Copy number variation and susceptibility to human disorders (Review)

Molecular Medicine Reports

Volumn 2, Issue 2, 2009, Pages 143-147

  Shastry, Barkur S ^a  

^a OAKLAND UNIVERSITY   (United States)

Author keywords

Arrays; Deletion; Duplication; Gene; Mutation; Polymorphism

Indexed keywords

ASTHMA; AUTISM; BIPOLAR DISORDER; COPY NUMBER VARIATION; CROHN DISEASE; DIABETES MELLITUS; DIGEORGE SYNDROME; EVOLUTION; GENE DOSAGE; GENE DUPLICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; GENE MUTATION; GENE NUMBER; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOMIC INSTABILITY; HAPPY PUPPET SYNDROME; HEREDITARY MOTOR SENSORY NEUROPATHY; HERITABILITY; HUMAN; NEUROLOGIC DISEASE; NONHUMAN; PHENOTYPE; PRADER WILLI SYNDROME; PROMOTER REGION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SPINAL MUSCULAR ATROPHY; VELOCARDIOFACIAL SYNDROME;

EID: 69249100939     PISSN: 17912997     EISSN: 17913004     Source Type: Journal    
DOI: 10.3892/mmr_00000074     Document Type: Review

References (58)

1. Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L, Aburatani H, Jones K, Reddon R, Hurles M, Armengol L, Estivill X, Mural RJ, Lee C, Scherer SW and Feuk L: Genome assembly comparison identifies structural variants in the human genome. Nat Genet 38:1413-1418, 2006. (Pubitemid 44837563)
2. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Brass JM, Schymick JC, Hernandez DG, Tyarnor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA and Singleton AR: Genotype, haplotype and copy number variation in world wide human populations. Nature 451: 998-1003, 2000.
3. Hind DA, Kloek AP, Jen M, Chen X and Frazer KA: Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 38: 82-85, 2006. (Pubitemid 43011886)
4. McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ and Altshuler DM: Common deletion polymorphisms in the human genome. Nat Genet 38: 86-92, 2006. (Pubitemid 43011887)
5. Conard DF, Andrews TD, Carter NP, Hurles ME and Pritchard JK: A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 38: 75-81, 2006. (Pubitemid 43011885)
6. Cappuzzo F, Hirsch FR, Rossi E, Bartolini S, Ceresoli GL, Bemis L, Haney J, Witta S, Danenberg K, Domenichini I, Ludovini V, Magrini E, Gregorc V, Doglioni C, Sidoni A, Tanato M, Franklin WA, Crino L, Bunn PA Jr and Varelia-Garcia M: Epidermal growth factor receptor gene and protein and gefitinib sensitivity in non-small-cell lung cancer. J Natl Cancer Inst 97: 643-655, 2005. (Pubitemid 40812628)
7. Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Rovin BH, Bradley W, Clark RA, Anderson SA, O'Connell RJ, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ and Ahuja SK: The influence of CCL3L1 gene-containing segmental duplication on HIV-1/AID susceptibility. Science 307:1434-1440, 2005. (Pubitemid 40321934)
8. Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, Mangion J, Roberton-Lowe C, Marshall AJ, Petretto E, Hodges MD, Bhangal G, Patel SG, Sheehan-Rooney K, Duda M, Cook PR, Evans DJ, Domin J, Flint J, Boyle JJ, Pusey CD and Cook HT: Copy number polymorphism in Fcgr 3 predisposes to glomerulonephritis in rats and humans. Nature 439: 851-855, 2006. (Pubitemid 43255703)
9. Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee Y-H, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimaki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King M-C, Skuse D, Geschwind DH, Gilliam TC, Ye K and Wigler M: Strong association of de novo copy number mutations with autism. Science 316: 445-449, 2007. (Pubitemid 46651493)
10. Reddon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conard DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Schere SW and Hurles ME: Global variation in copy number in the human genome. Nature 444: 444-454, 2006. (Pubitemid 44809057)
