Benign, pathogenic and copy number variations of unknown clinical significance in patients with congenital malformations and developmental delay

1Pennisi E. Breakthrough of the year. Human genetic variation. Science. 2007; 318(5858): 1842-1843.PennisiE. Breakthrough of the year. Human genetic variation Science. 2007 318 5858 1842 1843Search in Google Scholar

2Aldred PM, Hollox EJ, Armour JA. Copy number polymorphism and expression level variation of the human α-defensin genes DEFA1 and DEFA3. Hum Mol Genet. 2005; 14(14): 2045-2052.AldredPMHolloxEJArmourJA. Copy number polymorphism and expression level variation of the human α-defensin genes DEFA1 and DEFA3 Hum Mol Genet. 2005 14 14 2045 2052Search in Google Scholar

3Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science. 2005; 307(5714): 1434-1440.GonzalezEKulkarniHBolivarHManganoASanchezRCatanoG The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility Science. 2005 307 5714 14341440Search in Google Scholar

4Hollox EJ, Armour JA, Barber JC. Extensive normal copy number variation of a β-defensin antimicrobialgene cluster. Am J Hum Genet. 2003; 73(3): 591-600.HolloxEJArmourJABarberJC. Extensive normal copy number variation of a β-defensin antimicrobialgene cluster Am J Hum Genet. 2003 73 3 591 600Search in Google Scholar

5Linzmeier RM, Ganz T. Human defensin gene copy number polymorphisms: Comprehensive analysis of independent variation in α- and β-defensin regions at 8p22-p23. Genomics. 2005; 86(4): 423-430.LinzmeierRMGanzT. Human defensin gene copy number polymorphisms: Comprehensive analysis of independent variation in α- and β-defensin regions at 8p22-p23 Genomics. 2005 86 4 423 430Search in Google Scholar

6McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, et al. Common deletion polymorphisms in the human genome. Nat Genet. 2006; 38(1): 86-92.McCarrollSAHadnottTNPerryGHSabetiPCZodyMCBarrettJC Common deletion polymorphisms in the human genome Nat Genet. 2006 38 1 86 92Search in Google Scholar

7Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, et al. Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007; 39(10): 1256-1260.PerryGHDominyNJClawKGLeeASFieglerHRedonR Diet and the evolution of human amylase gene copy number variation Nat Genet. 2007 39 10 1256 1260Search in Google Scholar

8Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007; 315(5813): 848-853.StrangerBEForrestMSDunningMIngleCEBeazleyCThorneN Relative impact of nucleotide and copy number variation on gene expression phenotypes Science. 2007 315 5813 848 853Search in Google Scholar

9 Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature. 2006; 439(7078): 851-855.AitmanTJDongRVyseTJNorsworthyPJJohnsonMDSmithJ Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans Nature. 2006 439 7078 851 855Search in Google Scholar

10Fanciulli M, Norsworthy PJ, Petretto E, Dong R, Harper L, Kamesh L, et al. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet. 2007; 39(6): 721-723.FanciulliMNorsworthyPJPetrettoEDongRHarperLKameshL FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity Nat Genet. 2007 39 6 721 723Search in Google Scholar

11Fellermann K, Stange DE, Schaeffeler E, Schmalzl H, Wehkamp J, Bevins CL, et al. A chromosome 8 gene-cluster polymorphism with low human β-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am J Hum Genet. 2006; 79(3): 439-448.FellermannKStangeDESchaeffelerESchmalzlHWehkampJBevinsCL A chromosome 8 gene-cluster polymorphism with low human β-defensin 2 gene copy number predisposes to Crohn disease of the colon Am J Hum Genet. 2006 79 3 439 448Search in Google Scholar

12Gamazon ER, Nicolae DL, Cox NJ. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. PLoS Genet. 2011; 7(2): e1001292.GamazonERNicolaeDLCoxNJ. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci PLoS Genet. 2011 7 2 e1001292Search in Google Scholar

13Hollox EJ, Huffmeier U, Zeeuwen PL, Palla R, Lascorz J, Rodijk-Olthuis D, et al. Psoriasis is associated with increased β-defensin genomic copy number. Nat Genet. 2008; 40(1): 23-25.HolloxEJHuffmeierUZeeuwenPLPallaRLascorzJ Rodijk-OlthuisD Psoriasis is associated with increased β-defensin genomic copy number Nat Genet. 2008 40 1 23 25Search in Google Scholar

