Population genetic nature of copy number variation

Methods in Molecular Biology

Volumn 838, Issue , 2012, Pages 209-223

  Sjödin, Per ^a   Jakobsson, Mattias ^b  

^a UPPSALA UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Copy number variation; Demography; Mutation; Recombination; Selection

Indexed keywords

ARTICLE; COPY NUMBER VARIATION; GENE DELETION; GENE DUPLICATION; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETIC SELECTION; HUMAN; HUMAN GENOME; POPULATION GENETICS;

DNA COPY NUMBER VARIATIONS; GENE DELETION; GENE DUPLICATION; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; LINKAGE DISEQUILIBRIUM; RECOMBINATION, GENETIC; SELECTION, GENETIC;

MAMMALIA;

EID: 84856247679     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-507-7_10     Document Type: Article

References (92)

1. Lynch, M., and Conery, J.S. (2000) The evolutionary fate and consequences of duplicated genes Science 290, 1151-5.
2. Rubin, G.M., Yandell, M.D., Wortman, J.R., Gabor Miklos, G.L., Nelson, C.R., Hariharan, I.K., Fortini, M.E., Li, P.W., Apweiler, R., Fleischmann, W., Cherry, J.M., Henikoff, S., Skupski, M.P., Misra, S., Ashburner, M., Birney, E., Boguski, M.S., Brody, T., Brokstein, P., Celniker, S.E., Chervitz, S.A., Coates, D., Cravchik, A., Gabrielian, A., Galle, R.F., Gelbart, W.M., George, R.A., Goldstein, L.S., Gong, F., Guan, P., Harris, N.L., Hay, B.A., Hoskins, R.A., Li, J., Li, Z., Hynes, R.O., Jones, S.J., Kuehl, P.M., Lemaitre, B., Littleton, J.T., Morrison, D.K., Mungall, C., OFarrell, P.H., Pickeral, O.K., Shue, C., Vosshall, L.B., Zhang, J., Zhao, Q., Zheng, X.H., and Lewis, S. (2000) Comparative genomics of the eukaryotes Science 287, 2204-15. (Pubitemid 30177015)
3. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome Nature 409, 860-921.
4. Zhang, J. (2003) Evolution by gene duplication: an update Trends Ecol Evol 18, 292-8. (Pubitemid 36631749)
5. She, X., Cheng, Z., Zöllner, S., Church, D.M., and Eichler, E.E. (2008) Mouse segmental duplication and copy number variation Nat Genet 40, 909-14. (Pubitemid 351913656)
6. Dujon, B., Sherman, D., Fischer, G., Durrens, P., Casaregola, S., Lafontaine, I., De Montigny, J., Marck, C., Neuvéglise, C., Talla, E., Goffard, N., Frangeul, L., Aigle, M., Anthouard, V., Babour, A., Barbe, V., Barnay, S., Blanchin, S., Beckerich, J.M., Beyne, E., Bleykasten, C., Boisramé, A., Boyer, J., Cattolico, L., Confanioleri, F., De Daruvar, A., Despons, L., Fabre, E., Fairhead, C., Ferry-Dumazet, H., Groppi, A., Hantraye, F., Hennequin, C., Jauniaux, N., Joyet, P., Kachouri, R., Kerrest, A., Koszul, R., Lemaire, M., Lesur, I., Ma, L., Muller, H., Nicaud, J.M., Nikolski, M., Oztas, S., Ozier-Kalogeropoulos, O., Pellenz, S., Potier, S., Richard, G.F., Straub, M.L., Suleau, A., Swennen, D., Tekaia, F., Wésolowski-Louvel, M., Westhof, E., Wirth, B., Zeniou-Meyer, M., Zivanovic, I., Bolotin-Fukuhara, M., Thierry, A., Bouchier, C., Caudron, B., Scarpelli, C., Gaillardin, C., Weissenbach, J., Wincker, P., and Souciet, J.L. (2004) Genome evolution in yeasts Nature 430, 35-44. (Pubitemid 38915217)
7. Parkinson, J., Mitreva, M., Whitton, C., Thomson, M., Daub, J., Martin, J., Schmid, R., Hall, N., Barrell, B., Waterston, R.H., McCarter, J.P., and Blaxter, M.L. (2004) A transcriptomic analysis of the phylum Nematoda Nat Genet 36, 1259-67.
