A map of human genome variation from population-scale sequencing

David L. Altshuler, Richard M. Durbin, Gonçalo R. Abecasis, David R. Bentley, Aravinda Chakravarti, Andrew G. Clark, Francis S. Collins, Francisco M. De La Vega, Peter Donnelly, Michael Egholm, Paul Flicek, Stacey B. Gabriel, Richard A. Gibbs, Bartha M. Knoppers, Eric S. Lander, Hans Lehrach, Elaine R. Mardis, Gil A. McVean, Debbie A. Nickerson, Leena PeltonenAlan J. Schafer, Stephen T. Sherry, Jun Wang, Richard K. Wilson, David Deiros, Mike Metzker, Donna Muzny, Jeff Reid, David Wheeler, Shenzhen Jun Wang, Jingxiang Li, Min Jian, Guoqing Li, Ruiqiang Li, Huiqing Liang, Geng Tian, Bo Wang, Jian Wang, Wei Wang, Huanming Yang, Xiuqing Zhang, Huisong Zheng, Lauren Ambrogio, Toby Bloom, Kristian Cibulskis, Tim J. Fennell, David B. Jaffe, Erica Shefler, Carrie L. Sougnez, Illumina David R. Bentley, Niall Gormley, Sean Humphray, Zoya Kingsbury, Paula Koko-Gonzales, Jennifer Stone, Kevin J. Mc Kernan, Gina L. Costa, Jeffry K. Ichikawa, Clarence C. Lee, Ralf Sudbrak, Tatiana A. Borodina, Andreas Dahl, Alexey N. Davydov, Peter Marquardt, Florian Mertes, Wilfiried Nietfeld, Philip Rosenstiel, Stefan Schreiber, Aleksey V. Soldatov, Bernd Timmermann, Marius Tolzmann, Jason Affourtit, Dana Ashworth, Said Attiya, Melissa Bachorski, Eli Buglione, Adam Burke, Amanda Caprio, Christopher Celone, Shauna Clark, David Conners, Brian Desany, Lisa Gu, Lorri Guccione, Kalvin Kao, Andrew Kebbel, Jennifer Knowlton, Matthew Labrecque, Louise McDade, Craig Mealmaker, Melissa Minderman, Anne Nawrocki, Faheem Niazi, Kristen Pareja, Ravi Ramenani, David Riches, Wanmin Song, Cynthia Turcotte, Shally Wang, David Dooling, Lucinda Fulton, Robert Fulton, George Weinstock, John Burton, David M. Carter, Carol Churcher, Alison Coffey, Anthony Cox, Aarno Palotie, Michael Quail, Tom Skelly, James Stalker, Harold P. Swerdlow, Daniel Turner, Anniek De Witte, Shane Giles, Matthew Bainbridge, Danny Challis, Aniko Sabo, Fuli Yu, Jin Yu, Xiaodong Fang, Xiaosen Guo, Yingrui Li, Ruibang Luo, Shuaishuai Tai, Honglong Wu, Hancheng Zheng, Xiaole Zheng, Yan Zhou, Gabor T. Marth, Erik P. Garrison, Weichun Huang, Amit Indap, Deniz Kural, Wan Ping Lee, Wen Fung Leong, Aaron R. Quinlan, Chip Stewart, Michael P. Stromberg, Alistair N. Ward, Jiantao Wu, Charles Lee, Ryan E. Mills, Xinghua Shi, Mark J. Daly, Mark A. DePristo, Aaron D. Ball, Eric Banks, Brian L. Browning, Kiran V. Garimella, Sharon R. Grossman, Robert E. Handsaker, Matt Hanna, Chris Hartl, Andrew M. Kernytsky, Joshua M. Korn, Heng Li, Jared R. Maguire, Aaron McKenna, James C. Nemesh, Anthony A. Philippakis, Ryan E. Poplin, Alkes Price, Manuel A. Rivas, Pardis C. Sabeti, Stephen F. Schaffner, Ilya A. Shlyakhter, David N. Cooper, Edward V. Ball, Matthew Mort, Andrew D. Phillips, Peter D. Stenson, Jonathan Sebat, Vladimir Makarov, Kenny Ye, Seungtai C. Yoon, Carlos D. Bustamante, Adam Boyko, Jeremiah Degenhardt, Simon Gravel, Ryan N. Gutenkunst, Mark Kaganovich, Alon Keinan, Phil