The Fine-Scale and Complex Architecture of Human Copy-Number Variation

American Journal of Human Genetics

Volumn 82, Issue 3, 2008, Pages 685-695

  Perry, George H ^a,b   Ben Dor, Amir ^c   Tsalenko, Anya ^c   Sampas, Nick ^c   Rodriguez Revenga, Laia ^a   Tran, Charles W ^a   Scheffer, Alicia ^c   Steinfeld, Israel ^c   Tsang, Peter ^c   Yamada, N Alice ^c   Park, Han Soo ^d   Kim, Jong Il ^d   Seo, Jeong Sun ^d   Yakhini, Zohar ^c   Laderman, Stephen ^c   Bruhn, Laurakay ^c   Lee, Charles ^a,e  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c AGILENT TECHNOLOGIES   (United States)

^d Seoul National University   (South Korea)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; FEMALE; GENE DUPLICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOMIC INSTABILITY; HUMAN; HUMAN EXPERIMENT; HUMAN GENOME; MALE; MICROARRAY ANALYSIS; PRIORITY JOURNAL; DNA MICROARRAY; GENE DOSAGE; GENETICS; GENOME; METHODOLOGY; TANDEM REPEAT;

GENE DOSAGE; GENOME, HUMAN; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TANDEM REPEAT SEQUENCES; VARIATION (GENETICS);

EID: 41149140876     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2007.12.010     Document Type: Article

References (63)