8. Demuth, J.P., De Bie, T., Stajich, J.E., Cristianini, N., and Hahn, M.W. (2006) The evolution of mammalian gene families PLoS One 1, e85.
9. Hahn, M.W., Hanm M.V., and Han, S.G. (2007) Gene family evolution across 12 Drosophila genomes PLoS Genet 3, 2135-46. (Pubitemid 350291574)
10. Opazo, J.C., Hoffmann, F.G., and Storz, J.F. (2008) Differential loss of embryonic globin genes during the radiation of placental mammals Proc Natl Acad Sci USA 105, 12950-5.
11. Scherer, S.W., Lee, C., Birney, E., Altshuler, D.M., Eichler, E.E., Carter, N.P., Hurles, M.E., and Feuk, L. (2007) Challenges and standards in integrating surveys of structural variation Nat Genet 39, S7-15. (Pubitemid 47014477)
12. Johnson, M.E., Viggiano, L., Bailey, J.A., Abdul-Rauf, M., Goodwin, G., Rocchi, M., and Eichler, E.E. (2001) Positive selection of a gene family during the emergence of humans and African apes Nature 413, 514-19. (Pubitemid 32938748)
13. Nguyen, D.Q., Webber, C., and Ponting, C.P. (2006) Bias of selection on human copy-number variants PLoS Genet 2, e20.
14. Heger, A., and Ponting, C. P. (2007) Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes Genome Res 17, 1837-49. (Pubitemid 351360007)
15. 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., Carter, N.P., Lee, C., and Stone, A.C. (2007) Diet and the evolution of human amylase gene copy number variation Nat Genet 39, 1256-60. (Pubitemid 47482688)
16. Emerson, J.J., Cardoso-Moreira, M., Borevitz, J.O., and Long, M. (2008) Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster Science 320, 1629-31. (Pubitemid 351931251)
17. Xue, Y., Sun, D., Daly, A., Yang, F., Zhou, X., Zhao, M., Huang, N., Zerjal, T., Lee, C., Carter, N.P., Hurles, M.E., and Tyler-Smith, C. (2008) Adaptive evolution of UGT2B17 copy-number variation Am J Hum Genet 83, 337-46.
18. Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E., and Pritchard, J.K. (2006) A high-resolution survey of deletion polymorphism in the human genome Nat Genet 38, 75-81. (Pubitemid 43011885)
19. 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, and Eichler, E.E. (2006) Linkage disequilibrium and heritability of copynumber polymorphisms within duplicated regions of the human genome Am J Hum Genet 79, 275-90. (Pubitemid 44141826)
20. Dopman, E.B., and Hartl, D.L. (2007) A portrait of copy-number polymorphism in Drosophila melanogaster Proc Natl Acad Sci USA 104, 19920-5.
21. Nguyen, D.Q., Webber, C., Hehir-Kwa, J., Pfundt, R., Veltman, J., and Ponting, C.P. (2008) Reduced purifying selection prevails over positive selection in human copy number variant evolution Genome Res 18, 1711-23.