Lacroute, Xin Ma, Andy Reynolds, Laura Clarke, Fiona Cunningham, Javier Herrero, Stephen Keenen, Eugene Kulesha, Rasko Leinonen, William M. McLaren, Rajesh Radhakrishnan, Richard E. Smith, Vadim Zalunin, Jan O. Korbel, Adrian M. Stütz, Illumina Sean Humphray, Markus Bauer, R. Keira Cheetham, Tony Cox, Michael Eberle, Terena James, Scott Kahn, Lisa Murray, Kai Ye, Yutao Fu, Fiona C.L. Hyland, Jonathan M. Manning, F. McLaughlin Stephen, Heather E. Peckham, Onur Sakarya, Yongming A. Sun, Eric F. Tsung, A. Batzer Mark, Miriam K. Konkel, Jerilyn A. Walker, Marcus W. Albrecht, Vyacheslav S. Amstislavskiy, Ralf Herwig, Dimitri V. Parkhomchuk, Richa Agarwala, Hoda M. Khouri, Aleksandr O. Morgulis, Justin E. Paschall, Lon D. Phan, Kirill E. Rotmistrovsky, Robert D. Sanders, Martin F. Shumway, Chunlin Xiao, A. McVean Gil, Adam Auton, Zamin Iqbal, Gerton Lunter, Jonathan L. Marchini, Loukas Moutsianas, Simon Myers, Afidalina Tumian, James Knight, Roger Winer, David W. Craig, Steve M. Beckstrom-Sternberg, Alexis Christoforides, Ahmet A. Kurdoglu, John V. Pearson, Shripad A. Sinari, Waibhav D. Tembe, David Haussler, Angie S. Hinrichs, Sol J. Katzman, Andrew Kern, Robert M. Kuhn, Molly Przeworski, Ryan D. Hernandez, Bryan Howie, Joanna L. Kelley, S. Cord Melton, Yun Li, Paul Anderson, Tom Blackwell, Wei Chen, William O. Cookson, Jun Ding, Hyun Min Kang, Mark Lathrop, Liming Liang, Miriam F. Moffatt, Paul Scheet, Carlo Sidore, Matthew Snyder, Xiaowei Zhan, Sebastian Zöllner, Philip Awadalla, Ferran Casals, Youssef Idaghdour, John Keebler, Eric A. Stone, Martine Zilversmit, Lynn Jorde, Jinchuan Xing, Evan E. Eichler, Gozde Aksay, Can Alkan, Iman Hajirasouliha, Fereydoun Hormozdiari, Jeffrey M. Kidd, S. CenkSahinalp, Peter H. Sudmant, Ken Chen, Asif Chinwalla, Li Ding, Daniel C. Koboldt, Mike D. McLellan, John W. Wallis, Michael C. Wendl, Qunyuan Zhang, Cornelis A. Albers, Qasim Ayub, Senduran Balasubramaniam, Jeffrey C. Barrett, Yuan Chen, Don Conrad, Petr Danecek, Emmanouil T. Dermitzakis, Min Hu, Ni Huang, E. Hurles Matt, Hanjun Jin, Luke Jostins, Thomas M. Keane, Si Quang Le, Sarah Lindsay, Quan Long, Daniel G. MacArthur, Stephen B. Montgomery, Leopold Parts, Tyler-Smith Chris Tyler-Smith, Klaudia Walter, Yujun Zhang, Mark B. Gerstein, Michael Snyder, Alexej Abyzov, Suganthi Balasubramanian, Robert Bjornson, Fabian Grubert, Lukas Habegger, Rajini Haraksingh, Ekta Khurana, Hugo Y.K. Lam, Jing Leng, Xinmeng Jasmine Mu, Alexander E. Urban, Zhengdong Zhang, Steven A. McCarroll, Xiangqun Zheng-Bradley, Mark A. Batzer, Matt E. Hurles, Jiang Du, Justin Jee, Cristian Coafra, Huyen Dinh, Christie Kovar, Sandy Lee, Lynne Nazareth, Jane Wilkinson, Allison Coffey, Carol Scott, Chris Tyler-Smith, Neda Gharani, Jane S. Kaye, Alastair Kent, Taosha Li, Amy L. McGuire, Pilar N. Ossorio, Charles N. Rotimi, Yeyang Su, Lorraine H. Toji, Adam L. Felsenfeld, Jean E. McEwen, Assya Abdallah, Christopher R. Juenger, Nicholas C. Clemm, Audrey Duncanson, Eric D. Green, Mark S. Guyer, Jane L. Peterson

