis RA, Banin E, Lupski JR, Clark R, Katsanis N. Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic alleles to Bardet-Biedl syndrome. Am J Hum Genet. 2014 ;94(5):745-54.
Harel T, Yoon WHee, Garone C, Gu S, Coban-Akdemir Z, Eldomery MK, Posey JE, Jhangiani SN, Rosenfeld JA, Cho MT, Fox S, Withers M, Brooks SM, Chiang T, Duraine L, Erdin S, Yuan B, Shao Y, Moussallem E, Lamperti C, Donati MA, Smith JD, McLaughlin HM, Eng CM, Walkiewicz M, Xia F, Pippucci T, Magini P, Seri M, Zeviani M, Hirano M, Hunter JV, Srour M, Zanigni S, Lewis RAlan, Muzny DM, Lotze TE, Boerwinkle E, Gibbs RA, Hickey SE, Graham BH, Yang Y, Buhas D, Martin DM, Potocki L, Graziano C, Bellen HJ, Lupski JR. Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. Am J Hum Genet. 2016 ;99(4):831-845.
Gunning AC, Strucinska K, Oreja MMuñoz, Parrish A, Caswell R, Stals KL, Durigon R, Durlacher-Betzer K, Cunningham MH, Grochowski CM, Baptista J, Tysoe C, Baple E, Lahiri N, Homfray T, Scurr I, Armstrong C, Dean J, Pelayo UFernandez, Jones AWE, Taylor RW, Misra VK, Yoon WHee, Wright CF, Lupski JR, Spinazzola A, Harel T, Holt IJ, Ellard S. Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism. Am J Hum Genet. 2020 ;106(2):272-279.
Dai H, Zhu W, Yuan B, Walley N, Schoch K, Jiang Y-H, Phillips JA, Jones MS, Liu P, Murdock DR, Burrage LC, Lee B, Rosenfeld JA, Xiao R. A recurrent single-exon deletion in TBCK might be under-recognized in patients with infantile hypotonia and psychomotor delay. Hum Mutat. 2022 ;43(12):1816-1823.
Liu M, Zhong Y, Liu H, Liang D, Liu E, Zhang Y, Tian F, Liang Q, Cram DS, Wang H, Wu L, Yu F. REDBot: Natural language process methods for clinical copy number variation reporting in prenatal and products of conception diagnosis. Mol Genet Genomic Med. 2020 ;8(11):e1488.
Carvalho CMB, Pehlivan D, Ramocki MB, Fang P, Alleva B, Franco LM, Belmont JW, Hastings PJ, Lupski JR. Replicative mechanisms for CNV formation are error prone. Nat Genet. 2013 ;45(11):1319-26.
Ma X, Edmonson M, Yergeau D, Muzny DM, Hampton OA, Rusch M, Song G, Easton J, Harvey RC, Wheeler DA, Ma J, Doddapaneni H, Vadodaria B, Wu G, Nagahawatte P, Carroll WL, Chen I-M, Gastier-Foster JM, Relling MV, Smith MA, Devidas M, Auvil JMGuidry, Downing JR, Loh ML, Willman CL, Gerhard DS, Mullighan CG, Hunger SP, Zhang J. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia. Nat Commun. 2015 ;6:6604.
Pehlivan D, Beck CR, Okamoto Y, Harel T, Akdemir ZHC, Jhangiani SN, Withers MA, Goksungur MTuba, Carvalho CMB, Czesnik D, Gonzaga-Jauregui C, Wiszniewski W, Muzny DM, Gibbs RA, Rautenstrauss B, Sereda MW, Lupski JR. The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy. Genet Med. 2016 ;18(5):443-51.
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Chen Y, Zhao L, Wang Y, Cao M, Gelowani V, Xu M, Agrawal SA, Li Y, Daiger SP, Gibbs RA, Wang F, Chen R. SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. BMC Bioinformatics. 2017 ;18(1):147.