22. Iafrate, A.J., Feuk, L., Rivera, M.N., Listewnik, M.L., Donahoe, P.K., Qi, Y., Scherer, S.W., and Lee, C. (2004) Detection of large-scale variation in the human genome Nat Genet 36, 949-51. (Pubitemid 39167488)
23. Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M., Navin, N., Lucito, R., Healy, J., Hicks, J., Ye, K., Reiner, A., Gilliam, T.C., Trask, B., Patterson, N., Zetterberg, A., and Wigler, M. (2004) Large-scale copy number polymorphism in the human genome Science 305, 525-8. (Pubitemid 38971344)
24. 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., Cho, E.K., Dallaire, S., Freeman, J.L., González, J.R., Gratacòs, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J.R., Marshall, C.R., Mei, R., Montgomery, L., Nishimura, K., Okamura, K., Shen, F., Somerville, M.J., Tchinda, J., Valsesia, A., Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Zhang, J., Armengol, L., Conrad, D.F., Estivill, X., Tyler-Smith, C., Carter, N.P., Aburatani, H., Lee, C., Jones, K.W., Scherer, S.W., and Hurles, M.E. (2006) Global variation in copy number in the human genome Nature 444, 444-54. (Pubitemid 44809057)
25. 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., and Lam, W.L. (2007) A comprehensive analysis of common copy-number variations in the human genome Am J Hum Genet 80, 91-104. (Pubitemid 46047653)
26. Lupski, J.R., de Oca-Luna, R.M., Slaugenhaupt, S., Pentao, L., Guzzetta, V., Trask, B.J., Saucedo-Cardenas, O., Barker, D.F., Killian, J.M., Garcia, C.A., Chakravarti, A., and Patel, P.I. (1991) DNA duplication associated with Charcot-Marie-Tooth disease type 1A Cell 66, 219-32. (Pubitemid 121001361)
27. Singleton, A.B., Farrer, M., Johnson, J., Singleton, A., Hague, S., Kachergus, J., Hulihan, M., Peuralinna, T., Dutra, A., Nussbaum, R., Lincoln, S., Crawley, A., Hanson, M., Maraganore, D., Adler, C., Cookson, M.R., Muenter, M., Baptista, M., Miller, D., Blancato, J., Hardy, J., and Gwinn-Hardy, K. (2003) α-synuclein locus triplication causes Parkinsons disease Science 302, 841. (Pubitemid 37339619)
28. Gonzalez, E., Kulkarni, H., Bolivar, H., Mangano, A., Sanchez, R., Catano, G., Nibbs, R.J., Freedman, B.I., Quinones, M.P., Bamshad, M.J., Murthy, K.K., Rovin, B.H., Bradley, W., Clark, R.A., Anderson, S.A., Oconnell, R.J., Agan, B.K., Ahuja, S.S., Bologna, R., Sen, L., Dolan, M.J., and Ahuja, S.K. (2005) The influence of CCL3L1 genecontaining segmental duplications on HIV-1/AIDS susceptibility Science 307, 1434-40. (Pubitemid 40321934)
29. Beckmann, J.S., Estivill, X., and Antonarakis, S.E. (2007) Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability Nat Rev Genet 8, 639-46. (Pubitemid 47077281)
30. Mefford, H.C., Sharp, A.J., Baker, C., Itsara, A., Jiang, Z., Buysse, K., Huang, S., Maloney, V.K., Crolla, J.A., Baralle, D., Collins, A., Mercer, C., Norga, K., de Ravel, T., Devriendt, K., Bongers, E.M., de Leeuw, N., Reardon, W., Gimelli, S., Bena, F., Hennekam, R.C., Male, A., Gaunt, L., Clayton-Smith, J., Simonic, I., Park, S.M., Mehta, S.G., Nik-Zainal, S., Woods, C.G., Firth, H.V., Parkin, G., Fichera, M., Reitano, S., Lo Giudice, M., Li, K.E., Casuga, I., Broomer, A., Conrad, B., Schwerzmann, M., Räber, L., Gallati, S., Striano, P., Coppola, A., Tolmie, J.L., Tobias, E.S., Lilley, C., Armengol, L., Spysschaert, Y., Verloo, P., De Coene, A., Goossens, L., Mortier, G., Speleman, F., van Binsbergen, E., Nelen, M.R., Hochstenbach, R., Poot, M., Gallagher, L., Gill, M., McClellan, J., King, M.C., Regan, R., Skinner, C., Stevenson, R.E., Antonarakis, S.E., Chen, C., Estivill, X., Menten, B., Gimelli, G., Gribble, S., Schwartz, S., Sutcliffe, J.S., Walsh, T., Knight, S.J., Sebat, J., Romano, C., Schwartz, C.E., Veltman, J.A., de Vries, B.B., Vermeesch, J.R., Barber, J.C., Willatt, L., Tassabehji, M., and Eichler, E.E. (2008) Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes N Engl J Med 359, 1685-99.
31. Zhang, F., Gu, W., Hurles, M.E., and Lupski, J.R. (2009) Copy number variation in human health, disease, and evolution Annu Rev Genomics Hum Genet 10, 451-81.