Research output: Contribution to journalArticle

4984 Citations (Scopus)

Abstract

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10 g -8 per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.

Original languageEnglish (US)
Pages (from-to)1061-1073
Number of pages13
JournalNature
Volume467
Issue number7319
DOIs
StatePublished - Oct 28 2010
Externally publishedYes

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Human Genome
Genome
Population
Genetic Research
Genetic Selection
Medical Genetics
Gene Frequency
Fathers
Base Pairing
Haplotypes
Genes
Single Nucleotide Polymorphism
Exons
Genotype
Mothers
Phenotype
Mutation

ASJC Scopus subject areas

  • General

Cite this

Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., ... Peterson, J. L. (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061-1073. https://doi.org/10.1038/nature09534

A map of human genome variation from population-scale sequencing. / Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Shenzhen Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, Illumina David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; Mc Kernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Fang, Xiaodong; Guo, Xiaosen; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Korbel, Jan O.; Stütz, Adrian M.; Humphray, Illumina Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Ye, Kai; Fu, Yutao; Hyland, Fiona C.L.; Manning, Jonathan M.; Stephen, F. McLaughlin; Peckham, Heather E.; Sakarya, Onur; Sun, Yongming A.; Tsung, Eric F.; Mark, A. Batzer; Konkel, Miriam K.; Walker, Jerilyn A.; Albrecht, Marcus W.; Amstislavskiy, Vyacheslav S.; Herwig, Ralf; Parkhomchuk, Dimitri V.; Agarwala, Richa; Khouri, Hoda M.; Morgulis, Aleksandr O.; Paschall, Justin E.; Phan, Lon D.; Rotmistrovsky, Kirill E.; Sanders, Robert D.; Shumway, Martin F.; Xiao, Chunlin; Gil, A. McVean; Auton, Adam; Iqbal, Zamin; Lunter, Gerton; Marchini, Jonathan L.; Moutsianas, Loukas; Myers, Simon; Tumian, Afidalina; Knight, James; Winer, Roger; Craig, David W.; Beckstrom-Sternberg, Steve M.; Christoforides, Alexis; Kurdoglu, Ahmet A.; Pearson, John V.; Sinari, Shripad A.; Tembe, Waibhav D.; Haussler, David; Hinrichs, Angie S.; Katzman, Sol J.; Kern, Andrew; Kuhn, Robert M.; Przeworski, Molly; Hernandez, Ryan D.; Howie, Bryan; Kelley, Joanna L.; Melton, S. Cord; Li, Yun; Anderson, Paul; Blackwell, Tom; Chen, Wei; Cookson, William O.; Ding, Jun; Kang, Hyun Min; Lathrop, Mark; Liang, Liming; Moffatt, Miriam F.; Scheet, Paul; Sidore, Carlo; Snyder, Matthew; Zhan, Xiaowei; Zöllner, Sebastian; Awadalla, Philip; Casals, Ferran; Idaghdour, Youssef; Keebler, John; Stone, Eric A.; Zilversmit, Martine; Jorde, Lynn; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; CenkSahinalp, S.; Sudmant, Peter H.; Chen, Ken; Chinwalla, Asif; Ding, Li; Koboldt, Daniel C.; McLellan, Mike D.; Wallis, John W.; Wendl, Michael C.; Zhang, Qunyuan; Albers, Cornelis A.; Ayub, Qasim; Balasubramaniam, Senduran; Barrett, Jeffrey C.; Chen, Yuan; Conrad, Don; Danecek, Petr; Dermitzakis, Emmanouil T.; Hu, Min; Huang, Ni; Matt, E. Hurles; Jin, Hanjun; Jostins, Luke; Keane, Thomas M.; Quang Le, Si; Lindsay, Sarah; Long, Quan; MacArthur, Daniel G.; Montgomery, Stephen B.; Parts, Leopold; Chris Tyler-Smith, Tyler-Smith; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Balasubramanian, Suganthi; Bjornson, Robert; Grubert, Fabian; Habegger, Lukas; Haraksingh, Rajini; Khurana, Ekta; Lam, Hugo Y.K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; McCarroll, Steven A.; Zheng-Bradley, Xiangqun; Batzer, Mark A.; Hurles, Matt E.; Du, Jiang; Jee, Justin; Coafra, Cristian; Dinh, Huyen; Kovar, Christie; Lee, Sandy; Nazareth, Lynne; Wilkinson, Jane; Coffey, Allison; Scott, Carol; Tyler-Smith, Chris; Gharani, Neda; Kaye, Jane S.; Kent, Alastair; Li, Taosha; McGuire, Amy L.; Ossorio, Pilar N.; Rotimi, Charles N.; Su, Yeyang; Toji, Lorraine H.; Felsenfeld, Adam L.; McEwen, Jean E.; Abdallah, Assya; Juenger, Christopher R.; Clemm, Nicholas C.; Duncanson, Audrey; Green, Eric D.; Guyer, Mark S.; Peterson, Jane L.

In: Nature, Vol. 467, No. 7319, 28.10.2010, p. 1061-1073.