1. Ottolenghi S., Lanyon W.G., Paul J., Williamson R., Weatherall D.J., Clegg J.B., Pritchard J., Pootrakul S., and Boon W.H. The severe form of alpha thalassaemia is caused by a haemoglobin gene deletion. Nature 251 (1974) 389-392
2. Taylor J.M., Dozy A., Kan Y.W., Varmus H.E., Lie-Injo L.E., Ganesan J., and Todd D. Genetic lesion in homozygous alpha thalassaemia (hydrops fetalis). Nature 251 (1974) 392-393
3. Ottolenghi S., Comi P., Giglioni B., Tolstoshev P., Lanyon W.G., Mitchell G.J., Williamson R., Russo G., Musumeci S., Schillro G., et al. Delta-beta-thalassemia is due to a gene deletion. Cell 9 (1976) 71-80
4. Nathans J., Thomas D., and Hogness D.S. Molecular genetics of human color vision: The genes encoding blue, green, and red pigments. Science 232 (1986) 193-202
5. Awdeh Z.L., and Alper C.A. Inherited structural polymorphism of the fourth component of human complement. Proc. Natl. Acad. Sci. USA 77 (1980) 3576-3580
6. Groot P.C., Bleeker M.J., Pronk J.C., Arwert F., Mager W.H., Planta R.J., Eriksson A.W., and Frants R.R. The human alpha-amylase multigene family consists of haplotypes with variable numbers of genes. Genomics 5 (1989) 29-42
7. Colin Y., Cherif-Zahar B., Le Van Kim C., Raynal V., Van Huffel V., and Cartron J.P. Genetic basis of the RhD-positive and RhD-negative blood group polymorphism as determined by Southern analysis. Blood 78 (1991) 2747-2752
8. Trask B.J., Friedman C., Martin-Gallardo A., Rowen L., Akinbami C., Blankenship J., Collins C., Giorgi D., Iadonato S., Johnson F., et al. Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes. Hum. Mol. Genet. 7 (1998) 13-26
9. Buckland P.R. Polymorphically duplicated genes: Their relevance to phenotypic variation in humans. Ann. Med. 35 (2003) 308-315
10. Iafrate A.J., Feuk L., Rivera M.N., Listewnik M.L., Donahoe P.K., Qi Y., Scherer S.W., and Lee C. Detection of large-scale variation in the human genome. Nat. Genet. 36 (2004) 949-951
11. Sebat J., Lakshmi B., Troge J., Alexander J., Young J., Lundin P., Maner S., Massa H., Walker M., Chi M., et al. Large-scale copy number polymorphism in the human genome. Science 305 (2004) 525-528
12. Sharp A.J., Locke D.P., McGrath S.D., Cheng Z., Bailey J.A., Vallente R.U., Pertz L.M., Clark R.A., Schwartz S., Segraves R., et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77 (2005) 78-88
13. Tuzun E., Sharp A.J., Bailey J.A., Kaul R., Morrison V.A., Pertz L.M., Haugen E., Hayden H., Albertson D., Pinkel D., et al. Fine-scale structural variation of the human genome. Nat. Genet. 37 (2005) 727-732
14. Conrad D.F., Andrews T.D., Carter N.P., Hurles M.E., and Pritchard J.K. High-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38 (2006) 75-81
15. McCarroll S.A., Hadnott T.N., Perry G.H., Sabeti P.C., Zody M.C., Barrett J.C., Dallaire S., Gabriel S.B., Lee C., Daly M.J., et al. Common deletion polymorphisms in the human genome. Nat. Genet. 38 (2006) 86-92
16. Redon R., Ishikawa S., Fitch K.R., Feuk L., Perry G.H., Andrews T.D., Fiegler H., Shapero M.H., Carson A.R., Chen W., et al. Global variation in copy number in the human genome. Nature 444 (2006) 444-454
17. de Smith A.J., Tsalenko A., Sampas N., Scheffer A., Yamada N.A., Tsang P., Ben-Dor A., Yakhini Z., Ellis R.J., Bruhn L., et al. Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: Implications for association studies of complex diseases. Hum. Mol. Genet. 16 (2007) 2783-2794
18. Korbel J.O., Urban A.E., Affourtit J.P., Godwin B., Grubert F., Simons J.F., Kim P.M., Palejev D., Carriero N.J., Du L., et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318 (2007) 420-426
19. Wong K.K., deLeeuw R.J., Dosanjh N.S., Kimm L.R., Cheng Z., Horsman D.E., MacAulay C., Ng R.T., Brown C.J., Eichler E.E., et al. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet. 80 (2007) 91-104
20. Hollox E.J., Armour J.A., and Barber J.C. Extensive normal copy number variation of a beta-defensin antimicrobial-gene cluster. Am. J. Hum. Genet. 73 (2003) 591-600
21. Aldred P.M., Hollox E.J., and Armour J.A. Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3. Hum. Mol. Genet. 14 (2005) 2045-2052