32. McKim, K.S., Peters, K., and Rose, A.M. (1993) Two types of sites required for meiotic chromosome pairing in Caenorhabditis elegans Genetics 134, 749-68. (Pubitemid 23193575)
33. Hammarlund, M., Davis, M.W., Nguyen, H., Dayton, D., and Jorgensen, E.M. (2005) Heterozygous insertions alter crossover distribution but allow crossover interference in Caenorhabditis elegans Genetics 171, 1047-56. (Pubitemid 43234841)
34. Navarro, A., Betrán, E., Barbadilla, A., and Ruiz, A. (1997) Recombination and gene flux caused by gene conversion and crossing over in inversion heterokaryotypes Genetics 146, 695-709. (Pubitemid 27251405)
35. Shaw, C.J., and Lupski, J.R. (2004) Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease Hum Mol Genet 13, R57-64. (Pubitemid 38443799)
36. Lupski, J.R., and Stankiewicz, P., (2005) Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes PLoS Genet 1, e49.
37. Erdogan, F., Chen, W., Kirchhoff, M., Kalscheuer, V.M., Hultschig, C., Müller, I., Schulz, R., Menzel, C., Bryndorf, T., Ropers, H.H., and Ullmann, R. (2006) Impact of low copy repeats on the generation of balanced and unbalanced chromosomal aberrations in mental retardation Cytogenet Genome Res 115, 247-53. (Pubitemid 44832027)
38. Lindsay, S.J., Khajavi, M., Lupski, J.R., and Hurles, M.E. (2006) A chromosomal rearrangement hotspot can be identifi ed from population genetic variation and is coincident with a hotspot for allelic recombination Am J Hum Genet 79, 890-902. (Pubitemid 44763403)
39. Sun, X., Zhang, Y., Yang, S., Chen, J.Q., Hohn, B., and Tian, D. (2008) Insertion DNA Promotes Ectopic Recombination during Meiosis in Arabidopsis Mol Biol Evol 25, 2079-83.
40. Welz-Voegele, C., and Jinks-Robertson, S. (2008) Sequence divergence impedes crossover more than noncrossover events during mitotic gap repair in yeast Genetics 179, 1251-62.
41. Duret, L., and Galtier, N. (2009) Biased gene conversion and the evolution of mammalian genomic landscapes Annu Rev Genomics Hum Genet 10, 285-311.
42. Lamb, B.C. (1985) The effects of mispair and nonpair correction in hybrid DNA on base ratios (G + C content) and total amounts of DNA Mol Biol Evol 2, 175-88. (Pubitemid 15239738)
43. Bill, C.A., Taghian, D.G., Duran, W.A., and Nickoloff, J.A. (2001) Repair bias of large loop mismatches during recombination in mammalian cells depends on loop length and structure Mutat Res 485, 255-65. (Pubitemid 32232308)
44. White, S.J., Vissers, L.E., Geurts van Kessel, A., de Menezes, R.X., Kalay, E., Lehesjoki, A.E., Giordano, P.C., van de Vosse, E., Breuning, M.H., Brunner, H.G., den Dunnen, J.T., and Veltman, J.A.(2007) Variation of CNV distribution in five different ethnic populations Cytogenet Genome Res 118, 19-30. (Pubitemid 47492008)
45. Turner, D.J., Miretti, M., Rajan, D., Fiegler, H., Carter, N.P., Blayney, M.L., Beck, S., and Hurles, M.E. (2008) Germline rates of de novo meiotic deletions and duplications causing several genomic disorders Nat Genet 40, 90-5.
46. Kehrer-Sawatski, H., and Cooper, D.N. (2008) Comparative analysis of copy number variation in primate genomes Cytogenet Genome Res 123, 288-96.
47. Perry, G.H., Tchinda, J., McGrath, S.D., Zhang, J., Picker, S.R., Cáceres, A.M., Iafrate, A.J., Tyler-Smith, C., Scherer, S.W., Eichler, E.E., Stone, A.C., and Lee, C. (2006) Hotspots for copy number variation in chimpanzees and humans Proc Natl Acad Sci USA 103, 8006-11. (Pubitemid 43801043)
48. Ewens, W. J. (2004) Mathematical Population Genetics. Second Revised Edition. Springer-Verlag, New York.
49. Ohta, T., and Kimura, M. (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a fi nite population Genet Res 22, 201-4.
50. Conrad, D.F., and Hurles, M.E. (2007) The population genetics of structural variation Nat Genet 39, S30-6. (Pubitemid 47014472)
51. Cooper, G.M., Nickerson, D.A., and Eichler, E.E. (2007) Mutational and selective effects on copy-number variants in the human genome Nat Genet 39, S22-9. (Pubitemid 47014473)
52. Marques-Bonet, T., Girirajan, S., and Eichler, E.E. (2009) The origins and impact of primate segmental duplications Trends Genet 25, 443-54.
