Identification of copy number variation hotspots in human populations

American Journal of Human Genetics

Volumn 87, Issue 4, 2010, Pages 494-504

  Fu, Wenqing ^a   Zhang, Feng ^a   Wang, Yi ^a   Gu, Xun ^a,b   Jin, Li ^a,c  

^a FUDAN UNIVERSITY   (China)

^b IOWA STATE UNIVERSITY   (United States)

^c MAX PLANCK INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BETA DEFENSIN; COMPLEMENT COMPONENT C4A; COMPLEMENT COMPONENT C4B; GLUTATHIONE TRANSFERASE M1; GLUTATHIONE TRANSFERASE M2; RHESUS D ANTIBODY; SOMATOMEDIN B RECEPTOR; SOMATOMEDIN C RECEPTOR;

ADRA1B GENE; ARTICLE; BANP GENE; COPY NUMBER VARIATION; DLP GENE; DUSP22 GENE; ERICH1 GENE; ETV6 GENE; GENE; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENETIC TRAIT; GENOMIC INSTABILITY; GENOTYPE; GLUTATHIONE TRANSFERASE M4 GENE; GLUTATHIONE TRANSFERASE M5 GENE; GRM8 GENE; HEATR4 GENE; HP GENE; HPR GENE; HUMAN GENETICS; HUMAN GENOME; IFT52 GENE; INTS4 GENE; ITGB1 GENE; KLHL2 GENE; LSS GENE; MGAM GENE; MLL3 GENE; MRCL GENE; MUTATION RATE; OTOA GENE; PADI4 GENE; PARG GENE; PDPR GENE; PHYLOGENY; PIK3C2A GENE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SRGAP2 GENE; SYN3 GENE; TYW1B GENE; ZC3H6 GENE; ZNF28 GENE; ZNF468 GENE; ZNF57 GENE; ZNF658B GENE; ZNF700 GENE; ZZEF1 GENE; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETICS; HUMAN; MOLECULAR EVOLUTION; MUTATION;

ALGORITHMS; COMPUTER SIMULATION; DNA COPY NUMBER VARIATIONS; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; MODELS, GENETIC; MUTATION; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77957737256     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2010.09.006     Document Type: Article

References (41)