11. McCarroll SA and Altshuler DM: Copy number variation and association studies of human disease. Nat Genet 39: S37-S42, 2007. (Pubitemid 47014474)
12. Freeman JL, Perry GH, Feuk L, Reddon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW and Lee C: Copy number variation: new insight in genome diversity. Genome Res 16: 949-961, 2006. (Pubitemid 44162254)
13. Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y, Thiruvahindrapduram B, Fiebig A, Schrelber S, Friedman J, Ketelaars CE, Vos YJ, Ficicioglu C, Kirkpatrick S, Nicolson R, Sloman L, Summers A, Gibbons CA, Teebi A, Chitayat D, Weksberg R, Thompson A, Vardy C, Crosbie V, Luscombe S, Baatjes R, Zwaigenbaum L, Roberts W, Fernandez B, Szatmari P and Scherer SW: Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 82: 477-488, 2008.
14. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A and Wigler M: Large scale copy number polymorphism in the human genome. Science 305: 525-528, 2004. (Pubitemid 38971344)
15. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW and Lee C: Detection of large scale variation in the human genome. Nat Genet 36: 941-951, 2004. (Pubitemid 39167488)
16. Buckland PR: Polymorphically duplicated genes: their relevance to phenotypic variation in humans. Ann Med 35: 308-315, 2003.
17. De Stahl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjold M, Upadhyaya M, Komorowski J, Bruder CE and Dumanski JP: Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 KBAC-cloned-base array. Hum Mutat 29: 398-408, 2008.
18. Perry GH, Ben-Dor A, Tsalenko A, Sampas N, Rodriguez-Revenga L, Tran CW, Scheffer A, Steinfeld I, Tsang P, Yamada NA, Park HS, Kim JI, Seo JS, Yakhini Z, Laderman S, Bruhn L and Lee C: The fine scale and complex architecture of human copy number variation. Am J Hum Genet 82: 685-695, 2008.
19. Piotrowski A, Bruder CE, Andersson R, De Stahl TD, Menzel U, Sandgren J, Poplawski A, von Tell D, Crasto C, Bogdan A, Bartoszewski R, Bebok Z, Krzyzanowski M, Jankowski Z, Partridge EC, Komorowski J and Dumanski JP: Somatic mosaicism for copy number variation in differentiated human tissues. Hum Mutat 29:1118-1124, 2008.
20. Kehrer-Sawatzki H: What a difference copy number variation makes. BioEssays 29: 311-313, 2007. (Pubitemid 46597861)
21. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D and Eichler EE: Segmental duplication and copy number variation in the human genome. Am J Hum Genet 77: 78-88, 2005. (Pubitemid 40848038)
22. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV and Eichler EE: Fine-scale structural variation of the human genome. Nat Genet 37: 727-732, 2005. (Pubitemid 41754889)
23. Lee JA, Carvalho CM and Lupski JR: A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131: 1235-1247, 2007.
24. Li J, Jiang T, Mao JH, Balmain A, Peterson L, Harris C, Rao PH, Havlak P, Gibbs R and Cai WW: Genomic segmental polymorphisms in inbred mouse strains. Nat Genet 36: 952-954, 2004. (Pubitemid 39167489)
25. Adams DJ, Dermitzakis ET, Cox T, Smith J, Davies R, Banerjee R, Bonfield J, Mullikin JC, Chung YJ, Rogers J and Bradely A: Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains. Nat Genet 37: 532-536, 2005. (Pubitemid 40617283)
26. Lupski JR: Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 14: 417-422, 1998.
27. Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Caceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE, Stone AC and Lee C: Hotspots for copy number variation in chimpanzees and humans. Proc Nat Acad Sci USA 103: 8006-8011, 2006. (Pubitemid 43801043)
