Diversity of human copy number variation and multicopy genes

Peter H. Sudmant, Jacob O. Kitzman, Francesca Antonacci, Can Alkan, Maika Malig, Anya Tsalenko, Nick Sampas, Laurakay Bruhn, Jay Shendure, Evan E. Eichler, D. L. Altshuler, R. M. Durbin, G. R. Abecasis, D. R. Bentley, A. Chakravarti, A. G. Clark, F. S. Collins, F. M. De La Vega, P. Donnelly, M. EgholmP. Flicek, S. B. Gabriel, R. A. Gibbs, B. M. Knoppers, E. S. Lander, H. Lehrach, E. R. Mardis, G. A. McVean, D. A. Nickerson, L. Peltonen, A. J. Schafer, S. T. Sherry, J. Wang, R. K. Wilson, D. Deiros, M. Metzker, D. Muzny, J. Reid, D. Wheeler, J. Li, M. Jian, G. Li, R. Li, H. Liang, G. Tian, B. Wang, W. Wang, H. Yang, X. Zhang, H. Zheng, L. Ambrogio, T. Bloom, K. Cibulskis, T. J. Fennell, D. B. Jaffe, E. Shefler, C. L. Sougnez, N. Gormley, S. Humphray, Z. Kingsbury, P. Koko-Gonzales, J. Stone, K. J. McKernan, G. L. Costa, J. K. Ichikawa, C. C. Lee, R. Sudbrak, T. A. Borodina, A. Dahl, A. N. Davydov, P. Marquardt, F. Mertes, W. Nietfeld, P. Rosenstiel, S. Schreiber, A. V. Soldatov, B. Timmermann, M. Tolzmann, J. Affourtit, D. Ashworth, S. Attiya, M. Bachorski, E. Buglione, A. Burke, A. Caprio, C. Celone, S. Clark, D. Conners, B. Desany, L. Gu, L. Guccione, K. Kao, A. Kebbel, J. Knowlton, M. Labrecque, L. McDade, C. Mealmaker, M. Minderman, A. Nawrocki, F. Niazi, K. Pareja, R. Ramenani, D. Riches, W. Song, C. Turcotte, S. Wang, D. Dooling, L. Fulton, R. Fulton, G. Weinstock, J. Burton, D. M. Carter, C. Churcher, A. Coffey, A. Cox, A. Palotie, M. Quail, T. Skelly, J. Stalker, H. P. Swerdlow, D. Turner, A. De Witte, S. Giles, M. Bainbridge, D. Challis, A. Sabo, F. Yu, J. Yu, X. Fang, X. Guo, Y. Li, R. Luo, S. Tai, H. Wu, X. Zheng, Y. Zhou, G. T. Marth, E. P. Garrison, W. Huang, A. Indap, D. Kural, W. P. Lee, W. F. Leong, A. R. Quinlan, C. Stewart, M. P. Stromberg, A. N. Ward, J. Wu, C. Lee, R. E. Mills, X. Shi, M. J. Daly, M. A. DePristo, A. D. Ball, E. Banks, B. L. Browning, K. V. Garimella, S. R. Grossman, R. E. Handsaker, M. Hanna, C. Hartl, A. M. Kernytsky, J. M. Korn, H. Li, J. R. Maguire, S. A. McCarroll, A. McKenna, J. C. Nemesh, A. A. Philippakis, R. E. Poplin, A. Price, M. A. Rivas, P. C. Sabeti, S. F. Schaffner, I. A. Shlyakhter, D. N. Cooper, E. V. Ball, M. Mort, A. D. Phillips, P. D. Stenson, J. Sebat, V. Makarov, K. Ye, S. C. Yoon, C. D. Bustamante, A. Boyko, J. Degenhardt, S. Gravel, Ryan N Gutenkunst, M. Kaganovich, A. Keinan, P. Lacroute, X. Ma, A. Reynolds, L. Clarke, F. Cunningham, J. Herrero, S. Keenen, E. Kulesha, R. Leinonen, W. M. McLaren, R. Radhakrishnan, R. E. Smith, V. Zalunin, X. Zheng-Bradley, J. O. Korbel, A. M. Stütz, M. Bauer, R. K. Cheetham, T. Cox, M. Eberle, T. James, S. Kahn, L. Murray, Y. Fu, F. C. Hyland, J. M. Manning, S. F. McLaughlin, H. E. Peckham, O. Sakarya, Y. A. Sun, E. F. Tsung, M. A. Batzer, M. K. Konkel, J. A. Walker, M. W. Albrecht, V. S. Amstislavskiy, R. Herwig, D. V. Parkhomchuk, R. Agarwala, H. M. Khouri, A. O. Morgulis, J. E. Paschall, L. D. Phan, K. E. Rotmistrovsky, R. D. Sanders, M. F. Shumway, C. Xiao, A. Auton, Z. Iqbal, G. Lunter, J. L. Marchini, L. Moutsianas, S. Myers, A. Tumian, J. Knight, R. Winer, D. W. Craig, S. M. Beckstrom-Sternberg, A. Christoforides, A. A. Kurdoglu, J. V. Pearson, S. A. Sinari, W. D. Tembe, D. Haussler, A. S. Hinrichs, S. J. Katzman, A. Kern, R. M. Kuhn, M. Przeworski, R. D. Hernandez, B. Howie, J. L. Kelley, S. C. Melton, P. Anderson, T. Blackwell, W. Chen, W. O. Cookson, J. Ding, H. M. Kang, M. Lathrop, L. Liang, M. F. Moffatt, P. Scheet, C. Sidore, M. Snyder, X. Zhan, S. Zöllner, P. Awadalla, F. Casals, Y. Idaghdour, J. Keebler, E. A. Stone, M. Zilversmit, L. Jorde, J. Xing, G. Aksay, I. Hajirasouliha, F. Hormozdiari, J. M. Kidd, S. C. Sahinalp, K. Chen, A. Chinwalla, L. Ding, D. C. Koboldt, M. D. McLellan, J. W. Wallis, M. C. Wendl, Q. Zhang, C. A. Albers, Q. Ayub, S. Balasubramaniam, J. C. Barrett, Y. Chen, D. F. Conrad, P. Danecek, E. T. Dermitzakis, M. Hu, N. Huang, M. E. Hurles, H. Jin, L. Jostins, T. M. Keane, S. Q. Le, S. Lindsay, Q. Long, D. G. MacArthur, S. B. Montgomery, L. Parts, C. Tyler-Smith, K. Walter, Y. Zhang, M. B. Gerstein, A. Abyzov, S. Balasubramanian, R. Bjornson, J. Du, F. Grubert, L. Habegger, R. Haraksingh, J. Jee, E. Khurana, H. Y. Lam, J. Leng, X. J. Mu, A. E. Urban, Z. Zhang, C. Coafra, H. Dinh, C. Kovar, S. Lee, L. Nazareth, J. Wilkinson, C. Scott, N. Gharani, J. S. Kaye, A. Kent, T. Li, A. L. McGuire, P. N. Ossorio, C. N. Rotimi, Y. Su, L. H. Toji, L. D. Brooks, A. L. Felsenfeld, J. E. McEwen, A. Abdallah, C. R. Juenger, N. C. Clemm, A. Duncanson, E. D. Green, M. S. Guyer, J. L. Peterson

