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A global reference for human genetic variation

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Title: A global reference for human genetic variation
Author(s): Altshuler, DM
Durbin, RM
Abecasis, GR
Bentley, DR
Chakravarti, A
Clark, AG
Donnelly, P
Eichler, EE
Flicek, P
Gabriel, SB
Gibbs, RA
Green, ED
Hurles, ME
Knoppers, BM
Korbel, JO
Lander, ES
Lee, C
Lehrach, H
Mardis, ER
Marth, GT
McVean, GA
Nickerson, DA
Schmidt, JP
Sherry, ST
Wang, J
Wilson, RK
Gibbs, RA
Boerwinkle, E
Doddapaneni, H
Han, Y
Korchina, V
Kovar, C
Lee, S
Muzny, D
Reid, JG
Zhu, Y
Wang, J
Chang, Y
Feng, Q
Fang, X
Guo, X
Jian, M
Jiang, H
Jin, X
Lan, T
Li, G
Li, J
Li, Y
Liu, S
Liu, X
Lu, Y
Ma, X
Tang, M
Wang, B
Wang, G
Wu, H
Wu, R
Xu, X
Yin, Y
Zhang, D
Zhang, W
Zhao, J
Zhao, M
Zheng, X
Lander, ES
Altshuler, DM
Gabriel, SB
Gupta, N
Gharani, N
Toji, LH
Gerry, NP
Resch, AM
Flicek, P
Barker, J
Clarke, L
Gil, L
Hunt, SE
Kelman, G
Kulesha, E
Leinonen, R
McLaren, WM
Radhakrishnan, R
Roa, A
Smirnov, D
Smith, RE
Streeter, I
Thormann, A
Toneva, I
Vaughan, B
Zheng-Bradley, X
Bentley, DR
Grocock, R
Humphray, S
James, T
Kingsbury, Z
Lehrach, H
Sudbrak, R
Albrecht, MW
Amstislavskiy, VS
Borodina, TA
Lienhard, M
Mertes, F
Sultan, M
Timmermann, B
Yaspo, M-L
Mardis, ER
Wilson, RK
Fulton, L
Fulton, R
Sherry, ST
Ananiev, V
Belaia, Z
Beloslyudtsev, D
Bouk, N
Chen, C
Church, D
Cohen, R
Cook, C
Garner, J
Hefferon, T
Kimelman, M
Liu, C
Lopez, J
Meric, P
O'Sullivan, C
Ostapchuk, Y
Phan, L
Ponomarov, S
Schneider, V
Shekhtman, E
Sirotkin, K
Slotta, D
Zhang, H
McVean, GA
Durbin, RM
Balasubramaniam, S
Burton, J
Danecek, P
Keane, TM
Kolb-Kokocinski, A
McCarthy, S
Stalker, J
Quail, M
Schmidt, JP
Davies, CJ
Gollub, J
Webster, T
Wong, B
Zhan, Y
Auton, A
Campbell, CL
Kong, Y
Marcketta, A
Gibbs, RA
Yu, F
Antunes, L
Bainbridge, M
Muzny, D
Sabo, A
Huang, Z
Wang, J
Coin, LJM
Fang, L
Guo, X
Jin, X
Li, G
Li, Q
Li, Y
Li, Z
Lin, H
Liu, B
Luo, R
Shao, H
Xie, Y
Ye, C
Yu, C
Zhang, F
Zheng, H
Zhu, H
Alkan, C
Dal, E
Kahveci, F
Marth, GT
Garrison, EP
Kural, D
Lee, W-P
Leong, WF
Stromberg, M
Ward, AN
Wu, J
Zhang, M
Daly, MJ
DePristo, MA
Handsaker, RE
Altshuler, DM
Banks, E
Bhatia, G
Del Angel, G
Gabriel, SB
Genovese, G
Gupta, N
Li, H
Kashin, S
Lander, ES
McCarroll, SA
Nemesh, JC
Poplin, RE
Yoon, SC
Lihm, J
Makarov, V
Clark, AG
Gottipati, S
Keinan, A
Rodriguez-Flores, JL
Korbel, JO
Rausch, T
Fritz, MH
Stuetz, AM
Flicek, P
Beal, K
Clarke, L
Datta, A
Herrero, J
McLaren, WM
Ritchie, GRS
Smith, RE
Zerbino, D
Zheng-Bradley, X