Research output: Contribution to journalArticle

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, Wang, SJ, Li, J, Jian, M, Li, G, Li, R, Liang, H, Tian, G, Wang, B, Wang, J, Wang, W, Yang, H, Zhang, X, Zheng, H, Ambrogio, L, Bloom, T, Cibulskis, K, Fennell, TJ, Jaffe, DB, Shefler, E, Sougnez, CL, Bentley, IDR, Gormley, N, Humphray, S, Kingsbury, Z, Koko-Gonzales, P, Stone, J, Mc Kernan, 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, 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, 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, Korbel, JO, Stütz, AM, Humphray, IS, Bauer, M, Cheetham, RK, Cox, T, Eberle, M, James, T, Kahn, S, Murray, L, Ye, K, Fu, Y, Hyland, FCL, Manning, JM, Stephen, FM, Peckham, HE, Sakarya, O, Sun, YA, Tsung, EF, Mark, AB, 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, Gil, AM, 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, Li, Y, 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, Eichler, EE, Aksay, G, Alkan, C, Hajirasouliha, I, Hormozdiari, F, Kidd, JM, CenkSahinalp, S, Sudmant, PH, 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, D, Danecek, P, Dermitzakis, ET, Hu, M, Huang, N, Matt, EH, Jin, H, Jostins, L, Keane, TM, Quang Le, S, Lindsay, S, Long, Q, MacArthur, DG, Montgomery, SB, Parts, L, Chris Tyler-Smith, T-S, Walter, K, Zhang, Y, Gerstein, MB, Snyder, M, Abyzov, A, Balasubramanian, S, Bjornson, R, Grubert, F, Habegger, L, Haraksingh, R, Khurana, E, Lam, HYK, Leng, J, Mu, XJ, Urban, AE, Zhang, Z, McCarroll, SA, Zheng-Bradley, X, Batzer, MA, Hurles, ME, Du, J, Jee, J, Coafra, C, Dinh, H, Kovar, C, Lee, S, Nazareth, L, Wilkinson, J, Coffey, A, Scott, C, Tyler-Smith, C, Gharani, N, Kaye, JS, Kent, A, Li, T, McGuire, AL, Ossorio, PN, Rotimi, CN, Su, Y, Toji, LH, Felsenfeld, AL, McEwen, JE, Abdallah, A, Juenger, CR, Clemm, NC, Duncanson, A, Green, ED, Guyer, MS & Peterson, JL 2010, 'A map of human genome variation from population-scale sequencing', Nature, vol. 467, no. 7319, pp. 1061-1073. https://doi.org/10.1038/nature09534
Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG et al. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-1073. https://doi.org/10.1038/nature09534
Altshuler, David L. ; Durbin, Richard M. ; Abecasis, Gonçalo R. ; Bentley, David R. ; Chakravarti, Aravinda ; Clark, Andrew G. ; Collins, Francis S. ; De La Vega, Francisco M. ; Donnelly, Peter ; Egholm, Michael ; Flicek, Paul ; Gabriel, Stacey B. ; Gibbs, Richard A. ; Knoppers, Bartha M. ; Lander, Eric S. ; Lehrach, Hans ; Mardis, Elaine R. ; McVean, Gil A. ; Nickerson, Debbie A. ; Peltonen, Leena ; Schafer, Alan J. ; Sherry, Stephen T. ; Wang, Jun ; Wilson, Richard K. ; Deiros, David ; Metzker, Mike ; Muzny, Donna ; Reid, Jeff ; Wheeler, David ; Wang, Shenzhen Jun ; Li, Jingxiang ; Jian, Min ; Li, Guoqing ; Li, Ruiqiang ; Liang, Huiqing ; Tian, Geng ; Wang, Bo ; Wang, Jian ; Wang, Wei ; Yang, Huanming ; Zhang, Xiuqing ; Zheng, Huisong ; Ambrogio, Lauren ; Bloom, Toby ; Cibulskis, Kristian ; Fennell, Tim J. ; Jaffe, David B. ; Shefler, Erica ; Sougnez, Carrie L. ; Bentley, Illumina David R. ; Gormley, Niall ; Humphray, Sean ; Kingsbury, Zoya ; Koko-Gonzales, Paula ; Stone, Jennifer ; Mc Kernan, Kevin J. ; Costa, Gina L. ; Ichikawa, Jeffry K. ; Lee, Clarence C. ; Sudbrak, Ralf ; Borodina, Tatiana A. ; Dahl, Andreas ; Davydov, Alexey N. ; Marquardt, Peter ; Mertes, Florian ; Nietfeld, Wilfiried ; Rosenstiel, Philip ; Schreiber, Stefan ; Soldatov, Aleksey V. ; Timmermann, Bernd ; Tolzmann, Marius ; Affourtit, Jason ; Ashworth, Dana ; Attiya, Said ; Bachorski, Melissa ; Buglione, Eli ; Burke, Adam ; Caprio, Amanda ; Celone, Christopher ; Clark, Shauna ; Conners, David ; Desany, Brian ; Gu, Lisa ; Guccione, Lorri ; Kao, Kalvin ; Kebbel, Andrew ; Knowlton, Jennifer ; Labrecque, Matthew ; McDade, Louise ; Mealmaker, Craig ; Minderman, Melissa ; Nawrocki, Anne ; Niazi, Faheem ; Pareja, Kristen ; Ramenani, Ravi ; Riches, David ; Song, Wanmin ; Turcotte, Cynthia ; Wang, Shally ; Dooling, David ; Fulton, Lucinda ; Fulton, Robert ; Weinstock, George ; Burton, John ; Carter, David M. ; Churcher, Carol ; Coffey, Alison ; Cox, Anthony ; Palotie, Aarno ; Quail, Michael ; Skelly, Tom ; Stalker, James ; Swerdlow, Harold P. ; Turner, Daniel ; De