Research output: Contribution to journalArticle

399 Citations (Scopus)

Abstract

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ∼1000 genes accessible to genetic studies of disease association.

Original languageEnglish (US)
Pages (from-to)641-646
Number of pages6
JournalScience
Volume330
Issue number6004
DOIs
StatePublished - Oct 29 2010
Externally publishedYes

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Genes
Gene Conversion
Inborn Genetic Diseases
Population Genetics
Human Genome
Nucleotides
Genotype
Brain

ASJC Scopus subject areas

  • General

Cite this

Sudmant, P. H., Kitzman, J. O., Antonacci, F., Alkan, C., Malig, M., Tsalenko, A., ... Peterson, J. L. (2010). Diversity of human copy number variation and multicopy genes. Science, 330(6004), 641-646. https://doi.org/10.1126/science.1197005

Diversity of human copy number variation and multicopy genes. / Sudmant, Peter H.; Kitzman, Jacob O.; Antonacci, Francesca; Alkan, Can; Malig, Maika; Tsalenko, Anya; Sampas, Nick; Bruhn, Laurakay; Shendure, Jay; Eichler, Evan E.; Altshuler, D. L.; Durbin, R. M.; Abecasis, G. R.; Bentley, D. R.; Chakravarti, A.; Clark, A. G.; Collins, F. S.; De La Vega, F. M.; Donnelly, P.; Egholm, M.; Flicek, P.; Gabriel, S. B.; Gibbs, R. A.; Knoppers, B. M.; Lander, E. S.; Lehrach, H.; Mardis, E. R.; McVean, G. A.; Nickerson, D. A.; Peltonen, L.; Schafer, A. J.; Sherry, S. T.; Wang, J.; Wilson, R. K.; Deiros, D.; Metzker, M.; Muzny, D.; Reid, J.; Wheeler, D.; Li, J.; Jian, M.; Li, G.; Li, R.; Liang, H.; Tian, G.; Wang, B.; Wang, W.; Yang, H.; Zhang, X.; Zheng, H.; Ambrogio, L.; Bloom, T.; Cibulskis, K.; Fennell, T. J.; Jaffe, D. B.; Shefler, E.; Sougnez, C. L.; Gormley, N.; Humphray, S.; Kingsbury, Z.; Koko-Gonzales, P.; Stone, J.; McKernan, K. J.; Costa, G. L.; Ichikawa, J. K.; Lee, C. C.; Sudbrak, R.; Borodina, T. A.; Dahl, A.; Davydov, A. N.; Marquardt, P.; Mertes, F.; Nietfeld, W.; Rosenstiel, P.; Schreiber, S.; Soldatov, A. V.; Timmermann, B.; Tolzmann, M.; Affourtit, J.; Ashworth, D.; Attiya, S.; Bachorski, M.; Buglione, E.; Burke, A.; Caprio, A.; Celone, C.; Clark, S.; Conners, D.; Desany, B.; Gu, L.; Guccione, L.; Kao, K.; Kebbel, A.; Knowlton, J.; Labrecque, M.; McDade, L.; Mealmaker, C.; Minderman, M.; Nawrocki, A.; Niazi, F.; Pareja, K.; Ramenani, R.; Riches, D.; Song, W.; Turcotte, C.; Wang, S.; Dooling, D.; Fulton, L.; Fulton, R.; Weinstock, G.; Burton, J.; Carter, D. M.; Churcher, C.; Coffey, A.; Cox, A.; Palotie, A.; Quail, M.; Skelly, T.; Stalker, J.; Swerdlow, H. P.; Turner, D.; De Witte, A.; Giles, S.; Bainbridge, M.; Challis, D.; Sabo, A.; Yu, F.; Yu, J.; Fang, X.; Guo, X.; Li, Y.; Luo, R.; Tai, S.; Wu, H.; Zheng, X.; Zhou, Y.; Marth, G. T.; Garrison, E. P.; Huang, W.; Indap, A.; Kural, D.; Lee, W. P.; Leong, W. F.; Quinlan, A. R.; Stewart, C.; Stromberg, M. P.; Ward, A. N.; Wu, J.; Lee, C.; Mills, R. E.; Shi, X.; Daly, M. J.; DePristo, M. A.; Ball, A. D.; Banks, E.; Browning, B. L.; Garimella, K. V.; Grossman, S. R.; Handsaker, R. E.; Hanna, M.; Hartl, C.; Kernytsky, A. M.; Korn, J. M.; Li, H.; Maguire, J. R.; McCarroll, S. A.; McKenna, A.; Nemesh, J. C.; Philippakis, A. A.; Poplin, R. E.; Price, A.; Rivas, M. A.; Sabeti, P. C.; Schaffner, S. F.; Shlyakhter, I. A.; Cooper, D. N.; Ball, E. V.; Mort, M.; Phillips, A. D.; Stenson, P. D.; Sebat, J.; Makarov, V.; Ye, K.; Yoon, S. C.; Bustamante, C. D.; Boyko, A.; Degenhardt, J.; Gravel, S.; Gutenkunst, Ryan N; Kaganovich, M.; Keinan, A.; Lacroute, P.; Ma, X.; Reynolds, A.; Clarke, L.; Cunningham, F.; Herrero, J.; Keenen, S.; Kulesha, E.; Leinonen, R.; McLaren, W. M.; Radhakrishnan, R.; Smith, R. E.; Zalunin, V.; Zheng-Bradley, X.; Korbel, J. O.; Stütz, A. M.; Bauer, M.; Cheetham, R. K.; Cox, T.; Eberle, M.; James, T.; Kahn, S.; Murray, L.; Fu, Y.; Hyland, F. C.; Manning, J. M.; McLaughlin, S. F.; Peckham, H. E.; Sakarya, O.; Sun, Y. A.; Tsung, E. F.; Batzer, M. A.; Konkel, M. K.; Walker, J. A.; Albrecht, M. W.; Amstislavskiy, V. S.; Herwig, R.; Parkhomchuk, D. V.; Agarwala, R.; Khouri, H. M.; Morgulis, A. O.; Paschall, J. E.; Phan, L. D.; Rotmistrovsky, K. E.; Sanders, R. D.; Shumway, M. F.; Xiao, C.; Auton, A.; Iqbal, Z.; Lunter, G.; Marchini, J. L.; Moutsianas, L.; Myers, S.; Tumian, A.; Knight, J.; Winer, R.; Craig, D. W.; Beckstrom-Sternberg, S. M.; Christoforides, A.; Kurdoglu, A. A.; Pearson, J. V.; Sinari, S. A.; Tembe, W. D.; Haussler, D.; Hinrichs, A. S.; Katzman, S. J.; Kern, A.; Kuhn, R. M.; Przeworski, M.; Hernandez, R. D.; Howie, B.; Kelley, J. L.; Melton, S. C.; Anderson, P.; Blackwell, T.; Chen, W.; Cookson, W. O.; Ding, J.; Kang, H. M.; Lathrop, M.; Liang, L.; Moffatt, M. F.; Scheet, P.; Sidore, C.; Snyder, M.; Zhan, X.; Zöllner, S.; Awadalla, P.; Casals, F.; Idaghdour, Y.; Keebler, J.; Stone, E. A.; Zilversmit, M.; Jorde, L.; Xing, J.; Aksay, G.; Hajirasouliha, I.; Hormozdiari, F.; Kidd, J. M.; Sahinalp, S. C.; Chen, K.; Chinwalla, A.; Ding, L.; Koboldt, D. C.; McLellan, M. D.; Wallis, J. W.; Wendl, M. C.; Zhang, Q.; Albers, C. A.; Ayub, Q.; Balasubramaniam, S.; Barrett, J. C.; Chen, Y.; Conrad, D. F.; Danecek, P.; Dermitzakis, E. T.; Hu, M.; Huang, N.; Hurles, M. E.; Jin, H.; Jostins, L.; Keane, T. M.; Le, S. Q.; Lindsay, S.; Long, Q.; MacArthur, D. G.; Montgomery, S. B.; Parts, L.; Tyler-Smith, C.; Walter, K.; Zhang, Y.; Gerstein, M. B.; Abyzov, A.; Balasubramanian, S.; Bjornson, R.; Du, J.; Grubert, F.; Habegger, L.; Haraksingh, R.; Jee, J.; Khurana, E.; Lam, H. Y.; Leng, J.; Mu, X. J.; Urban, A. E.; Zhang, Z.; Coafra, C.; Dinh, H.; Kovar, C.; Lee, S.; Nazareth, L.; Wilkinson, J.; Scott, C.; Gharani, N.; Kaye, J. S.; Kent, A.; Li, T.; McGuire, A. L.; Ossorio, P. N.; Rotimi, C. N.; Su, Y.; Toji, L. H.; Brooks, L. D.; Felsenfeld, A. L.; McEwen, J. E.; Abdallah, A.; Juenger, C. R.; Clemm, N. C.; Duncanson, A.; Green, E. D.; Guyer, M. S.; Peterson, J. L.