53. Liu, G.E., Ventura, M., Cellamare, A., Chen, L., Cheng, Z., Zhu, B., Li, C., Song, J., and Eichler, E.E. (2009) Analysis of recent segmental duplications in the bovine genome BMC Genomics 10, 571.
54. Bailey, J.A., Liu, G.E., and Eichler, E.E. (2003) An Alu Transposition Model for the Origin and Expansion of Human Segmental Duplications Am J Hum Genet 73, 823-34. (Pubitemid 37271886)
55. Kim, P.M., Lam, H.Y., Urban, A.E., Korbel, J.O., Affourtit, J., Grubert, F., Chen, X., Weissman, S., Snyder, M., and Gerstein, M.B. (2008) Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history Genome Res 18, 1865-74.
56. Tian, D., Wang, Q., Zhang, P., Araki, H., Yang, S., Kreitman, M., Nagylaki, T., Hudson, R., Bergelson, J., and Chen, J.Q. (2008) Singlenucleotide mutation rate increases close to insertions/deletions in eukaryotes Nature 455, 105-8.
57. Petrov, D.A., and Hartl, D.L. (2000) Pseudogene evolution and natural selection for a compact genome J Heredity 91, 221-7. (Pubitemid 30314325)
58. Petrov, D.A. (2002) Mutational Equilibrium Model of Genome Size Evolution Theor Pop Biol 61, 533-46. (Pubitemid 38051056)
59. Taylor, M.S., Ponting, C.P., and Copley, R.R. (2004) Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes Genome Res 14, 555-66. (Pubitemid 38500226)
60. Taylor, M.S., Kai, C., Kawai, J., Carninci, P., Hayashizaki Y, and Semple, C.A. (2006) Heterotachy in mammalian promoter evolution PLoS Genet 2, e30.
61. Kim, J., He, X., and Sinha, S. (2009) Evolution of Regulatory Sequences in 12 Drosophila Species PLoS Genet 5, e1000330.
62. Sjödin, P., Bataillon, T., and Schierup, M.H. (2010) Insertion and deletion processes in recent human history PLoS One 5, e8650.
63. Tuzun, E., Sharp, A.J., Bailey, J.A., Kaul, R., Morrison, V.A., Pertz, L.M., Haugen, E., Hayden, H., Albertson, D., Pinkel, D., Olson, M.V., and Eichler, E.E. (2005) Finescale structural variation of the human genome Nat Genet 37, 727-32. (Pubitemid 41754889)
64. Nicholas, T.J., Cheng, Z., Ventura, M., Mealey, K., Eichler, E.E., and Akey, J.M. (2009) The genomic architecture of segmental duplications and associated copy number variants in dogs Genome Res 19, 491-9.
65. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome Nature 420, 520-62.
66. Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature 428, 493-521.
67. Conrad, D.F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T.D., Barnes, C., Campbell, P., Fitzgerald, T., Hu, M., Ihm, C.H., Kristiansson, K., Macarthur, D.G., Macdonald, J.R., Onyiah, I., Pang, A.W., Robson, S., Stirrups, K., Valsesia, A., Walter, K., Wei, J., The Wellcome Trust Case Control Consortium, Tyler-Smith, C., Carter, N.P., Lee, C., Scherer, S.W., and Hurles, M.E. (2010) Origins and functional impact of copy number variation in the human genome Nature 464, 704-12.
68. Perry, G.H., Yang, F., Marques-Bonet, T., Murphy, C., Fitzgerald, T., Lee, A.S., Hyland, C., Stone, A.C., Hurles, M.E., Tyler-Smith, C., Eichler, E.E., Carter, N.P., Lee, C., and Redon, R. (2008) Copy number variation and evolution in humans and chimpanzees Genome Res 18, 1698-710.
69. Korbel, J.O., Kim, P.M., Chen, X., Urban, A.E., Weissman, S., Snyder, M., and Gerstein, M.B. (2008) The current excitement about copy-number variation: how it relates to gene duplications and protein families Curr Opin Struct Biol 18, 366-74.