1. R. Redon, S. Ishikawa, K.R. Fitch, L. Feuk, G.H. Perry, T.D. Andrews, H. Fiegler, M.H. Shapero, A.R. Carson, and W. Chen Global variation in copy number in the human genome Nature 444 2006 444 454 (Pubitemid 44809057)
2. D.F. Conrad, D. Pinto, R. Redon, L. Feuk, O. Gokcumen, Y. Zhang, J. Aerts, T.D. Andrews, C. Barnes, P. Campbell Wellcome Trust Case Control Consortium Origins and functional impact of copy number variation in the human genome Nature 464 2010 704 712
3. F. Zhang, W. Gu, M.E. Hurles, and J.R. Lupski Copy number variation in human health, disease, and evolution Annu. Rev. Genomics Hum. Genet. 10 2009 451 481
4. R. Beroukhim, C.H. Mermel, D. Porter, G. Wei, S. Raychaudhuri, J. Donovan, J. Barretina, J.S. Boehm, J. Dobson, and M. Urashima The landscape of somatic copy-number alteration across human cancers Nature 463 2010 899 905
5. C.M. Egan, S. Sridhar, M. Wigler, and I.M. Hall Recurrent DNA copy number variation in the laboratory mouse Nat. Genet. 39 2007 1384 1389
6. G.J. van Ommen Frequency of new copy number variation in humans Nat. Genet. 37 2005 333 334
7. K.W. Lam, and A.J. Jeffreys Processes of copy-number change in human DNA: the dynamics of alpha-globin gene deletion Proc. Natl. Acad. Sci. USA 103 2006 8921 8927
8. K.W. Lam, and A.J. Jeffreys Processes of de novo duplication of human alpha-globin genes Proc. Natl. Acad. Sci. USA 104 2007 10950 10955
9. J.R. Lupski Genomic rearrangements and sporadic disease Nat. Genet. 39 7 Suppl 2007 S43 S47
10. D.J. Turner, M. Miretti, D. Rajan, H. Fiegler, N.P. Carter, M.L. Blayney, S. Beck, and M.E. Hurles Germline rates of de novo meiotic deletions and duplications causing several genomic disorders Nat. Genet. 40 2008 90 95
11. S. Abu Bakar, E.J. Hollox, and J.A. Armour Allelic recombination between distinct genomic locations generates copy number diversity in human beta-defensins Proc. Natl. Acad. Sci. USA 106 2009 853 858
12. S.A. McCarroll, F.G. Kuruvilla, J.M. Korn, S. Cawley, J. Nemesh, A. Wysoker, M.H. Shapero, P.I. de Bakker, J.B. Maller, and A. Kirby Integrated detection and population-genetic analysis of SNPs and copy number variation Nat. Genet. 40 2008 1166 1174
13. J.L. Freeman, G.H. Perry, L. Feuk, R. Redon, S.A. McCarroll, D.M. Altshuler, H. Aburatani, K.W. Jones, C. Tyler-Smith, and M.E. Hurles Copy number variation: new insights in genome diversity Genome Res. 16 2006 949 961 (Pubitemid 44162254)
14. D.P. Locke, A.J. Sharp, S.A. McCarroll, S.D. McGrath, T.L. Newman, Z. Cheng, S. Schwartz, D.G. Albertson, D. Pinkel, D.M. Altshuler, and E.E. Eichler Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome Am. J. Hum. Genet. 79 2006 275 290
15. M.J. Minichiello, and R. Durbin Mapping trait loci by use of inferred ancestral recombination graphs Am. J. Hum. Genet. 79 2006 910 922
16. M. Kato, Y. Nakamura, and T. Tsunoda An algorithm for inferring complex haplotypes in a region of copy-number variation Am. J. Hum. Genet. 83 2008 157 169
17. G. Laval, and L. Excoffier SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history Bioinformatics 20 2004 2485 2487
18. B. Weir, and C. Cockerham Estimating F-statistics for the analysis of population structure Evolution 38 1984 1358 1370
19. S.F. Schaffner, C. Foo, S. Gabriel, D. Reich, M.J. Daly, and D. Altshuler Calibrating a coalescent simulation of human genome sequence variation Genome Res. 15 2005 1576 1583 (Pubitemid 41545011)
20. A. Kong, D.F. Gudbjartsson, J. Sainz, G.M. Jonsdottir, S.A. Gudjonsson, B. Richardsson, S. Sigurdardottir, J. Barnard, B. Hallbeck, and G. Masson A high-resolution recombination map of the human genome Nat. Genet. 31 2002 241 247
21. S. Myers, L. Bottolo, C. Freeman, G. McVean, and P. Donnelly A fine-scale map of recombination rates and hotspots across the human genome Science 310 2005 321 324