In: Science, Vol. 330, No. 6004, 29.10.2010, p. 641-646.

Research output: Contribution to journalArticle

Sudmant, PH, Kitzman, JO, Antonacci, F, Alkan, C, Malig, M, Tsalenko, A, Sampas, N, Bruhn, L, Shendure, J, Eichler, EE, Altshuler, DL, Durbin, RM, Abecasis, GR, Bentley, DR, Chakravarti, A, Clark, AG, Collins, FS, De La Vega, FM, Donnelly, P, Egholm, M, Flicek, P, Gabriel, SB, Gibbs, RA, Knoppers, BM, Lander, ES, Lehrach, H, Mardis, ER, McVean, GA, Nickerson, DA, Peltonen, L, Schafer, AJ, Sherry, ST, Wang, J, Wilson, RK, Deiros, D, Metzker, M, Muzny, D, Reid, J, Wheeler, D, Li, J, Jian, M, Li, G, Li, R, Liang, H, Tian, G, Wang, B, Wang, W, Yang, H, Zhang, X, Zheng, H, Ambrogio, L, Bloom, T, Cibulskis, K, Fennell, TJ, Jaffe, DB, Shefler, E, Sougnez, CL, Gormley, N, Humphray, S, Kingsbury, Z, Koko-Gonzales, P, Stone, J, McKernan, KJ, Costa, GL, Ichikawa, JK, Lee, CC, Sudbrak, R, Borodina, TA, Dahl, A, Davydov, AN, Marquardt, P, Mertes, F, Nietfeld, W, Rosenstiel, P, Schreiber, S, Soldatov, AV, Timmermann, B, Tolzmann, M, Affourtit, J, Ashworth, D, Attiya, S, Bachorski, M, Buglione, E, Burke, A, Caprio, A, Celone, C, Clark, S, Conners, D, Desany, B, Gu, L, Guccione, L, Kao, K, Kebbel, A, Knowlton, J, Labrecque, M, McDade, L, Mealmaker, C, Minderman, M, Nawrocki, A, Niazi, F, Pareja, K, Ramenani, R, Riches, D, Song, W, Turcotte, C, Wang, S, Dooling, D, Fulton, L, Fulton, R, Weinstock, G, Burton, J, Carter, DM, Churcher, C, Coffey, A, Cox, A, Palotie, A, Quail, M, Skelly, T, Stalker, J, Swerdlow, HP, Turner, D, De Witte, A, Giles, S, Bainbridge, M, Challis, D, Sabo, A, Yu, F, Yu, J, Fang, X, Guo, X, Li, Y, Luo, R, Tai, S, Wu, H, Zheng, X, Zhou, Y, Marth, GT, Garrison, EP, Huang, W, Indap, A, Kural, D, Lee, WP, Leong, WF, Quinlan, AR, Stewart, C, Stromberg, MP, Ward, AN, Wu, J, Lee, C, Mills, RE, Shi, X, Daly, MJ, DePristo, MA, Ball, AD, Banks, E, Browning, BL, Garimella, KV, Grossman, SR, Handsaker, RE, Hanna, M, Hartl, C, Kernytsky, AM, Korn, JM, Li, H, Maguire, JR, McCarroll, SA, McKenna, A, Nemesh, JC, Philippakis, AA, Poplin, RE, Price, A, Rivas, MA, Sabeti, PC, Schaffner, SF, Shlyakhter, IA, Cooper, DN, Ball, EV, Mort, M, Phillips, AD, Stenson, PD, Sebat, J, Makarov, V, Ye, K, Yoon, SC, Bustamante, CD, Boyko, A, Degenhardt, J, Gravel, S, Gutenkunst, RN, Kaganovich, M, Keinan, A, Lacroute, P, Ma, X, Reynolds, A, Clarke, L, Cunningham, F, Herrero, J, Keenen, S, Kulesha, E, Leinonen, R, McLaren, WM, Radhakrishnan, R, Smith, RE, Zalunin, V, Zheng-Bradley, X, Korbel, JO, Stütz, AM, Bauer, M, Cheetham, RK, Cox, T, Eberle, M, James, T, Kahn, S, Murray, L, Fu, Y, Hyland, FC, Manning, JM, McLaughlin, SF, Peckham, HE, Sakarya, O, Sun, YA, Tsung, EF, Batzer, MA, Konkel, MK, Walker, JA, Albrecht, MW, Amstislavskiy, VS, Herwig, R, Parkhomchuk, DV, Agarwala, R, Khouri, HM, Morgulis, AO, Paschall, JE, Phan, LD, Rotmistrovsky, KE, Sanders, RD, Shumway, MF, Xiao, C, Auton, A, Iqbal, Z, Lunter, G, Marchini, JL, Moutsianas, L, Myers, S, Tumian, A, Knight, J, Winer, R, Craig, DW, Beckstrom-Sternberg, SM, Christoforides, A, Kurdoglu, AA, Pearson, JV, Sinari, SA, Tembe, WD, Haussler, D, Hinrichs, AS, Katzman, SJ, Kern, A, Kuhn, RM, Przeworski, M, Hernandez, RD, Howie, B, Kelley, JL, Melton, SC, Anderson, P, Blackwell, T, Chen, W, Cookson, WO, Ding, J, Kang, HM, Lathrop, M, Liang, L, Moffatt, MF, Scheet, P, Sidore, C, Snyder, M, Zhan, X, Zöllner, S, Awadalla, P, Casals, F, Idaghdour, Y, Keebler, J, Stone, EA, Zilversmit, M, Jorde, L, Xing, J, Aksay, G, Hajirasouliha, I, Hormozdiari, F, Kidd, JM, Sahinalp, SC, Chen, K, Chinwalla, A, Ding, L, Koboldt, DC, McLellan, MD, Wallis, JW, Wendl, MC, Zhang, Q, Albers, CA, Ayub, Q, Balasubramaniam, S, Barrett, JC, Chen, Y, Conrad, DF, Danecek, P, Dermitzakis, ET, Hu, M, Huang, N, Hurles, ME, Jin, H, Jostins, L, Keane, TM, Le, SQ, Lindsay, S, Long, Q, MacArthur, DG, Montgomery, SB, Parts, L, Tyler-Smith, C, Walter, K, Zhang, Y, Gerstein, MB, Abyzov, A, Balasubramanian, S, Bjornson, R, Du, J, Grubert, F, Habegger, L, Haraksingh, R, Jee, J, Khurana, E, Lam, HY, Leng, J, Mu, XJ, Urban, AE, Zhang, Z, Coafra, C, Dinh, H, Kovar, C, Lee, S, Nazareth, L, Wilkinson, J, Scott, C, Gharani, N, Kaye, JS, Kent, A, Li, T, McGuire, AL, Ossorio, PN, Rotimi, CN, Su, Y, Toji, LH, Brooks, LD, Felsenfeld, AL, McEwen, JE, Abdallah, A, Juenger, CR, Clemm, NC, Duncanson, A, Green, ED, Guyer, MS & Peterson, JL 2010, 'Diversity of human copy number variation and multicopy genes', Science, vol. 330, no. 6004, pp. 641-646. https://doi.org/10.1126/science.1197005