28. She X, Cheng Z, Zollner S, Church DM and Eichler EE: Mouse segment duplication and copy number variation. Nat Genet 40: 909-914, 2008. (Pubitemid 351913656)
29. Nobrega MA, Zhu Y, Plajzer-Frick I, Afzal V and Rubin EM: Megabase deletions of gene deserts result in viable mice. Nature 431: 988-993, 2004. (Pubitemid 39434420)
30. Nguyen DQ, Webber C and Ponting CP: Basis of selection on human copy number variants. PLoS Genet 2: 198-207, 2006.
31. Fortna A, Kim Y, MacLaren E, Marshall K, Hahan G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, Karimpour-Fard A, Glueck D, McGavran L, Berry R, Pollack J and Sikela JM: Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol 2: E207-E222, 2004. (Pubitemid 39234408)
32. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, DeJong P, Wilson RK, Paabo S, Rocchi M and Eichler EE: A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 43: 788-793, 2005. (Pubitemid 41613429)
33. Newman TL, Tuzun E, Morrison VA, Hayden KE, Ventura M, McGrath SD, Rocchi M and Eichler EE: A genome-wide survey of structural variation between human and chimpanzee. Genome Res 15: 1344-1356, 2005. (Pubitemid 41400900)
34. Kid JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tuzun E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR and Eichler EE: Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64, 2008. (Pubitemid 351630326)
35. Emerson JJ, Cardoso-Moreira M, Borevitz JO and Long M: Natural selection shapes genome wide patterns of copy number polymorphism in Drosophila melanogaster. Science 320: 1629-1631, 2008.
36. Dopman EB and Hartl DL: A portrait of copy number polymorphism in Drosophila melanogaster. Proc Nat Acad Sci USA 104: 19920-19925, 2007.
37. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thome N, Reddon R, Bird CP, De Grassi A, Lee C, Tyler- Smith C, Scherer SW, Tavare S, Deloukas P, Hurles ME and Dermitzakis ET: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853, 2007. (Pubitemid 46255837)
38. Inoue K and Lupski JR: Molecular mechanisms for genomic disorders. Ann Rev Genomics Hum Genet 3: 199-242, 2002.
39. Lee JA and Lupski JR: Genomic rearrangements and copy number alterations as a cause of nervous system disorders. Neuron 52: 103-121, 2006.
40. Esch HV, Bauters M, Ignatius J, Jansen M, Raynaud M, Hollanders K, Lugtenberg D, Bienvenu T, Jensen LR, Gecz J, Moraine C, Marynen P, Fryns J-P and Froyen G: Duplication of the MECP2 region is a frequent cause of severe mental retardation and progressive neurological symptoms in males. Am J Hum Genet 77: 442-453, 2005. (Pubitemid 41192650)
41. Lupski JR: Genomic rearrangements and sporadic disease. Nat Genet 39: S43-S47, 2007.
42. Willcocks LC, Lyons PA, Clatworthy MR, Robinson JI, Yang W, Newland SA, Plagnol V, McGovern NN, Condliffe AM, Chilvers ER, Adu D, Jolly EC, Watts R, Lau YL, Morgan AW, Nash G and Smith KG: Copy number of FCGR3B, which is associated with systemic lupus erythematosus, correlates with protein expression and immune complex uptake. J Exp Med 205: 1575-1582, 2008. (Pubitemid 351962021)
43. Fellermann K, Stange DE, Shaeffeler E, Schmalzl H, Wehkamp J, Bevins CL, Reinisch W, Teml A, Schwab M, Lichter P, Radlwimmer B and Stange EF: A chromosome 8 gene cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am J Hum Genet 79: 439-448, 2006. (Pubitemid 44384253)
44. Lachman HM, Perdosa E, Petruolo OA, Cockerham M, Papolos A, Novak T, Papolos DF and Stopkova P: Increase in GSK3 beta gene copy number variation in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 144B: 259-265, 2007. (Pubitemid 46642013)
45. Gabriel SB, Scaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ and Altshuler D: The structure of haploid blocks in the human genome. Science 296: 2225-2229, 2002. (Pubitemid 34680308)