70. Rosenberg, N.A., Mahajan, S., Ramachandran, S., Zhao, C., Pritchard, J.K., and Feldman, M.W. (2005) Clines, clusters, and the effect of study design on the inference of human population structure PLoS Genet 1, e70.
71. Li, J.Z., Absher, D.M., Tang, H., Southwick, A.M., Casto, A.M., Ramachandran, S., Cann, H.M., Barsh, G.S., Feldman, M., Cavalli-Sforza, L.L., and Myers, R.M. (2008) Worldwide human relationships inferred from genome-wide patterns of variation Science 319, 1100-4. (Pubitemid 351300793)
72. 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., Oseroff, V.V., Albertson, D.G., Pinkel, D., and Eichler, E.E. (2005) Segmental duplications and copy-number variation in the human genome Am J Hum Genet 77, 78-88. (Pubitemid 40848038)
73. Jakobsson, M., Scholz, S.W., Scheet, P., Gibbs, J.R., VanLiere, J.M., Fung, H.C., Szpiech, Z.A., Degnan, J.H., Wang, K., Guerreiro, R., Bras, J.M., Schymick, J.C., Hernandez, D.G., Traynor, B.J., Simon-Sanchez, J., Matarin, M., Britton, A., van de Leemput, J., Rafferty, I., Bucan, M., Cann, H.M., Hardy, J.A., Rosenberg, N.A., and Singleton, A.B. (2008) Genotype, haplotype, and copy-number variation in worldwide human populations Nature 451, 998-1003. (Pubitemid 351301742)
74. Wang, C., Szpiech, Z.A., Degnan, J.H., Jakobsson, M., Pemberton, T.J., Hardy, J.A., Singleton, A. B., and Rosenberg, N.A. (2010) Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis Stat Appl in Genet and Mol Biol 9, Article 13.
75. Cann, H.M., Cohen, D., and Dausset, J. (1987) Diagnosis of genetic disease by linkage analysis Birth Defects Orig Artic Ser 23, 33-60.
76. Garrigan, D., and Hammer, M.F. (2006) Reconstructing human origins in the genomic era Nat Rev Genet 7, 669-80. (Pubitemid 44260003)
77. The International HapMap Consortium (2005) A haplotype map of the human genome Nature 437, 1299-320.
78. 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., Altshuler, D.M., and International HapMap Consortium (2006) Common deletion polymorphisms in the human genome Nat Genet 38, 86-92. (Pubitemid 43011887)
79. Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S.F., Hakonarson, H., and Bucan, M. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in wholegenome SNP genotyping data Genome Res 17, 1665-74. (Pubitemid 350074862)
80. Kidd, J.M., Cooper, G.M., Donahue, W.F., Hayden, H.S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., Haugen, E., Zerr, T., Yamada, N.A., Tsang, P., Newman, T.L., Tüzün, E., Cheng, Z., Ebling, H.M., Tusneem, N., David, R., Gillett, W., Phelps, K.A., Weaver, M., Saranga, D., Brand, A., Tao, W., Gustafson, E., McKernan, K., Chen, L., Malig, M., Smith, J.D., Korn, J.M., McCarroll, S.A., Altshuler, D.A., Peiffer, D.A., Dorschner, M., Stamatoyannopoulos, J., Schwartz, D., Nickerson, D.A., Mullikin, J.C., Wilson, R.K., Bruhn, L., Olson, M.V., Kaul, R., Smith, D.R., and Eichler, E.E. (2008) Mapping and sequencing of structural variation from eight human genomes Nature 453, 56-64. (Pubitemid 351630326)
81. Armengol, L., Villatoro, S., González, J.R., Pantano, L., García-Aragonés, M., Rabionet, R., Cáceres, M., and Estivill, X. (2009) Identifi cation of copy number variants defining genomic differences among major human groups PLoS One 4, e7230.
82. Takahashi, N., Satoh, Y., Kodaira, M., and Katayama, H. (2008) Large-scale copy number variants (CNVs) detected in different ethnic human populations Cytogenet Genome Res 123, 224-33.
83. Kato, M., Kawaguchi, T., Ishikawa, S., Umeda, T., Nakamichi, R., Shapero, M.H., Jones, K.W., Nakamura, Y., Aburatani, H., and Tsunoda, T. (2010) Population-genetic nature of copy number variations in the human genome Hum Mol Genet 19, 761-73.