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A et al. Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29;330(6004):641-646. https://doi.org/10.1126/science.1197005
Sudmant, Peter H. ; Kitzman, Jacob O. ; Antonacci, Francesca ; Alkan, Can ; Malig, Maika ; Tsalenko, Anya ; Sampas, Nick ; Bruhn, Laurakay ; Shendure, Jay ; Eichler, Evan E. ; Altshuler, D. L. ; Durbin, R. M. ; Abecasis, G. R. ; Bentley, D. R. ; Chakravarti, A. ; Clark, A. G. ; Collins, F. S. ; De La Vega, F. M. ; Donnelly, P. ; Egholm, M. ; Flicek, P. ; Gabriel, S. B. ; Gibbs, R. A. ; Knoppers, B. M. ; Lander, E. S. ; Lehrach, H. ; Mardis, E. R. ; McVean, G. A. ; Nickerson, D. A. ; Peltonen, L. ; Schafer, A. J. ; Sherry, S. T. ; Wang, J. ; Wilson, R. K. ; Deiros, D. ; Metzker, M. ; Muzny, D. ; Reid, J. ; Wheeler, D. ; Li, J. ; Jian, M. ; Li, G. ; Li, R. ; Liang, H. ; Tian, G. ; Wang, B. ; Wang, W. ; Yang, H. ; Zhang, X. ; Zheng, H. ; Ambrogio, L. ; Bloom, T. ; Cibulskis, K. ; Fennell, T. J. ; Jaffe, D. B. ; Shefler, E. ; Sougnez, C. L. ; Gormley, N. ; Humphray, S. ; Kingsbury, Z. ; Koko-Gonzales, P. ; Stone, J. ; McKernan, K. J. ; Costa, G. L. ; Ichikawa, J. K. ; Lee, C. C. ; Sudbrak, R. ; Borodina, T. A. ; Dahl, A. ; Davydov, A. N. ; Marquardt, P. ; Mertes, F. ; Nietfeld, W. ; Rosenstiel, P. ; Schreiber, S. ; Soldatov, A. V. ; Timmermann, B. ; Tolzmann, M. ; Affourtit, J. ; Ashworth, D. ; Attiya, S. ; Bachorski, M. ; Buglione, E. ; Burke, A. ; Caprio, A. ; Celone, C. ; Clark, S. ; Conners, D. ; Desany, B. ; Gu, L. ; Guccione, L. ; Kao, K. ; Kebbel, A. ; Knowlton, J. ; Labrecque, M. ; McDade, L. ; Mealmaker, C. ; Minderman, M. ; Nawrocki, A. ; Niazi, F. ; Pareja, K. ; Ramenani, R. ; Riches, D. ; Song, W. ; Turcotte, C. ; Wang, S. ; Dooling, D. ; Fulton, L. ; Fulton, R. ; Weinstock, G. ; Burton, J. ; Carter, D. M. ; Churcher, C. ; Coffey, A. ; Cox, A. ; Palotie, A. ; Quail, M. ; Skelly, T. ; Stalker, J. ; Swerdlow, H. P. ; Turner, D. ; De Witte, A. ; Giles, S. ; Bainbridge, M. ; Challis, D. ; Sabo, A. ; Yu, F. ; Yu, J. ; Fang, X. ; Guo, X. ; Li, Y. ; Luo, R. ; Tai, S. ; Wu, H. ; Zheng, X. ; Zhou, Y. ; Marth, G. T. ; Garrison, E. P. ; Huang, W. ; Indap, A. ; Kural, D. ; Lee, W. P. ; Leong, W. F. ; Quinlan, A. R. ; Stewart, C. ; Stromberg, M. P. ; Ward, A. N. ; Wu, J. ; Lee, C. ; Mills, R. E. ; Shi, X. ; Daly, M. J. ; DePristo, M. A. ; Ball, A. D. ; Banks, E. ; Browning, B. L. ; Garimella, K. V. ; Grossman, S. R. ; Handsaker, R. E. ; Hanna, M. ; Hartl, C. ; Kernytsky, A. M. ; Korn, J. M. ; Li, H. ; Maguire, J. R. ; McCarroll, S. A. ; McKenna, A. ; Nemesh, J. C. ; Philippakis, A. A. ; Poplin, R. E. ; Price, A. ; Rivas, M. A. ; Sabeti, P. C. ; Schaffner, S. F. ; Shlyakhter, I. A. ; Cooper, D. N. ; Ball, E. V. ; Mort, M. ; Phillips, A. D. ; Stenson, P. D. ; Sebat, J. ; Makarov, V. ; Ye, K. ; Yoon, S. C. ; Bustamante, C. D. ; Boyko, A. ; Degenhardt, J. ; Gravel, S. ; Gutenkunst, Ryan N ; Kaganovich, M. ; Keinan, A. ; Lacroute, P. ; Ma, X. ; Reynolds, A. ; Clarke, L. ; Cunningham, F. ; Herrero, J. ; Keenen, S. ; Kulesha, E. ; Leinonen, R. ; McLaren, W. M. ; Radhakrishnan, R. ; Smith, R. E. ; Zalunin, V. ; Zheng-Bradley, X. ; Korbel, J. O. ; Stütz, A. M. ; Bauer, M. ; Cheetham, R. K. ; Cox, T. ; Eberle, M. ; James, T. ; Kahn, S. ; Murray, L. ; Fu, Y. ; Hyland, F. C. ; Manning, J. M. ; McLaughlin, S. F. ; Peckham, H. E. ; Sakarya, O. ; Sun, Y. A. ; Tsung, E. F. ; Batzer, M. A. ; Konkel, M. K. ; Walker, J. A. ; Albrecht, M. W. ; Amstislavskiy, V. S. ; Herwig, R. ; Parkhomchuk, D. V. ; Agarwala, R. ; Khouri, H. M. ; Morgulis, A. O. ; Paschall, J. E. ; Phan, L. D. ; Rotmistrovsky, K. E. ; Sanders, R. D. ; Shumway, M. F. ; Xiao, C. ; Auton, A. ; Iqbal, Z. ; Lunter, G. ; Marchini, J. L. ; Moutsianas, L. ; Myers, S. ; Tumian, A. ; Knight, J. ; Winer, R. ; Craig, D. W. ; Beckstrom-Sternberg, S. M. ; Christoforides, A. ; Kurdoglu, A