46. Locke DP, Sharp AJ, McCarroll SA, McGrath SD, Newman TL, Cheng Z, Schwartz S, Albertson DG, Pinkel D, Altshuler DM and Eichler EE: Linkage disequilibrium and heritability of copy number polymorphisms within duplicated regions of the human genome. Am J Hum Genet 79: 275-290, 2006. (Pubitemid 44141826)
47. Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, Zhang J, Liu G, Ihara S, Nakamura H, Hurles ME, Lee C, Scherer SW, Jones KW, Shapero MH, Huang J and Aburatani H: Genome wide deletion of human copy number variations using high-density DNA oligonucleotide arrays. Genomic Res 16: 1575-1584, 2006. (Pubitemid 44878496)
48. Estivill X and Armengol L: Copy number variants and common disorders: filling the gap and exploring complexity in genome wide association studies. PLoS Genetics 3: e190-e203, 2007. (Pubitemid 350072046)
49. Thomas DC, Haile RW and Duggan D: Recent developments in genome-wide association scan: a workshop summary and review. Am J Hum Genet 77: 337-345, 2005.
50. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR and Meyerson M: An integrated view of copy number and allelic alterations in the cancer genome using single oligonucleotide polymorphism arrays. Cancer Res 64: 3060-3071, 2004. (Pubitemid 38581405)
51. Franke L, De Kovel CG, Aulchenko YS, Trynka G, Zhernakova A, Hunt KA, Blauw HM, van den Berg LH, Ophoff R, Deloukas P, van Heel DA and Wijmenga C: Deletion, imputation and association analysis of small deletions and null alleles on oligonucleotide arrays. Am J Hum Genet 82: 1316-1333, 2008. (Pubitemid 351749608)
52. Auer H, Newsom DL, Nowak NJ, McHugh KM, Sunita S, Yu C-Y, Yang Y, Wenger GD, Gastier-Foster JM and Kornacker KL: Gene resolution analysis of DNA copy number variation using oligonucleotide expression microarrays. BMC Genomics 8: 111-117, 2007. (Pubitemid 46767844)
53. Carter NP: Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 39: S16-S21, 2007. (Pubitemid 47014471)
54. Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B, Hebert M, Jones KN, Shu Y, Kitzmiller K, Bianchong CA, McBride KL, Higgins GC, Rennebohm RM, Rice RR, Hackshaw KV, Roubey RA, Grossman JM, Tsao BP, Birmingham DJ, Rovin BH, Hebert LA and Yu CY: 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 80: 1037-1054, 2007. (Pubitemid 47579341)
55. Fanciulli M, Norsworthy PJ, Petretto E, Dong R, Harper L, Kamesh L, Heward JM, Gough SC, De Smith A, Blakemore AI, Froguel P, Owen CJ, Pearce SH, Teixeira L, Guillevin L, Graham DS, Pusey CD, Cook HT, Vyse TJ and Aitman TJ: FCGR3B copy number variation is associated with susceptibility to systemic but not organ-specific autoimmunity. Nat Genet 39: 721-723, 2007. (Pubitemid 46848593)
56. Fiegler H, Reddon R, Andrews D, Scott C, Andrews R, Carder C, Clark R, Dovey O, Ellis P, Feuk L, French L, Hunt P, Kalaitzopoulos D, Larkin J, Montgomery L, Perry GH, Plumb BW, Porter K, Rigby RE, Rigler D, Valsesia A, Langford C, Humphray SJ, Scherer SW, Lee C, Hurles ME and Carter NP: Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res 16: 1566-1574, 2006. (Pubitemid 44878495)
57. Dhami P, Coffey AJ, Abbs S, Vermeesch JR, Dumanski JP, Woodward KJ, Andrews RM, Langford C and Vetrie D: Exon array CGH: detection of copy number changes at the resolution of individual exons in the human genome. Am J Hum Genet 76: 750-762, 2005. (Pubitemid 40563097)
58. Babcock M, Yatsenko S, Hopkins J, Brenton M, Cao Q, De Jong P, Stankiewicz P, Lupski JR, Sikela JM and Morrow BE: Hominoid lineage specific amplification of low copy repeats on 22q11.2 (LCR22s) associated with velo-cardo-facial/digeorge syndrome. Hum Mol Genet 16: 2560-2571, 2007. (Pubitemid 47617723)