22. Gonzalez E., Kulkarni H., Bolivar H., Mangano A., Sanchez R., Catano G., Nibbs R.J., Freedman B.I., Quinones M.P., Bamshad M.J., et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307 (2005) 1434-1440
23. Linzmeier R.M., and Ganz T. Human defensin gene copy number polymorphisms: comprehensive analysis of independent variation in alpha- and beta-defensin regions at 8p22-p23. Genomics 86 (2005) 423-430
24. Perry G.H., Dominy N.J., Claw K.G., Lee A.S., Fiegler H., Redon R., Werner J., Villanea F.A., Mountain J.L., Misra R., et al. Diet and the evolution of human amylase gene copy number variation. Nat. Genet. 39 (2007) 1256-1260
25. Stranger B.E., Forrest M.S., Dunning M., Ingle C.E., Beazley C., Thorne N., Redon R., Bird C.P., de Grassi A., Lee C., et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315 (2007) 848-853
26. Aitman T.J., Dong R., Vyse T.J., Norsworthy P.J., Johnson M.D., Smith J., Mangion J., Roberton-Lowe C., Marshall A.J., Petretto E., et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439 (2006) 851-855
27. Fellermann K., Stange D.E., Schaeffeler E., Schmalzl H., Wehkamp J., Bevins C.L., Reinisch W., Teml A., Schwab M., Lichter P., et al. 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 (2006) 439-448
28. Park J., Chen L., Ratnashinge L., Sellers T.A., Tanner J.P., Lee J.H., Dossett N., Lang N., Kadlubar F.F., Ambrosone C.B., et al. Deletion polymorphism of UDP-glucuronosyltransferase 2B17 and risk of prostate cancer in African American and Caucasian men. Cancer Epidemiol. Biomarkers Prev. 15 (2006) 1473-1478
29. Fanciulli M., Norsworthy P.J., Petretto E., Dong R., Harper L., Kamesh L., Heward J.M., Gough S.C., de Smith A., Blakemore A.I., et al. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat. Genet. 39 (2007) 721-723
30. Yang Y., Chung E.K., Wu Y.L., Savelli S.L., Nagaraja H.N., Zhou B., Hebert M., Jones K.N., Shu Y., Kitzmiller K., 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. 80 (2007) 1037-1054
31. Hollox, E.J., Huffmeier, U., Zeeuwen, P.L.J.M., Palla, R., Lascorz, J., Rodijk-Olthuis, D., van de Kerkhof, P.C.M., Traupe, H., de Jongh, G., den Heijer, M., et al. Psoriasis is associated with increased beta-defensin genomic copy number. Nat. Genet. 40, 23-25.
32. HapMap. A haplotype map of the human genome. Nature 437 (2005) 1299-1320
33. Barrett M.T., Scheffer A., Ben-Dor A., Sampas N., Lipson D., Kincaid R., Tsang P., Curry B., Baird K., Meltzer P.S., et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl. Acad. Sci. USA 101 (2004) 17765-17770
34. Bailey J.A., Gu Z., Clark R.A., Reinert K., Samonte R.V., Schwartz S., Adams M.D., Myers E.W., Li P.W., and Eichler E.E. Recent segmental duplications in the human genome. Science 297 (2002) 1003-1007
35. Cooper G.M., Nickerson D.A., and Eichler E.E. Mutational and selective effects on copy-number variants in the human genome. Nat. Genet. 39 (2007) S22-S29
36. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
37. Lipson, D., Tsalenko, A., Yakhini, Z., and Ben-Dor, A. (2005). Interval scores for quality annotated CGH data. In Workshop on Genomic Signal Processing and Statistics (GENSIPS) (Newport, Rhode Island).
38. Lipson D., Aumann Y., Ben-Dor A., Linial N., and Yakhini Z. Efficient calculation of interval scores for DNA copy number data analysis. J. Comput. Biol. 13 (2006) 215-228
39. Pinto D., Marshall C., Feuk L., and Scherer S.W. Copy-number variation in control population cohorts. Hum. Mol. Genet. 16 (2007) R168-R173
40. Conrad D.F., and Hurles M.E. The population genetics of structural variation. Nat. Genet. 39 (2007) S30-S36
41. Khaja R., Zhang J., MacDonald J.R., He Y., Joseph-George A.M., Wei J., Rafiq M.A., Qian C., Shago M., Pantano L., et al. Genome assembly comparison identifies structural variants in the human genome. Nat. Genet. 38 (2006) 1413-1418
42. Newman T.L., Rieder M.J., Morrison V.A., Sharp A.J., Smith J.D., Sprague L.J., Kaul R., Carlson C.S., Olson M.V., Nickerson D.A., et al. High-throughput genotyping of intermediate-size structural variation. Hum. Mol. Genet. 15 (2006) 1159-1167