. A. ; Pearson, J. V. ; Sinari, S. A. ; Tembe, W. D. ; Haussler, D. ; Hinrichs, A. S. ; Katzman, S. J. ; Kern, A. ; Kuhn, R. M. ; Przeworski, M. ; Hernandez, R. D. ; Howie, B. ; Kelley, J. L. ; Melton, S. C. ; Anderson, P. ; Blackwell, T. ; Chen, W. ; Cookson, W. O. ; Ding, J. ; Kang, H. M. ; Lathrop, M. ; Liang, L. ; Moffatt, M. F. ; Scheet, P. ; Sidore, C. ; Snyder, M. ; Zhan, X. ; Zöllner, S. ; Awadalla, P. ; Casals, F. ; Idaghdour, Y. ; Keebler, J. ; Stone, E. A. ; Zilversmit, M. ; Jorde, L. ; Xing, J. ; Aksay, G. ; Hajirasouliha, I. ; Hormozdiari, F. ; Kidd, J. M. ; Sahinalp, S. C. ; Chen, K. ; Chinwalla, A. ; Ding, L. ; Koboldt, D. C. ; McLellan, M. D. ; Wallis, J. W. ; Wendl, M. C. ; Zhang, Q. ; Albers, C. A. ; Ayub, Q. ; Balasubramaniam, S. ; Barrett, J. C. ; Chen, Y. ; Conrad, D. F. ; Danecek, P. ; Dermitzakis, E. T. ; Hu, M. ; Huang, N. ; Hurles, M. E. ; Jin, H. ; Jostins, L. ; Keane, T. M. ; Le, S. Q. ; Lindsay, S. ; Long, Q. ; MacArthur, D. G. ; Montgomery, S. B. ; Parts, L. ; Tyler-Smith, C. ; Walter, K. ; Zhang, Y. ; Gerstein, M. B. ; Abyzov, A. ; Balasubramanian, S. ; Bjornson, R. ; Du, J. ; Grubert, F. ; Habegger, L. ; Haraksingh, R. ; Jee, J. ; Khurana, E. ; Lam, H. Y. ; Leng, J. ; Mu, X. J. ; Urban, A. E. ; Zhang, Z. ; Coafra, C. ; Dinh, H. ; Kovar, C. ; Lee, S. ; Nazareth, L. ; Wilkinson, J. ; Scott, C. ; Gharani, N. ; Kaye, J. S. ; Kent, A. ; Li, T. ; McGuire, A. L. ; Ossorio, P. N. ; Rotimi, C. N. ; Su, Y. ; Toji, L. H. ; Brooks, L. D. ; Felsenfeld, A. L. ; McEwen, J. E. ; Abdallah, A. ; Juenger, C. R. ; Clemm, N. C. ; Duncanson, A. ; Green, E. D. ; Guyer, M. S. ; Peterson, J. L. / Diversity of human copy number variation and multicopy genes. In: Science. 2010 ; Vol. 330, No. 6004. pp. 641-646.
@article{24cbc349ce404278a361e1be3d2b3c90,
title = "Diversity of human copy number variation and multicopy genes",
abstract = "Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million {"}singly unique nucleotide{"} positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ∼1000 genes accessible to genetic studies of disease association.",
author = "Sudmant, {Peter H.} and Kitzman, {Jacob O.} and Francesca Antonacci and Can Alkan and Maika Malig and Anya Tsalenko and Nick Sampas and Laurakay Bruhn and Jay Shendure and Eichler, {Evan E.} and Altshuler, {D. L.} and Durbin, {R. M.} and Abecasis, {G. R.} and Bentley, {D. R.} and A. Chakravarti and Clark, {A. G.} and Collins, {F. S.} and {De La Vega}, {F. M.} and P. Donnelly and M. Egholm and P. Flicek and Gabriel, {S. B.} and Gibbs, {R. A.} and Knoppers, {B. M.} and Lander, {E. S.} and H. Lehrach and Mardis, {E. R.} and McVean, {G. A.} and Nickerson, {D. A.} and L. Peltonen and Schafer, {A. J.} and Sherry, {S. T.} and J. Wang and Wilson, {R. K.} and D. Deiros and M. Metzker and D. Muzny and J. Reid and D. Wheeler and J. Li and M. Jian and G. Li and R. Li and H. Liang and G. Tian and B. Wang and W. Wang and H. Yang and X. Zhang and H. Zheng and L. Ambrogio and T. Bloom and K. Cibulskis and Fennell, {T. J.} and Jaffe, {D. B.} and E. Shefler and Sougnez, {C. L.} and N. Gormley and S. Humphray and Z. Kingsbury and P. Koko-Gonzales and J. Stone and McKernan, {K. J.} and Costa, {G. L.} and Ichikawa, {J. K.} and Lee, {C. C.} and R. Sudbrak and Borodina, {T. A.} and A. Dahl and Davydov, {A. N.} and P. Marquardt and F. Mertes and W. Nietfeld and P. Rosenstiel and S. Schreiber and Soldatov, {A. V.} and B. Timmermann and M. Tolzmann and J. Affourtit and D. Ashworth and S. Attiya and M. Bachorski and E. Buglione and A. Burke and A. Caprio and C. Celone and S. Clark and D. Conners and B. Desany and L. Gu and L. Guccione and K. Kao and A. Kebbel and J. Knowlton and M. Labrecque and L. McDade and C. Mealmaker and M. Minderman and A. Nawrocki and F. Niazi and K. Pareja and R. Ramenani and D. Riches and W. Song and C. Turcotte and S. Wang and D. Dooling and L. Fulton and R. Fulton and G. Weinstock and J. Burton and Carter, {D. M.} and C. Churcher and A. Coffey and A. Cox and A. Palotie and M. Quail and T. Skelly and J. Stalker and Swerdlow, {H. P.} and D. Turner and {De Witte}, A. and S. Giles and M. Bainbridge and D. Challis and A. Sabo and F. Yu and J. Yu and X. Fang and X. Guo and Y. Li and R. Luo and S. Tai and H. Wu and X. Zheng and Y. Zhou and Marth, {G. T.