Sabeti, PC
Shlyakhter, I
Schaffner, SF
Vitti, J
Cooper, DN
Ball, EV
Stenson, PD
Bentley, DR
Barnes, B
Bauer, M
Cheetham, RK
Cox, A
Eberle, M
Humphray, S
Kahn, S
Murray, L
Peden, J
Shaw, R
Kenny, EE
Batzer, MA
Konkel, MK
Walker, JA
MacArthur, DG
Lek, M
Sudbrak, R
Amstislavskiy, VS
Herwig, R
Mardis, ER
Ding, L
Koboldt, DC
Larson, D
Ye, K
Gravel, S
Swaroop, A
Chew, E
Lappalainen, T
Erlich, Y
Gymrek, M
Willems, TF
Simpson, JT
Shriver, MD
Rosenfeld, JA
Bustamante, CD
Montgomery, SB
De La Vega, FM
Byrnes, JK
Carroll, AW
DeGorter, MK
Lacroute, P
Maples, BK
Martin, AR
Moreno-Estrada, A
Shringarpure, SS
Zakharia, F
Halperin, E
Baran, Y
Lee, C
Cerveira, E
Hwang, J
Malhotra, A
Plewczynski, D
Radew, K
Romanovitch, M
Zhang, C
Hyland, FCL
Craig, DW
Christoforides, A
Homer, N
Izatt, T
Kurdoglu, AA
Sinari, SA
Squire, K
Sherry, ST
Xiao, C
Sebat, J
Antaki, D
Gujral, M
Noor, A
Ye, K
Burchard, EG
Hernandez, RD
Gignoux, CR
Haussler, D
Katzman, SJ
Kent, WJ
Howie, B
Ruiz-Linares, A
Dermitzakis, ET
Devine, SE
Goncalo, RA
Kang, HM
Kidd, JM
Blackwell, T
Caron, S
Chen, W
Emery, S
Fritsche, L
Fuchsberger, C
Jun, G
Li, B
Lyons, R
Scheller, C
Sidore, C
Song, S
Sliwerska, E
Taliun, D
Tan, A
Welch, R
Wing, MK
Zhan, X
Awadalla, P
Hodgkinson, A
Li, Y
Shi, X
Quitadamo, A
Lunter, G
McVean, GA
Marchini, JL
Myers, S
Churchhouse, C
Delaneau, O
Gupta-Hinch, A
Kretzschmar, W
Iqbal, Z
Mathieson, I
Menelaou, A
Rimmer, A
Xifara, DK
Oleksyk, TK
Fu, Y
Liu, X
Xiong, M
Jorde, L
Witherspoon, D
Xing, J
Eichler, EE
Browning, BL
Browning, SR
Hormozdiari, F
Sudmant, PH
Khurana, E
Durbin, RM
Hurles, ME
Tyler-Smith, C
Albers, CA
Ayub, Q
Balasubramaniam, S
Chen, Y
Colonna, V
Danecek, P
Jostins, L
Keane, TM
McCarthy, S
Walter, K
Xue, Y
Gerstein, MB
Abyzov, A
Balasubramanian, S
Chen, J
Clarke, D
Fu, Y
Harmanci, AO
Jin, M
Lee, D
Liu, J
Mu, XJ
Zhang, J
Zhang, Y
Li, Y
Luo, R
Zhu, H
Alkan, C
Dal, E
Kahveci, F
Marth, GT
Garrison, EP
Kural, D
Lee, W-P
Ward, AN
Wu, J
Zhang, M
McCarroll, SA
Handsaker, RE
Altshuler, DM
Banks, E
Del Angel, G
Genovese, G
Hartl, C
Li, H
Kashin, S
Nemesh, JC
Shakir, K
Yoon, SC
Lihm, J
Makarov, V
Degenhardt, J
Korbel, JO
Fritz, MH
Meiers, S
Raeder, B
Rausch, T
Stuetz, AM
Flicek, P
Casale, FP
Clarke, L
Smith, RE
Stegle, O
Zheng-Bradley, X
Bentley, DR
Barnes, B
Cheetham, RK
Eberle, M
Humphray, S
Kahn, S
Murray, L
Shaw, R
Lameijer, E-W
Batzer, MA
Konkel, MK
Walker, JA
Ding, L
Hall, I
Ye, K
Lacroute, P
Lee, C
Cerveira, E
Malhotra, A
Hwang, J
Plewczynski, D
Radew, K
Romanovitch, M
Zhang, C
Craig, DW
Homer, N
Church, D
Xiao, C