22. K.A. Frazer, D.G. Ballinger, D.R. Cox, D.A. Hinds, L.L. Stuve, R.A. Gibbs, J.W. Belmont, A. Boudreau, P. Hardenbol, S.M. Leal International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs Nature 449 2007 851 861
23. P. Stankiewicz, and J.R. Lupski Genome architecture, rearrangements and genomic disorders Trends Genet. 18 2002 74 82
24. J.A. Bailey, and E.E. Eichler Primate segmental duplications: crucibles of evolution, diversity and disease Nat. Rev. Genet. 7 2006 552 564
25. E.J. Hollox, U. Huffmeier, P.L. Zeeuwen, R. Palla, J. Lascorz, D. Rodijk-Olthuis, P.C. van de Kerkhof, H. Traupe, G. de Jongh, and M. den Heijer Psoriasis is associated with increased beta-defensin genomic copy number Nat. Genet. 40 2008 23 25
26. F. Zhang, M. Khajavi, A.M. Connolly, C.F. Towne, S.D. Batish, and J.R. Lupski The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans Nat. Genet. 41 2009 849 853
27. A. Itsara, G.M. Cooper, C. Baker, S. Girirajan, J. Li, D. Absher, R.M. Krauss, R.M. Myers, P.M. Ridker, and D.I. Chasman Population analysis of large copy number variants and hotspots of human genetic disease Am. J. Hum. Genet. 84 2009 148 161
28. M. Stephens, N.J. Smith, and P. Donnelly A new statistical method for haplotype reconstruction from population data Am. J. Hum. Genet. 68 2001 978 989
29. S. Repping, S.K. van Daalen, L.G. Brown, C.M. Korver, J. Lange, J.D. Marszalek, T. Pyntikova, F. van der Veen, H. Skaletsky, D.C. Page, and S. Rozen High mutation rates have driven extensive structural polymorphism among human Y chromosomes Nat. Genet. 38 2006 463 467
30. W. Gu, F. Zhang, and J.R. Lupski Mechanisms for human genomic rearrangements Pathogenetics 1 2008 4
31. J.L. Argueso, J. Westmoreland, P.A. Mieczkowski, M. Gawel, T.D. Petes, and M.A. Resnick Double-strand breaks associated with repetitive DNA can reshape the genome Proc. Natl. Acad. Sci. USA 105 2008 11845 11850
32. F. Zhang, C.M. Carvalho, and J.R. Lupski Complex human chromosomal and genomic rearrangements Trends Genet. 25 2009 298 307
33. P.J. Hastings, J.R. Lupski, S.M. Rosenberg, and G. Ira Mechanisms of change in gene copy number Nat. Rev. Genet. 10 2009 551 564
34. Y. Yang, E.K. Chung, Y.L. Wu, S.L. Savelli, H.N. Nagaraja, B. Zhou, M. Hebert, K.N. Jones, Y. Shu, and K. Kitzmiller 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
35. R.S. Huang, P. Chen, S. Wisel, S. Duan, W. Zhang, E.H. Cook, S. Das, N.J. Cox, and M.E. Dolan Population-specific GSTM1 copy number variation Hum. Mol. Genet. 18 2009 366 372
36. Y. Colin, B. Chérif-Zahar, C. Le Van Kim, V. Raynal, V. Van Huffel, and J.P. Cartron Genetic basis of the RhD-positive and RhD-negative blood group polymorphism as determined by Southern analysis Blood 78 1991 2747 2752
37. H. Park, J.I. Kim, Y.S. Ju, O. Gokcumen, R.E. Mills, S. Kim, S. Lee, D. Suh, D. Hong, and H.P. Kang Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing Nat. Genet. 42 2010 400 405
38. W.A. Ester, H.A. van Duyvenvoorde, C.C. de Wit, A.J. Broekman, C.A. Ruivenkamp, L.C. Govaerts, J.M. Wit, A.C. Hokken-Koelega, and M. Losekoot Two short children born small for gestational age with insulin-like growth factor 1 receptor haploinsufficiency illustrate the heterogeneity of its phenotype J. Clin. Endocrinol. Metab. 94 2009 4717 4727
39. I. Cuscó, A. Medrano, B. Gener, M. Vilardell, F. Gallastegui, O. Villa, E. González, B. Rodríguez-Santiago, E. Vilella, M. Del Campo, and L.A. Pérez-Jurado Autism-specific copy number variants further implicate the phosphatidylinositol signaling pathway and the glutamatergic synapse in the etiology of the disorder Hum. Mol. Genet. 18 2009 1795 1804
40. N. Brunetti-Pierri, J.S. Berg, F. Scaglia, J. Belmont, C.A. Bacino, T. Sahoo, S.R. Lalani, B. Graham, B. Lee, and M. Shinawi Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities Nat. Genet. 40 2008 1466 1471
41. L. Excoffier, and M. Slatkin Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population Mol. Biol. Evol. 12 1995 921 927