84. Hinds, D.A., Kloek, A.P., Jen, M., Chen, X., and Frazer, K.A. (2006) Common deletions and SNPs are in linkage disequilibrium in the human genome Nat Genet 38, 82-5. (Pubitemid 43011886)
85. de Ståhl, T.D., Sandgren, J., Piotrowski, A., Nord, H., Andersson, R., Menzel, U., Bogdan, A., Thuresson, A.C., Poplawski, A., von Tell, D., Hansson, C.M., Elshafi e, A.I., Elghazali, G., Imreh, S., Nordenskjöld, M., Upadhyaya, M., Komorowski, J., Bruder, C.E., and Dumanski, J.P. (2008) Profi ling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array Hum Mutat 29, 398-408. (Pubitemid 351364942)
86. Cann, H.M., de Toma, C., Cazes, L., Legrand, M.F., Morel, V., Piouffre, L., Bodmer, J., Bodmer, W.F., Bonne-Tamir, B., Cambon-Thomsen, A., Chen, Z., Chu, J., Carcassi, C., Contu, L., Du, R., Excoffi er, L., Ferrara, G.B., Friedlaender, J.S., Groot, H., Gurwitz, D., Jenkins, T., Herrera, R.J., Huang, X., Kidd, J., Kidd, K.K., Langaney, A., Lin, A.A., Mehdi, S.Q., Parham, P., Piazza, A., Pistillo, M.P., Qian, Y., Shu, Q., Xu, J., Zhu, S., Weber, J.L., Greely, H.T., Feldman, M.W., Thomas, G., Dausset, J., and Cavalli-Sforza LL. (2002) A human genome diversity cell line panel Science 296, 261-2. (Pubitemid 34303653)
87. Itsara, A., Cooper, G.M., Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R.M., Myers, R.M., Ridker, P.M., Chasman, D.I., Mefford, H., Ying, P., Nickerson, D.A., and Eichler, E.E. (2009) Population analysis of large copy number variants and hotspots of human genetic disease Am J Hum Genet 84, 148-61.
88. McCarroll, S.A., Kuruvilla, F.G., Korn, J.M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M.H., de Bakker, P.I., Maller, J.B., Kirby, A., Elliott, A.L., Parkin, M., Hubbell, E., Webster, T., Mei, R., Veitch, J., Collins, P.J., Handsaker, R., Lincoln, S., Nizzari, M., Blume, J., Jones, K.W., Rava, R., Daly, M.J., Gabriel, S.B., and Altshuler, D. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation Nat Genet 40, 1166-74.
89. Kalinowski, S.T. (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs Conserv Genet 5, 539-43. (Pubitemid 39225128)
90. Schrider, D.R., and Hahn, M.W. (2010) Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications Mol Biol Evol 27, 103-11.
91. Branton, D., Deamer, D.W., Marziali, A., Bayley, H., Benner, S.A., Butler, T., Di Ventra, M., Garaj, S., Hibbs, A., Huang, X., Jovanovich, S.B., Krstic, P.S., Lindsay, S., Ling, X.S., Mastrangelo, C.H., Meller, A., Oliver, J.S., Pershin, Y.V., Ramsey, J.M., Riehn, R., Soni, G.V., Tabard-Cossa, V., Wanunu, M., Wiggin, M., and Schloss, J.A. (2008) The potential and challenges of nanopore sequencing Nat Biotechnol 26, 1146-53.
92. Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., Bibillo, A., Bjornson, K., Chaudhuri, B., Christians, F., Cicero, R., Clark, S., Dalal, R., Dewinter, A., Dixon, J., Foquet, M., Gaertner, A., Hardenbol, P., Heiner, C., Hester, K., Holden, D., Kearns, G., Kong, X., Kuse, R., Lacroix, Y., Lin, S., Lundquist, P., Ma, C., Marks, P., Maxham, M., Murphy, D., Park, I., Pham, T., Phillips, M., Roy, J., Sebra, R., Shen, G., Sorenson, J., Tomaney, A., Travers, K., Trulson, M., Vieceli, J., Wegener, J., Wu, D., Yang, A., Zaccarin, D., Zhao, P., Zhong, F., Korlach, J., and Turner, S. (2009) Real-time DNA sequencing from single polymerase molecules Science 323, 133-8.