Sebat, J
Antaki, D
Bafna, V
Michaelson, J
Ye, K
Devine, SE
Gardner, EJ
Abecasis, GR
Kidd, JM
Mills, RE
Dayama, G
Emery, S
Jun, G
Shi, X
Quitadamo, A
Lunter, G
McVean, GA
Chen, K
Fan, X
Chong, Z
Chen, T
Witherspoon, D
Xing, J
Eichler, EE
Chaisson, MJ
Hormozdiari, F
Huddleston, J
Malig, M
Nelson, BJ
Sudmant, PH
Parrish, NF
Khurana, E
Hurles, ME
Blackburne, B
Lindsay, SJ
Ning, Z
Walter, K
Zhang, Y
Gerstein, MB
Abyzov, A
Chen, J
Clarke, D
Lam, H
Mu, XJ
Sisu, C
Zhang, J
Zhang, Y
Gibbs, RA
Yu, F
Bainbridge, M
Challis, D
Evani, US
Kovar, C
Lu, J
Muzny, D
Nagaswamy, U
Reid, JG
Sabo, A
Yu, J
Guo, X
Li, W
Li, Y
Wu, R
Marth, GT
Garrison, EP
Leong, WF
Ward, AN
Del Angel, G
DePristo, MA
Gabriel, SB
Gupta, N
Hartl, C
Poplin, RE
Clark, AG
Rodriguez-Flores, JL
Flicek, P
Clarke, L
Smith, RE
Zheng-Bradley, X
MacArthur, DG
Mardis, ER
Fulton, R
Koboldt, DC
Gravel, S
Bustamante, CD
Craig, DW
Christoforides, A
Homer, N
Izatt, T
Sherry, ST
Xiao, C
Dermitzakis, ET
Abecasis, GR
Kang, HM
McVean, GA
Gerstein, MB
Balasubramanian, S
Habegger, L
Yu, H
Flicek, P
Clarke, L
Cunningham, F
Dunham, I
Zerbino, D
Zheng-Bradley, X
Lage, K
Jespersen, JB
Horn, H
Montgomery, SB
DeGorter, MK
Khurana, E
Tyler-Smith, C
Chen, Y
Colonna, V
Xue, Y
Gerstein, MB
Balasubramanian, S
Fu, Y
Kim, D
Auton, A
Marcketta, A
Desalle, R
Narechania, A
Sayres, MAW
Garrison, EP
Handsaker, RE
Kashin, S
McCarroll, SA
Rodriguez-Flores, JL
Flicek, P
Clarke, L
Zheng-Bradley, X
Erlich, Y
Gymrek, M
Willems, TF
Bustamante, CD
Mendez, FL
Poznik, GD
Underhill, PA
Lee, C
Cerveira, E
Malhotra, A
Romanovitch, M
Zhang, C
Abecasis, GR
Coin, L
Shao, H
Mittelman, D
Tyler-Smith, C
Ayub, Q
Banerjee, R
Cerezo, M
Chen, Y
Fitzgerald, T
Louzada, S
Massaia, A
McCarthy, S
Ritchie, GR
Xue, Y
Yang, F
Gibbs, RA
Kovar, C
Kalra, D
Hale, W
Muzny, D
Reid, JG
Wang, J
Dan, X
Guo, X
Li, G
Li, Y
Ye, C
Zheng, X
Altshuler, DM
Flicek, P
Clarke, L
Zheng-Bradley, X
Bentley, DR
Cox, A
Humphray, S
Kahn, S
Sudbrak, R
Albrecht, MW
Lienhard, M
Larson, D
Craig, DW
Izatt, T
Kurdoglu, AA
Sherry, ST
Xiao, C
Haussler, D
Abecasis, GR
McVean, GA
Durbin, RM
Balasubramaniam, S
Keane, TM
McCarthy, S
Stalker, J
Chakravarti, A
Knoppers, BM
Abecasis, GR
Barnes, KC
Beiswanger, C
Burchard, EG
Bustamante, CD
Cai, H
Cao, H
Durbin, RM
Gerry, NP
Gharani, N
Gibbs, RA
Gignoux, CR
Gravel, S
Henn, B
Jones, D
Jorde, L
Kaye, JS
Keinan, A
Kent, A
Kerasidou, A
Li, Y
Mathias, R
McVean, GA
Moreno-Estrada, A
Ossorio, PN
Parker, M
Resch, AM
Rotimi, CN
Royal, CD
Sandoval, K
Su, Y
Sudbrak, R
Tian, Z
Tishkoff, S
Toji, LH
Tyler-Smith, C