14Park J, Chen L, Ratnashinge L, Sellers TA, Tanner JP, Lee JH, et al. Deletion polymorphism of UDP-glucuronosyltransferase 2B17 and risk of prostate cancer in African American and Caucasian men. Cancer Epidemiol Biomarkers Prev. 2006; 15(8): 1473-1478.ParkJChenLRatnashingeLSellersTATannerJPLeeJH Deletion polymorphism of UDP-glucuronosyltransferase 2B17 and risk of prostate cancer in African American and Caucasian men Cancer Epidemiol Biomarkers Prev. 2006 15 8 1473 1478Search in Google Scholar

15Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B, et al. Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): Low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet. 2007; 80(6): 1037-1054.YangYChungEKWuYLSavelliSLNagarajaHNZhouB Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): Low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans Am J Hum Genet. 2007 80 6 1037 1054Search in Google Scholar

16Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011; 21(6): 974-984.AbyzovAUibanAESnyderMGersteinM. CNVnator: An approach to discover genotype, and characterize typical and atypical CNVs from family and population genome sequencing Genome Res. 2011 21 6 974 984Search in Google Scholar

17Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, Malig M, et al. Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet. 2011; 88(3): 317-332.CampbellCDSampasNTsalenkoASudmantPHKiddJMMaligM Population-genetic properties of differentiated human copy-number polymorphisms Am J Hum Genet. 2011 88 3 317 332Search in Google Scholar

18Fu Y, Chen Z, Blakemore AI, Orwoll E, Cohen DM. Absence of AVPR2 copy number variation in eunatremic and dysnatremic subjects in non-Hispanic Caucasian populations. Physiol Genomics. 2010; 40(3): 121-127.FuYChenZBlakemoreAIOrwollECohenDM. Absence of AVPR2 copy number variation in eunatremic and dysnatremic subjects in non-Hispanic Caucasian populations Physiol Genomics. 2010 40 3 121 127Search in Google Scholar

19Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, et al. Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet. 2009; 84(2): 148-161.ItsaraACooperGMBakerCGirirajanSLiJAbsherD Population analysis of large copy number variants and hotspots of human genetic disease Am J Hum Genet. 2009 84 2 148 161Search in Google Scholar

20Pinto D, Marshall C, Feuk L, Scherer SW. Copy-number variation in control population cohorts. Hum Mol Genet. 2007; 16(Spec No. 2): R168-R173.PintoDMarshallCFeukLSchererSW. Copy-number variation in control population cohorts Hum Mol Genet. 2007 16 2 R168R173Search in Google Scholar

21Zhang LN, Meng Z, He ZW, Li DF, Luo XY, Liang LY. [Clinical phenotypes and copy number variations in children with microdeletion and microduplication syndromes: An analysis of 50 cases]. Zhongguo Dang Dai Er Ke Za Zhi. 2016; 18(9): 840-845.ZhangLNMengZHeZWLiDFLuoXYLiangLY. [Clinical phenotypes and copy number variations in children with microdeletion and microduplication syndromes: An analysis of 50 cases] Zhongguo Dang Dai Er Ke Za Zhi. 2016 18 9 840 845Search in Google Scholar

22Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006; 7(2): 85-97.FeukLCarsonARSchererSW. Structural variation in the human genome Nat Rev Genet. 2006 7 2 85 97Search in Google Scholar

23Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet. 2007; 39(7 Suppl): S48-S54.LeeCIafrateAJBrothmanAR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders Nat Genet. 2007 39 7 S48S54Search in Google Scholar

24Freeman JL, Perry GH, Feuk L, Redon R, McCar-roll SA, Altshuler DM, et al. Copy number variation: New insights in genome diversity. Genome Res. 2006; 16(8): 949-961.FreemanJLPerryGHFeukLRedonR McCar-rollSAAltshulerDM Copy number variation: New insights in genome diversity Genome Res. 2006 16 8 949 961Search in Google Scholar

25Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, et al. Challenges and standards in integrating surveys of structural variation. Nat Genet. 2007; 39(7 Suppl): S7-S15.SchererSWLeeCBirneyEAltshulerDMEichlerEECarterNP Challenges and standards in integrating surveys of structural variation Nat Genet. 2007 39 7 S7S15Search in Google Scholar

26Alaerts M, Del-Favero J. Searching genetic risk factors for schizophrenia and bipolar disorder: Learn from the past and back to the future. Hum Mutat. 2009; 30(8): 1139-1152.AlaertsM Del-FaveroJ. Searching genetic risk factors for schizophrenia and bipolar disorder: Learn from the past and back to the future Hum Mutat. 2009 30 8 1139 1152Search in Google Scholar

27Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, et al. Detection of large-scale variation in the human genome. Nat Genet. 2004; 36(9): 949-951.IafrateAJFeukLRiveraMNListewnikMLDonahoePKQiY Detection of large-scale variation in the human genome Nat Genet. 2004 36 9 949 951Search in Google Scholar

28Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, et al. Large-scale copy number polymorphism in the human genome. Science. 2004; 305(5683): 525-528.SebatJLakshmiBTrogeJAlexanderJYoungJLundinP Large-scale copy number polymorphism in the human genome Science. 2004 305 5683 525 528Search in Google Scholar

29Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, et al. Global variation in copy number in the human genome. Nature. 2006; 444(7118): 444-454.RedonRIshikawaSFitchKRFeukLPerryGHAndrewsTD Global variation in copy number in the human genome Nature. 2006 444 7118 444454Search in Google Scholar

30Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, et al. The diploid genome sequence of an individual human. PLoS Biol. 2007; 5(10): e254.LevySSuttonGNgPCFeukLHalpernALWalenzBP The diploid genome sequence of an individual human PLoS Biol. 2007 5 10 e254Search in Google Scholar

31Venter JC. Multiple personal genomes await. Nature. 2010; 464(7289): 676-677.VenterJC. Multiple personal genomes await Nature. 2010 464 7289 676 677Search in Google Scholar

32Caramaschi E, Stanghellini I, Magini P, Giuffrida MG, Scullin S, Giuva T, et al. Predictive diagnostic value for the clinical features accompanying intellectual disability in children with pathogenic copy number variations: A multivariate analysis. Ital J Pediatr. 2014; 40: 39. 10.1186/1824-7288-40-39.CaramaschiEStanghelliniIMaginiPGiuffridaMGScullinSGiuvaT Predictive diagnostic value for the clinical features accompanying intellectual disability in children with pathogenic copy number variations: A multivariate analysis Ital J Pediatr. 2014 40 39 10.1186/1824-7288-40-39Open DOISearch in Google Scholar

33Choufani S, Cytrynbaum C, Chung BH, Turinsky AL, Grafodatskaya D, Chen YA, et al. NSD1 mutations generate a genome-wide DNA methylation signature. Nat Commun. 2015; 6: 10207. 10.1038/ncomms10207.ChoufaniSCytrynbaumCChungBHTurinskyALGrafodatskayaDChenYA NSD1 mutations generate a genome-wide DNA methylation signature Nat Commun. 2015 6 10207 10.1038/ncomms10207Open DOISearch in Google Scholar

34Courtens W, Wuyts W, Rooms L, Pera SB, Wauters J. A subterminal deletion of the long arm of chromosome 10: A clinical report and review. Am J Med Genet A. 2006; 140(4): 402-409.CourtensWWuytsWRoomsLPeraSBWautersJ. A subterminal deletion of the long arm of chromosome 10: A clinical report and review Am J Med Genet A. 2006 140 4 402 409Search in Google Scholar

35Kalsner L, Chamberlain SJ. Prader-Willi, Angelman, and 15q11-q13 duplication syndromes. Pediatr Clin North Am. 2015; 62(3): 587-606.KalsnerLChamberlainSJ. Prader-Willi, Angelman, and 15q11-q13 duplication syndromes Pediatr Clin North Am. 2015 62 3 587 606Search in Google Scholar

36Tan ES, Yong MH, Lim EC, Li ZH, Brett MS, Tan EC. Chromosome 15q11-q13 copy number gain detected by array-CGH in two cases with a maternal methylation pattern. Mol Cytogenet. 2014; 7: 32. 10.1186/17558166-7-32.TanESYongMHLimECLiZHBrettMSTanEC. Chromosome 15q11-q13 copy number gain detected by array-CGH in two cases with a maternal methylation pattern Mol Cytogenet. 2014 7 32 10.1186/17558166-7-32Open DOISearch in Google Scholar

37Kooy RF. Distinct disorders affecting the brain share common genetic origins. F1000 Biol Rep. 2010; 2: 11. 10.3410/B2-11. (http://f1000.com/reports/b/2/11.)KooyRF. Distinct disorders affecting the brain share common genetic origins F1000 Biol Rep. 2010 2 11 10.3410/B2-11 (http://f1000.com/reports/b/2/11.)Open DOISearch in Google Scholar

38Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, et al. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature. 2010; 464(7289): 713-720.CraddockNHurlesMECardinNPearsonRDPlagnolVRobsonS Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls Nature. 2010 464 7289 713 720Search in Google Scholar

39Diskin SJ, Hou C, Glessner JT, Attiyeh EF, Laudenslager M, Bosse K, et al. Copy number variation at 1q21.1 associated with neuroblastoma. Nature. 2009; 459(7249): 987-991.DiskinSJHouCGlessnerJTAttiyehEFLaudenslagerMBosseK Copy number variation at 1q21.1 associated with neuroblastoma Nature. 2009 459 7249 987 991Search in Google Scholar