} and Garrison, {E. P.} and W. Huang and A. Indap and D. Kural and Lee, {W. P.} and Leong, {W. F.} and Quinlan, {A. R.} and C. Stewart and Stromberg, {M. P.} and Ward, {A. N.} and J. Wu and C. Lee and Mills, {R. E.} and X. Shi and Daly, {M. J.} and DePristo, {M. A.} and Ball, {A. D.} and E. Banks and Browning, {B. L.} and Garimella, {K. V.} and Grossman, {S. R.} and Handsaker, {R. E.} and M. Hanna and C. Hartl and Kernytsky, {A. M.} and Korn, {J. M.} and H. Li and Maguire, {J. R.} and McCarroll, {S. A.} and A. McKenna and Nemesh, {J. C.} and Philippakis, {A. A.} and Poplin, {R. E.} and A. Price and Rivas, {M. A.} and Sabeti, {P. C.} and Schaffner, {S. F.} and Shlyakhter, {I. A.} and Cooper, {D. N.} and Ball, {E. V.} and M. Mort and Phillips, {A. D.} and Stenson, {P. D.} and J. Sebat and V. Makarov and K. Ye and Yoon, {S. C.} and Bustamante, {C. D.} and A. Boyko and J. Degenhardt and S. Gravel and Gutenkunst, {Ryan N} and M. Kaganovich and A. Keinan and P. Lacroute and X. Ma and A. Reynolds and L. Clarke and F. Cunningham and J. Herrero and S. Keenen and E. Kulesha and R. Leinonen and McLaren, {W. M.} and R. Radhakrishnan and Smith, {R. E.} and V. Zalunin and X. Zheng-Bradley and Korbel, {J. O.} and St{\"u}tz, {A. M.} and M. Bauer and Cheetham, {R. K.} and T. Cox and M. Eberle and T. James and S. Kahn and L. Murray and Y. Fu and Hyland, {F. C.} and Manning, {J. M.} and McLaughlin, {S. F.} and Peckham, {H. E.} and O. Sakarya and Sun, {Y. A.} and Tsung, {E. F.} and Batzer, {M. A.} and Konkel, {M. K.} and Walker, {J. A.} and Albrecht, {M. W.} and Amstislavskiy, {V. S.} and R. Herwig and Parkhomchuk, {D. V.} and R. Agarwala and Khouri, {H. M.} and Morgulis, {A. O.} and Paschall, {J. E.} and Phan, {L. D.} and Rotmistrovsky, {K. E.} and Sanders, {R. D.} and Shumway, {M. F.} and C. Xiao and A. Auton and Z. Iqbal and G. Lunter and Marchini, {J. L.} and L. Moutsianas and S. Myers and A. Tumian and J. Knight and R. Winer and Craig, {D. W.} and Beckstrom-Sternberg, {S. M.} and A. Christoforides and Kurdoglu, {A. A.} and Pearson, {J. V.} and Sinari, {S. A.} and Tembe, {W. D.} and D. Haussler and Hinrichs, {A. S.} and Katzman, {S. J.} and A. Kern and Kuhn, {R. M.} and M. Przeworski and Hernandez, {R. D.} and B. Howie and Kelley, {J. L.} and Melton, {S. C.} and P. Anderson and T. Blackwell and W. Chen and Cookson, {W. O.} and J. Ding and Kang, {H. M.} and M. Lathrop and L. Liang and Moffatt, {M. F.} and P. Scheet and C. Sidore and M. Snyder and X. Zhan and S. Z{\"o}llner and P. Awadalla and F. Casals and Y. Idaghdour and J. Keebler and Stone, {E. A.} and M. Zilversmit and L. Jorde and J. Xing and G. Aksay and I. Hajirasouliha and F. Hormozdiari and Kidd, {J. M.} and Sahinalp, {S. C.} and K. Chen and A. Chinwalla and L. Ding and Koboldt, {D. C.} and McLellan, {M. D.} and Wallis, {J. W.} and Wendl, {M. C.} and Q. Zhang and Albers, {C. A.} and Q. Ayub and S. Balasubramaniam and Barrett, {J. C.} and Y. Chen and Conrad, {D. F.} and P. Danecek and Dermitzakis, {E. T.} and M. Hu and N. Huang and Hurles, {M. E.} and H. Jin and L. Jostins and Keane, {T. M.} and Le, {S. Q.} and S. Lindsay and Q. Long and MacArthur, {D. G.} and Montgomery, {S. B.} and L. Parts and C. Tyler-Smith and K. Walter and Y. Zhang and Gerstein, {M. B.} and A. Abyzov and S. Balasubramanian and R. Bjornson and J. Du and F. Grubert and L. Habegger and R. Haraksingh and J. Jee and E. Khurana and Lam, {H. Y.} and J. Leng and Mu, {X. J.} and Urban, {A. E.} and Z. Zhang and C. Coafra and H. Dinh and C. Kovar and S. Lee and L. Nazareth and J. Wilkinson and C. Scott and N. Gharani and Kaye, {J. S.} and A. Kent and T. Li and McGuire, {A. L.} and Ossorio, {P. N.} and Rotimi, {C. N.} and Y. Su and Toji, {L. H.} and Brooks, {L. D.} and Felsenfeld, {A. L.} and McEwen, {J. E.} and A. Abdallah and Juenger, {C. R.} and Clemm, {N. C.} and A. Duncanson and Green, {E. D.} and Guyer, {M. S.} and Peterson, {J. L.}",
year = "2010",
month = "10",
day = "29",
doi = "10.1126/science.1197005",
language = "English (US)",
volume = "330",
pages = "641--646",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6004",