Via, M
Wang, Y
Yang, H
Yang, L
Zhu, J
Bodmer, W
Bedoya, G
Ruiz-Linares, A
Cai, Z
Gao, Y
Chu, J
Peltonen, L
Garcia-Montero, A
Orfao, A
Dutil, J
Martinez-Cruzado, JC
Oleksyk, TK
Barnes, KC
Mathias, RA
Hennis, A
Watson, H
McKenzie, C
Qadri, F
LaRocque, R
Sabeti, PC
Zhu, J
Deng, X
Sabeti, PC
Asogun, D
Folarin, O
Happi, C
Omoniwa, O
Stremlau, M
Tariyal, R
Jallow, M
Joof, FS
Corrah, T
Rockett, K
Kwiatkowski, D
Kooner, J
Tran, TH
Dunstan, SJ
Nguyen, TH
Fonnie, R
Garry, R
Kanneh, L
Moses, L
Sabeti, PC
Schieffelin, J
Grant, DS
Gallo, C
Poletti, G
Saleheen, D
Rasheed, A
Brook, LD
Felsenfeld, A
McEwen, JE
Vaydylevich, Y
Green, ED
Duncanson, A
Dunn, M
Schloss, JA
Wang, J
Yang, H
Auton, A
Brooks, LD
Durbin, RM
Garrison, EP
Kang, HM
Korbel, JO
Marchini, JL
McCarthy, S
McVean, GA
Abecasis, GR
Item Type: Journal Article
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
Publication Date: 30-Sep-2015
Date of Acceptance: 20-Aug-2015
URI: http://hdl.handle.net/10044/1/40662
DOI: http://dx.doi.org/10.1038/nature15393
ISSN: 0028-0836
Publisher: Nature Publishing Group
Start Page: 68
End Page: 74
Journal / Book Title: Nature
Volume: 526
Issue: 7571
Copyright Statement: This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported licence. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.
Keywords: Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
GENOME-WIDE ASSOCIATION
COMPLEMENT FACTOR-H
MACULAR DEGENERATION
POPULATION HISTORY
BAYES FACTORS
MUTATION
DISEASE
VARIANT
SUSCEPTIBILITY
INDIVIDUALS
Datasets as Topic
Demography
Disease Susceptibility
Exome
Genetic Variation
Genetics, Medical
Genetics, Population
Genome, Human
Genome-Wide Association Study
Genomics
Genotype
Haplotypes
High-Throughput Nucleotide Sequencing
Humans
INDEL Mutation
Internationality
Physical Chromosome Mapping
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Rare Diseases
Reference Standards
Sequence Analysis, DNA
1000 Genomes Project Consortium
Humans
Disease Susceptibility
Rare Diseases
Physical Chromosome Mapping
Sequence Analysis, DNA
Genetics, Medical
Genetics, Population
Genomics
Demography
Genotype
Haplotypes
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Genome, Human
Reference Standards
Internationality
INDEL Mutation
Genetic Variation
Genome-Wide Association Study
High-Throughput Nucleotide Sequencing
Exome
Datasets as Topic
General Science & Technology
MD Multidisciplinary
Publication Status: Published
Appears in Collections:Faculty of Medicine



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