Witte, Anniek ; Giles, Shane ; Bainbridge, Matthew ; Challis, Danny ; Sabo, Aniko ; Yu, Fuli ; Yu, Jin ; Fang, Xiaodong ; Guo, Xiaosen ; Li, Yingrui ; Luo, Ruibang ; Tai, Shuaishuai ; Wu, Honglong ; Zheng, Hancheng ; Zheng, Xiaole ; Zhou, Yan ; Marth, Gabor T. ; Garrison, Erik P. ; Huang, Weichun ; Indap, Amit ; Kural, Deniz ; Lee, Wan Ping ; Leong, Wen Fung ; Quinlan, Aaron R. ; Stewart, Chip ; Stromberg, Michael P. ; Ward, Alistair N. ; Wu, Jiantao ; Lee, Charles ; Mills, Ryan E. ; Shi, Xinghua ; Daly, Mark J. ; DePristo, Mark A. ; Ball, Aaron D. ; Banks, Eric ; Browning, Brian L. ; Garimella, Kiran V. ; Grossman, Sharon R. ; Handsaker, Robert E. ; Hanna, Matt ; Hartl, Chris ; Kernytsky, Andrew M. ; Korn, Joshua M. ; Li, Heng ; Maguire, Jared R. ; McKenna, Aaron ; Nemesh, James C. ; Philippakis, Anthony A. ; Poplin, Ryan E. ; Price, Alkes ; Rivas, Manuel A. ; Sabeti, Pardis C. ; Schaffner, Stephen F. ; Shlyakhter, Ilya A. ; Cooper, David N. ; Ball, Edward V. ; Mort, Matthew ; Phillips, Andrew D. ; Stenson, Peter D. ; Sebat, Jonathan ; Makarov, Vladimir ; Ye, Kenny ; Yoon, Seungtai C. ; Bustamante, Carlos D. ; Boyko, Adam ; Degenhardt, Jeremiah ; Gravel, Simon ; Gutenkunst, Ryan N. ; Kaganovich, Mark ; Keinan, Alon ; Lacroute, Phil ; Ma, Xin ; Reynolds, Andy ; Clarke, Laura ; Cunningham, Fiona ; Herrero, Javier ; Keenen, Stephen ; Kulesha, Eugene ; Leinonen, Rasko ; McLaren, William M. ; Radhakrishnan, Rajesh ; Smith, Richard E. ; Zalunin, Vadim ; Korbel, Jan O. ; Stütz, Adrian M. ; Humphray, Illumina Sean ; Bauer, Markus ; Cheetham, R. Keira ; Cox, Tony ; Eberle, Michael ; James, Terena ; Kahn, Scott ; Murray, Lisa ; Ye, Kai ; Fu, Yutao ; Hyland, Fiona C.L. ; Manning, Jonathan M. ; Stephen, F. McLaughlin ; Peckham, Heather E. ; Sakarya, Onur ; Sun, Yongming A. ; Tsung, Eric F. ; Mark, A. Batzer ; Konkel, Miriam K. ; Walker, Jerilyn A. ; Albrecht, Marcus W. ; Amstislavskiy, Vyacheslav S. ; Herwig, Ralf ; Parkhomchuk, Dimitri V. ; Agarwala, Richa ; Khouri, Hoda M. ; Morgulis, Aleksandr O. ; Paschall, Justin E. ; Phan, Lon D. ; Rotmistrovsky, Kirill E. ; Sanders, Robert D. ; Shumway, Martin F. ; Xiao, Chunlin ; Gil, A. McVean ; Auton, Adam ; Iqbal, Zamin ; Lunter, Gerton ; Marchini, Jonathan L. ; Moutsianas, Loukas ; Myers, Simon ; Tumian, Afidalina ; Knight, James ; Winer, Roger ; Craig, David W. ; Beckstrom-Sternberg, Steve M. ; Christoforides, Alexis ; Kurdoglu, Ahmet A. ; Pearson, John V. ; Sinari, Shripad A. ; Tembe, Waibhav D. ; Haussler, David ; Hinrichs, Angie S. ; Katzman, Sol J. ; Kern, Andrew ; Kuhn, Robert M. ; Przeworski, Molly ; Hernandez, Ryan D. ; Howie, Bryan ; Kelley, Joanna L. ; Melton, S. Cord ; Li, Yun ; Anderson, Paul ; Blackwell, Tom ; Chen, Wei ; Cookson, William O. ; Ding, Jun ; Kang, Hyun Min ; Lathrop, Mark ; Liang, Liming ; Moffatt, Miriam F. ; Scheet, Paul ; Sidore, Carlo ; Snyder, Matthew ; Zhan, Xiaowei ; Zöllner, Sebastian ; Awadalla, Philip ; Casals, Ferran ; Idaghdour, Youssef ; Keebler, John ; Stone, Eric A. ; Zilversmit, Martine ; Jorde, Lynn ; Xing, Jinchuan ; Eichler, Evan E. ; Aksay, Gozde ; Alkan, Can ; Hajirasouliha, Iman ; Hormozdiari, Fereydoun ; Kidd, Jeffrey M. ; CenkSahinalp, S. ; Sudmant, Peter H. ; Chen, Ken ; Chinwalla, Asif ; Ding, Li ; Koboldt, Daniel C. ; McLellan, Mike D. ; Wallis, John W. ; Wendl, Michael C. ; Zhang, Qunyuan ; Albers, Cornelis A. ; Ayub, Qasim ; Balasubramaniam, Senduran ; Barrett, Jeffrey C. ; Chen, Yuan ; Conrad, Don ; Danecek, Petr ; Dermitzakis, Emmanouil T. ; Hu, Min ; Huang, Ni ; Matt, E. Hurles ; Jin, Hanjun ; Jostins, Luke ; Keane, Thomas M. ; Quang Le, Si ; Lindsay, Sarah ; Long, Quan ; MacArthur, Daniel G. ; Montgomery, Stephen B. ; Parts, Leopold ; Chris Tyler-Smith, Tyler-Smith ; Walter, Klaudia ; Zhang, Yujun ; Gerstein, Mark B. ; Snyder, Michael ; Abyzov, Alexej ; Balasubramanian, Suganthi ; Bjornson, Robert ; Grubert, Fabian ; Habegger, Lukas ; Haraksingh, Rajini ; Khurana, Ekta ; Lam, Hugo Y.K. ; Leng, Jing ; Mu, Xinmeng Jasmine ; Urban, Alexander E. ; Zhang, Zhengdong ; McCarroll, Steven A. ; Zheng-Bradley, Xiangqun ; Batzer, Mark A. ; Hurles, Matt E. ; Du, Jiang ; Jee, Justin ; Coafra, Cristian ; Dinh, Huyen ; Kovar, Christie ; Lee, Sandy ; Nazareth, Lynne ; Wilkinson, Jane ; Coffey, Allison ; Scott, Carol ; Tyler-Smith, Chris ; Gharani, Neda ; Kaye, Jane S. ; Kent, Alastair ; Li, Taosha ; McGuire, Amy L. ; Ossorio, Pilar N. ; Rotimi, Charles N. ; Su, Yeyang ; Toji, Lorraine H. ; Felsenfeld, Adam L. ; McEwen, Jean E. ; Abdallah, Assya ; Juenger, Christopher R. ; Clemm, Nicholas C. ; Duncanson, Audrey ; Green, Eric D. ; Guyer, Mark S. ; Peterson, Jane L. / A map of human genome variation from population-scale sequencing. In: Nature. 2010 ; Vol. 467, No. 7319. pp. 1061-1073.