}

TY - JOUR

T1 - Diversity of human copy number variation and multicopy genes

AU - Sudmant, Peter H.

AU - Kitzman, Jacob O.

AU - Antonacci, Francesca

AU - Alkan, Can

AU - Malig, Maika

AU - Tsalenko, Anya

AU - Sampas, Nick

AU - Bruhn, Laurakay

AU - Shendure, Jay

AU - Eichler, Evan E.

AU - Altshuler, D. L.

AU - Durbin, R. M.

AU - Abecasis, G. R.

AU - Bentley, D. R.

AU - Chakravarti, A.

AU - Clark, A. G.

AU - Collins, F. S.

AU - De La Vega, F. M.

AU - Donnelly, P.

AU - Egholm, M.

AU - Flicek, P.

AU - Gabriel, S. B.

AU - Gibbs, R. A.

AU - Knoppers, B. M.

AU - Lander, E. S.

AU - Lehrach, H.

AU - Mardis, E. R.

AU - McVean, G. A.

AU - Nickerson, D. A.

AU - Peltonen, L.

AU - Schafer, A. J.

AU - Sherry, S. T.

AU - Wang, J.

AU - Wilson, R. K.

AU - Deiros, D.

AU - Metzker, M.

AU - Muzny, D.

AU - Reid, J.

AU - Wheeler, D.

AU - Li, J.

AU - Jian, M.

AU - Li, G.

AU - Li, R.

AU - Liang, H.

AU - Tian, G.

AU - Wang, B.

AU - Wang, W.

AU - Yang, H.

AU - Zhang, X.

AU - Zheng, H.

AU - Ambrogio, L.

AU - Bloom, T.

AU - Cibulskis, K.

AU - Fennell, T. J.

AU - Jaffe, D. B.

AU - Shefler, E.

AU - Sougnez, C. L.

AU - Gormley, N.

AU - Humphray, S.

AU - Kingsbury, Z.

AU - Koko-Gonzales, P.

AU - Stone, J.

AU - McKernan, K. J.

AU - Costa, G. L.

AU - Ichikawa, J. K.

AU - Lee, C. C.

AU - Sudbrak, R.

AU - Borodina, T. A.

AU - Dahl, A.

AU - Davydov, A. N.

AU - Marquardt, P.

AU - Mertes, F.

AU - Nietfeld, W.

AU - Rosenstiel, P.

AU - Schreiber, S.

AU - Soldatov, A. V.

AU - Timmermann, B.

AU - Tolzmann, M.

AU - Affourtit, J.

AU - Ashworth, D.

AU - Attiya, S.

AU - Bachorski, M.

AU - Buglione, E.

AU - Burke, A.

AU - Caprio, A.

AU - Celone, C.

AU - Clark, S.