43. Urban A.E., Korbel J.O., Selzer R., Richmond T., Hacker A., Popescu G.V., Cubells J.F., Green R., Emanuel B.S., Gerstein M.B., et al. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 103 (2006) 4534-4539
44. Korbel J.O., Urban A.E., Grubert F., Du J., Royce T.E., Starr P., Zhong G., Emanuel B.S., Weissman S.M., Snyder M., et al. Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc. Natl. Acad. Sci. USA 104 (2007) 10110-10115
45. Pfeiffer P., Goedecke W., and Obe G. Mechanisms of DNA double-strand break repair and their potential to induce chromosomal aberrations. Mutagenesis 15 (2000) 289-302
46. Rothkamm K., Kruger I., Thompson L.H., and Lobrich M. Pathways of DNA double-strand break repair during the mammalian cell cycle. Mol. Cell. Biol. 23 (2003) 5706-5715
47. Linardopoulou E.V., Williams E.M., Fan Y., Friedman C., Young J.M., and Trask B.J. Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437 (2005) 94-100
48. Eden E., Lipson D., Yogev S., and Yakhini Z. Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol 3 (2007) e39
49. Bacolla A., and Wells R.D. Non-B DNA conformations, genomic rearrangements, and human disease. J. Biol. Chem. 279 (2004) 47411-47414
50. Bacolla A., Jaworski A., Larson J.E., Jakupciak J.P., Chuzhanova N., Abeysinghe S.S., O'Connell C.D., Cooper D.N., and Wells R.D. Breakpoints of gross deletions coincide with non-B DNA conformations. Proc. Natl. Acad. Sci. USA 101 (2004) 14162-14167
51. Lobachev K.S., Stenger J.E., Kozyreva O.G., Jurka J., Gordenin D.A., and Resnick M.A. Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J. 19 (2000) 3822-3830
52. Stenger J.E., Lobachev K.S., Gordenin D., Darden T.A., Jurka J., and Resnick M.A. Biased distribution of inverted and direct Alus in the human genome: Implications for insertion, exclusion, and genome stability. Genome Res. 11 (2001) 12-27
53. Hinds D.A., Kloek A.P., Jen M., Chen X., and Frazer K.A. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat. Genet. 38 (2006) 82-85
54. Locke D.P., Sharp A.J., McCarroll S.A., McGrath S.D., Newman T.L., Cheng Z., Schwartz S., Albertson D.G., Pinkel D., Altshuler D.M., et al. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet. 79 (2006) 275-290
55. McCarroll S.A., and Altshuler D. Copy number variation and association studies of human disease. Nat. Genet. 39 (2007) S37-S42
56. Goidts V., Cooper D.N., Armengol L., Schempp W., Conroy J., Estivill X., Nowak N., Hameister H., and Kehrer-Sawatzki H. Complex patterns of copy number variation at sites of segmental duplications: An important category of structural variation in the human genome. Hum. Genet. 120 (2006) 270-284
57. Perry G.H., Tchinda J., McGrath S.D., Zhang J., Picker S.R., Caceres A.M., Iafrate A.J., Tyler-Smith C., Scherer S.W., Eichler E.E., et al. Hotspots for copy number variation in chimpanzees and humans. Proc. Natl. Acad. Sci. USA 103 (2006) 8006-8011
58. Repping S., van Daalen S.K., Brown L.G., Korver C.M., Lange J., Marszalek J.D., Pyntikova T., van der Veen F., Skaletsky H., Page D.C., et al. High mutation rates have driven extensive structural polymorphism among human Y chromosomes. Nat. Genet. 38 (2006) 463-467
59. Egan C.M., Sridhar S., Wigler M., and Hall I.M. Recurrent DNA copy number variation in the laboratory mouse. Nat. Genet. 39 (2007) 1384-1389
60. Jobling M.A., Lo I.C., Turner D.J., Bowden G.R., Lee A.C., Xue Y., Carvalho-Silva D., Hurles M.E., Adams S.M., Chang Y.M., et al. Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y. Hum. Mol. Genet. 16 (2007) 307-316
61. Simon-Sanchez J., Scholz S., Del Mar Matarin M., Fung H.C., Hernandez D., Gibbs J.R., Britton A., Hardy J., and Singleton A. Genomewide SNP assay reveals mutations underlying Parkinson disease. Hum. Mutat. (2007) 10.1002/humu.20626 Published online November 9, 2007
62. Wang K., Li M., Hadley D., Liu R., Glessner J., Grant S.F., Hakonarson H., and Bucan M. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17 (2007) 1665-1674
63. Zogopoulos G., Ha K.C., Naqib F., Moore S., Kim H., Montpetit A., Robidoux F., Laflamme P., Cotterchio M., Greenwood C., et al. Germ-line DNA copy number variation frequencies in a large North American population. Hum. Genet. 122 (2007) 345-353