@article{c65ed439410246f9af14e97cc4000fae,
title = "A map of human genome variation from population-scale sequencing",
abstract = "The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95{\%} of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10 g -8 per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.",
author = "Altshuler, {David L.} and Durbin, {Richard M.} and Abecasis, {Gon{\cc}alo R.} and Bentley, {David R.} and Aravinda Chakravarti and Clark, {Andrew G.} and Collins, {Francis S.} and {De La Vega}, {Francisco M.} and Peter Donnelly and Michael Egholm and Paul Flicek and Gabriel, {Stacey B.} and Gibbs, {Richard A.} and Knoppers, {Bartha M.} and Lander, {Eric S.} and Hans Lehrach and Mardis, {Elaine R.} and McVean, {Gil A.} and Nickerson, {Debbie A.} and Leena Peltonen and Schafer, {Alan J.} and Sherry, {Stephen T.} and Jun Wang and Wilson, {Richard K.} and David Deiros and Mike Metzker and Donna Muzny and Jeff Reid and David Wheeler and Wang, {Shenzhen Jun} and Jingxiang Li and Min Jian and Guoqing Li and Ruiqiang Li and Huiqing Liang and Geng Tian and Bo Wang and Jian Wang and Wei Wang and Huanming Yang and Xiuqing Zhang and Huisong Zheng and Lauren Ambrogio and Toby Bloom and Kristian Cibulskis and Fennell, {Tim J.} and Jaffe, {David B.} and Erica Shefler and Sougnez, {Carrie L.} and Bentley, {Illumina David R.} and Niall Gormley and Sean Humphray and Zoya Kingsbury and Paula Koko-Gonzales and Jennifer Stone and {Mc Kernan}, {Kevin J.} and Costa, {Gina L.} and Ichikawa, {Jeffry K.} and Lee, {Clarence C.} and Ralf Sudbrak and Borodina, {Tatiana A.} and Andreas Dahl and Davydov, {Alexey N.} and Peter Marquardt and Florian Mertes and Wilfiried Nietfeld and Philip Rosenstiel and Stefan Schreiber and Soldatov, {Aleksey V.} and Bernd Timmermann and Marius Tolzmann and Jason Affourtit and Dana Ashworth and Said Attiya and Melissa Bachorski and Eli Buglione and Adam Burke and Amanda Caprio and Christopher Celone and Shauna Clark and David Conners and Brian Desany and Lisa Gu and Lorri Guccione and Kalvin Kao and Andrew Kebbel and Jennifer Knowlton and Matthew Labrecque and Louise McDade and Craig Mealmaker and Melissa Minderman and Anne Nawrocki and Faheem Niazi and Kristen Pareja and Ravi Ramenani and David Riches and Wanmin Song and Cynthia Turcotte and Shally Wang and David Dooling and Lucinda Fulton and Robert Fulton and George Weinstock and John Burton and Carter, {David M.} and Carol Churcher and Alison Coffey and Anthony Cox and Aarno Palotie and Michael Quail and Tom Skelly and James Stalker and Swerdlow, {Harold P.} and Daniel Turner and {De Witte}, Anniek and Shane Giles and Matthew Bainbridge and Danny Challis and Aniko Sabo and Fuli Yu and Jin Yu and Xiaodong Fang and Xiaosen Guo and Yingrui Li and Ruibang Luo and Shuaishuai Tai and Honglong Wu and Hancheng Zheng and Xiaole Zheng and Yan Zhou and Marth, {Gabor T.} and Garrison, {Erik P.} and Weichun Huang and Amit Indap and Deniz Kural and Lee, {Wan Ping} and Leong, {Wen Fung} and Quinlan, {Aaron R.} and Chip Stewart and Stromberg, {Michael P.} and Ward, {Alistair N.} and Jiantao Wu and Charles Lee and Mills, {Ryan E.} and Xinghua Shi and Daly, {Mark J.} and DePristo, {Mark A.} and Ball, {Aaron D.} and Eric Banks and Browning, {Brian L.} and Garimella, {Kiran V.} and Grossman, {Sharon R.} and Handsaker, {Robert E.} and Matt Hanna and Chris Hartl and Kernytsky, {Andrew M.} and Korn, {Joshua M.} and Heng Li and Maguire, {Jared R.} and Aaron McKenna and Nemesh, {James C.} and Philippakis, {Anthony A.} and Poplin, {Ryan E.} and Alkes Price and Rivas, {Manuel A.} and Sabeti, {Pardis C.} and Schaffner, {Stephen F.} and Shlyakhter, {Ilya A.} and Cooper, {David N.} and Ball, {Edward V.} and Matthew Mort and Phillips, {Andrew D.