AU - Conners, D.

AU - Desany, B.

AU - Gu, L.

AU - Guccione, L.

AU - Kao, K.

AU - Kebbel, A.

AU - Knowlton, J.

AU - Labrecque, M.

AU - McDade, L.

AU - Mealmaker, C.

AU - Minderman, M.

AU - Nawrocki, A.

AU - Niazi, F.

AU - Pareja, K.

AU - Ramenani, R.

AU - Riches, D.

AU - Song, W.

AU - Turcotte, C.

AU - Wang, S.

AU - Dooling, D.

AU - Fulton, L.

AU - Fulton, R.

AU - Weinstock, G.

AU - Burton, J.

AU - Carter, D. M.

AU - Churcher, C.

AU - Coffey, A.

AU - Cox, A.

AU - Palotie, A.

AU - Quail, M.

AU - Skelly, T.

AU - Stalker, J.

AU - Swerdlow, H. P.

AU - Turner, D.

AU - De Witte, A.

AU - Giles, S.

AU - Bainbridge, M.

AU - Challis, D.

AU - Sabo, A.

AU - Yu, F.

AU - Yu, J.

AU - Fang, X.

AU - Guo, X.

AU - Li, Y.

AU - Luo, R.

AU - Tai, S.

AU - Wu, H.

AU - Zheng, X.

AU - Zhou, Y.

AU - Marth, G. T.

AU - Garrison, E. P.

AU - Huang, W.

AU - Indap, A.

AU - Kural, D.

AU - Lee, W. P.

AU - Leong, W. F.

AU - Quinlan, A. R.

AU - Stewart, C.

AU - Stromberg, M. P.

AU - Ward, A. N.

AU - Wu, J.

AU - Lee, C.

AU - Mills, R. E.

AU - Shi, X.

AU - Daly, M. J.

AU - DePristo, M. A.

AU - Ball, A. D.

AU - Banks, E.

AU - Browning, B. L.

AU - Garimella, K. V.

AU - Grossman, S. R.

AU - Handsaker, R. E.

AU - Hanna, M.

AU - Hartl, C.

AU - Kernytsky, A. M.

AU - Korn, J. M.

AU - Li, H.

AU - Maguire, J. R.

AU - McCarroll, S. A.

AU - McKenna, A.

AU - Nemesh, J. C.

AU - Philippakis, A. A.

AU - Poplin, R. E.

AU - Price, A.

AU - Rivas, M. A.

AU - Sabeti, P. C.

AU - Schaffner, S. F.

AU - Shlyakhter, I. A.

AU - Cooper, D. N.

AU - Ball, E. V.

AU - Mort, M.

AU - Phillips, A. D.

AU - Stenson, P. D.

AU - Sebat, J.

AU - Makarov, V.

AU - Ye, K.

AU - Yoon, S. C.

AU - Bustamante, C. D.

AU - Boyko, A.

AU - Degenhardt, J.

AU - Gravel, S.

AU - Gutenkunst, Ryan N

AU - Kaganovich, M.

AU - Keinan, A.

AU - Lacroute, P.

AU - Ma, X.

AU - Reynolds, A.

AU - Clarke, L.

AU - Cunningham, F.

AU - Herrero, J.

AU - Keenen, S.

AU - Kulesha, E.

AU - Leinonen, R.

AU - McLaren, W. M.

AU - Radhakrishnan, R.

AU - Smith, R. E.

AU - Zalunin, V.

AU - Zheng-Bradley, X.

AU - Korbel, J. O.

AU - Stütz, A. M.

AU - Bauer, M.

AU - Cheetham, R. K.

AU - Cox, T.

AU - Eberle, M.

AU - James, T.

AU - Kahn, S.

AU - Murray, L.

AU - Fu, Y.

AU - Hyland, F. C.

AU - Manning, J. M.

AU - McLaughlin, S. F.

AU - Peckham, H. E.

AU - Sakarya, O.

AU - Sun, Y. A.

AU - Tsung, E. F.

AU - Batzer, M. A.

AU - Konkel, M. K.

AU - Walker, J. A.

AU - Albrecht, M. W.

AU - Amstislavskiy, V. S.

AU - Herwig, R.

AU - Parkhomchuk, D. V.

AU - Agarwala, R.

AU - Khouri, H. M.

AU - Morgulis, A. O.

AU - Paschall, J. E.

AU - Phan, L. D.

AU - Rotmistrovsky, K. E.

AU - Sanders, R. D.

AU - Shumway, M. F.

AU - Xiao, C.

AU - Auton, A.

AU - Iqbal, Z.

AU - Lunter, G.

AU - Marchini, J. L.

AU - Moutsianas, L.

AU - Myers, S.

AU - Tumian, A.

AU - Knight, J.

AU - Winer, R.

AU - Craig, D. W.

AU - Beckstrom-Sternberg, S. M.

AU - Christoforides, A.

AU - Kurdoglu, A. A.

AU - Pearson, J. V.

AU - Sinari, S. A.

AU - Tembe, W. D.

AU - Haussler, D.

AU - Hinrichs, A. S.

AU - Katzman, S. J.

AU - Kern, A.

AU - Kuhn, R. M.

AU - Przeworski, M.

AU - Hernandez, R. D.

AU - Howie, B.

AU - Kelley, J. L.

AU - Melton, S. C.

AU - Anderson, P.

AU - Blackwell, T.

AU - Chen, W.

AU - Cookson, W. O.

AU - Ding, J.

AU - Kang, H. M.

AU - Lathrop, M.

AU - Liang, L.

AU - Moffatt, M. F.

AU - Scheet, P.

AU - Sidore, C.

AU - Snyder, M.

AU - Zhan, X.

AU - Zöllner, S.

AU - Awadalla, P.

AU - Casals, F.

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PY - 2010/10/29

Y1 - 2010/10/29

N2 - Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ∼1000 genes accessible to genetic studies of disease association.

AB - Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ∼1000 genes accessible to genetic studies of disease association.

UR - http://www.scopus.com/inward/record.url?scp=78049412267&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78049412267&partnerID=8YFLogxK

U2 - 10.1126/science.1197005

DO - 10.1126/science.1197005

M3 - Article

C2 - 21030649

AN - SCOPUS:78049412267

VL - 330

SP - 641

EP - 646

JO - Science

JF - Science

SN - 0036-8075

IS - 6004

ER -