} and Stenson, {Peter D.} and Jonathan Sebat and Vladimir Makarov and Kenny Ye and Yoon, {Seungtai C.} and Bustamante, {Carlos D.} and Adam Boyko and Jeremiah Degenhardt and Simon Gravel and Gutenkunst, {Ryan N.} and Mark Kaganovich and Alon Keinan and Phil Lacroute and Xin Ma and Andy Reynolds and Laura Clarke and Fiona Cunningham and Javier Herrero and Stephen Keenen and Eugene Kulesha and Rasko Leinonen and McLaren, {William M.} and Rajesh Radhakrishnan and Smith, {Richard E.} and Vadim Zalunin and Korbel, {Jan O.} and St{\"u}tz, {Adrian M.} and Humphray, {Illumina Sean} and Markus Bauer and Cheetham, {R. Keira} and Tony Cox and Michael Eberle and Terena James and Scott Kahn and Lisa Murray and Kai Ye and Yutao Fu and Hyland, {Fiona C.L.} and Manning, {Jonathan M.} and Stephen, {F. McLaughlin} and Peckham, {Heather E.} and Onur Sakarya and Sun, {Yongming A.} and Tsung, {Eric F.} and Mark, {A. Batzer} and Konkel, {Miriam K.} and Walker, {Jerilyn A.} and Albrecht, {Marcus W.} and Amstislavskiy, {Vyacheslav S.} and Ralf Herwig and Parkhomchuk, {Dimitri V.} and Richa Agarwala and Khouri, {Hoda M.} and Morgulis, {Aleksandr O.} and Paschall, {Justin E.} and Phan, {Lon D.} and Rotmistrovsky, {Kirill E.} and Sanders, {Robert D.} and Shumway, {Martin F.} and Chunlin Xiao and Gil, {A. McVean} and Adam Auton and Zamin Iqbal and Gerton Lunter and Marchini, {Jonathan L.} and Loukas Moutsianas and Simon Myers and Afidalina Tumian and James Knight and Roger Winer and Craig, {David W.} and Beckstrom-Sternberg, {Steve M.} and Alexis Christoforides and Kurdoglu, {Ahmet A.} and Pearson, {John V.} and Sinari, {Shripad A.} and Tembe, {Waibhav D.} and David Haussler and Hinrichs, {Angie S.} and Katzman, {Sol J.} and Andrew Kern and Kuhn, {Robert M.} and Molly Przeworski and Hernandez, {Ryan D.} and Bryan Howie and Kelley, {Joanna L.} and Melton, {S. Cord} and Yun Li and Paul Anderson and Tom Blackwell and Wei Chen and Cookson, {William O.} and Jun Ding and Kang, {Hyun Min} and Mark Lathrop and Liming Liang and Moffatt, {Miriam F.} and Paul Scheet and Carlo Sidore and Matthew Snyder and Xiaowei Zhan and Sebastian Z{\"o}llner and Philip Awadalla and Ferran Casals and Youssef Idaghdour and John Keebler and Stone, {Eric A.} and Martine Zilversmit and Lynn Jorde and Jinchuan Xing and Eichler, {Evan E.} and Gozde Aksay and Can Alkan and Iman Hajirasouliha and Fereydoun Hormozdiari and Kidd, {Jeffrey M.} and S. CenkSahinalp and Sudmant, {Peter H.} and Ken Chen and Asif Chinwalla and Li Ding and Koboldt, {Daniel C.} and McLellan, {Mike D.} and Wallis, {John W.} and Wendl, {Michael C.} and Qunyuan Zhang and Albers, {Cornelis A.} and Qasim Ayub and Senduran Balasubramaniam and Barrett, {Jeffrey C.} and Yuan Chen and Don Conrad and Petr Danecek and Dermitzakis, {Emmanouil T.} and Min Hu and Ni Huang and Matt, {E. Hurles} and Hanjun Jin and Luke Jostins and Keane, {Thomas M.} and {Quang Le}, Si and Sarah Lindsay and Quan Long and MacArthur, {Daniel G.} and Montgomery, {Stephen B.} and Leopold Parts and {Chris Tyler-Smith}, Tyler-Smith and Klaudia Walter and Yujun Zhang and Gerstein, {Mark B.} and Michael Snyder and Alexej Abyzov and Suganthi Balasubramanian and Robert Bjornson and Fabian Grubert and Lukas Habegger and Rajini Haraksingh and Ekta Khurana and Lam, {Hugo Y.K.} and Jing Leng and Mu, {Xinmeng Jasmine} and Urban, {Alexander E.} and Zhengdong Zhang and McCarroll, {Steven A.} and Xiangqun Zheng-Bradley and Batzer, {Mark A.} and Hurles, {Matt E.} and Jiang Du and Justin Jee and Cristian Coafra and Huyen Dinh and Christie Kovar and Sandy Lee and Lynne Nazareth and Jane Wilkinson and Allison Coffey and Carol Scott and Chris Tyler-Smith and Neda Gharani and Kaye, {Jane S.} and Alastair Kent and Taosha Li and McGuire, {Amy L.} and Ossorio, {Pilar N.} and Rotimi, {Charles N.} and Yeyang Su and Toji, {Lorraine H.} and Felsenfeld, {Adam L.} and McEwen, {Jean E.} and Assya Abdallah and Juenger, {Christopher R.} and Clemm, {Nicholas C.} and Audrey Duncanson and Green, {Eric D.} and Guyer, {Mark S.} and Peterson, {Jane L.}",
year = "2010",
month = "10",
day = "28",
doi = "10.1038/nature09534",
language = "English (US)",
volume = "467",
pages = "1061--1073",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7319",

}

TY - JOUR

T1 - A map of human genome variation from population-scale sequencing

AU - Altshuler, David L.

AU - Durbin, Richard M.

AU - Abecasis, Gonçalo R.

AU - Bentley, David R.

AU - Chakravarti, Aravinda

AU - Clark, Andrew G.

AU - Collins, Francis S.

AU - De La Vega, Francisco M.

AU - Donnelly, Peter

AU - Egholm, Michael

AU - Flicek, Paul

AU - Gabriel, Stacey B.

AU - Gibbs, Richard A.

AU - Knoppers, Bartha M.

AU - Lander, Eric S.

AU - Lehrach, Hans

AU - Mardis, Elaine R.

AU - McVean, Gil A.

AU - Nickerson, Debbie A.

AU - Peltonen, Leena

AU - Schafer, Alan J.

AU - Sherry, Stephen T.

AU - Wang, Jun

AU - Wilson, Richard K.

AU - Deiros, David

AU - Metzker, Mike

AU - Muzny, Donna

AU - Reid, Jeff

AU - Wheeler, David

AU - Wang, Shenzhen Jun

AU - Li, Jingxiang

AU - Jian, Min

AU - Li, Guoqing

AU - Li, Ruiqiang

AU - Liang, Huiqing

AU - Tian, Geng

AU - Wang, Bo

AU - Wang, Jian

AU - Wang, Wei

AU - Yang, Huanming

AU - Zhang, Xiuqing

AU - Zheng, Huisong

AU - Ambrogio, Lauren

AU - Bloom, Toby

AU - Cibulskis, Kristian

AU - Fennell, Tim J.

AU - Jaffe, David B.

AU - Shefler, Erica

AU - Sougnez, Carrie L.

AU - Bentley, Illumina David R.

AU - Gormley, Niall

AU - Humphray, Sean

AU - Kingsbury, Zoya

AU - Koko-Gonzales, Paula

AU - Stone, Jennifer

AU - Mc Kernan, Kevin J.

AU - Costa, Gina L.

AU - Ichikawa, Jeffry K.

AU - Lee, Clarence C.

AU - Sudbrak, Ralf

AU - Borodina, Tatiana A.

AU - Dahl, Andreas

AU - Davydov, Alexey N.

AU - Marquardt, Peter

AU - Mertes, Florian

AU - Nietfeld, Wilfiried

AU - Rosenstiel, Philip

AU - Schreiber, Stefan

AU - Soldatov, Aleksey V.

AU - Timmermann, Bernd

AU - Tolzmann, Marius

AU - Affourtit, Jason

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PY - 2010/10/28

Y1 - 2010/10/28

N2 - The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10 g -8 per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.

AB - The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10 g -8 per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.

UR - http://www.scopus.com/inward/record.url?scp=84975742565&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84975742565&partnerID=8YFLogxK

U2 - 10.1038/nature09534

DO - 10.1038/nature09534

M3 - Article

AN - SCOPUS:84975742565

VL - 467

SP - 1061

EP - 1073

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7319

ER -