Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Olivier Delaneau, Jonathan Marchini, Gil A. McVeanh, Peter Donnelly, Gerton Lunter, Jonathan L. Marchini, Simon Myers, Anjali Gupta-Hinch, Zamin Iqbal, Iain Mathieson, Andy Rimmer, Dionysia K. Xifara, Angeliki Kerasidou, Claire Churchhouse, David M. Altshuler, Stacey B. Gabriel, Eric S. Lander, Namrata Gupta, Mark J. Daly, Mark A. DePristoEric Banks, Gaurav Bhatia, Mauricio O. Carneiro, Guillermo Del Angel, Giulio Genovese, Robert E. Handsaker, Chris Hartl, Steven A. McCarroll, James C. Nemesh, Ryan E. Poplin, Stephen F. Schaffner, Khalid Shakir, Pardis C. Sabeti, Sharon R. Grossman, Shervin Tabrizi, Ridhi Tariyal, Heng Li, David Reich, Richard M. Durbin, Matthew E. Hurles, Senduran Balasubramaniam, John Burton, Petr Danecek, Thomas M. Keane, Anja Kolb-Kokocinski, Shane McCarthy, James Stalker, Michael Quail, Qasim Ayub, Yuan Chen, Alison J. Coffey, Vincenza Colonna, Ni Huang, Luke Jostins, Aylwyn Scally, Klaudia Walter, Yali Xue, Yujun Zhang, Ben Blackburne, Sarah J. Lindsay, Zemin Ning, Adam Frankish, Jennifer Harrow, Tyler S. Chris, Gonalo R. Abecasis, Hyun Min Kang, Paul Anderson, Tom Blackwell, Fabio Busonero, Christian Fuchsberger, Goo Jun, Andrea Maschio, Eleonora Porcu, Carlo Sidore, Adrian Tan, Mary Kate Trost, David R. Bentley, Russell Grocock, Sean Humphray, Terena James, Zoya Kingsbury, Markus Bauer, R. Keira Cheetham, Tony Cox, Michael Eberle, Lisa Murray, Richard Shaw, Aravinda Chakravarti, Andrew G. Clark, Alon Keinan, Juan L. Rodriguez-Flores, Francisco M. De LaVega, Jeremiah Degenhardt, Evan E. Eichler, Paul Flicek, Laura Clarke, Rasko Leinonen, Richard E. Smith, Xiangqun Zheng-Bradley, Kathryn Beal, Fiona Cunningham, Javier Herrero, William M. McLaren, Graham R.S. Ritchie, Jonathan Barker, Gavin Kelman, Eugene Kulesha, Rajesh Radhakrishnan, Asier Roa, Dmitriy Smirnov, Ian Streeter, Iliana Toneva, Richard A. Gibbs, Huyen Dinh, Christie Kovar, Sandra Lee, Lora Lewis, Donna Muzny, Jeff Reid, Min Wang, Fuli Yu, Matthew Bainbridge, Danny Challis, Uday S. Evani, James Lu, Uma Nagaswamy, Aniko Sabo, Yi Wang, Jin Yu, Gerald Fowler, Walker Hale, Divya Kalra, Eric D. Green, Bartha M. Knoppers, Jan O. Korbel, Tobias Rausch, Adrian M. Sttz, Charles Lee, Lauren Griffin, Chih Heng Hsieh, Ryan E. Mills, Marcin Von Grotthuss, Chengsheng Zhang, Xinghua Shi, Hans Lehrach, Ralf Sudbrak, Vyacheslav S. Amstislavskiy, Matthias Lienhard, Florian Mertes, Marc Sultan, Bernd Timmermann, Marie Laure Yaspo, Sudbrak Ralf Herwig, Elaine R. Mardis, Richard K. Wilson, Lucinda Fulton, Robert Fulton, George M. Weinstock, Asif Chinwalla, Li Ding, David Dooling, Daniel C. Koboldt, Michael D. McLellan, John W. Wallis, Michael C. Wendl, Qunyuan Zhang, Gabor T. Marth, Erik P. Garrison, Deniz Kural, Wan Ping Lee, Wen Fung Leong, Alistair N. Ward, Jiantao Wu, Mengyao Zhang, Deborah A. Nickerson, Can Alkan, Fereydoun Hormozdiari, Arthur Ko, Peter H. Sudmant, Jeanette P. Schmidt, Christopher J. Davies, Jeremy Gollub, Teresa Webster, Brant Wong, Yiping Zhan, Stephen T. Sherry, Chunlin Xiao, Deanna Church, Victor Ananiev, Zinaida Belaia, Dimitriy Beloslyudtsev, Nathan Bouk, Chao Chen, Robert Cohen, Charles Cook, John Garner, Timothy Hefferon, Mikhail Kimelman, Chunlei Liu, John Lopez, Peter Meric, Yuri Ostapchuk, Lon Phan, Sergiy Ponomarov, Valerie Schneider, Eugene Shekhtman, Karl Sirotkin, Douglas Slotta, Hua Zhang, Jun Wang, Xiaodong Fang, Xiaosen Guo, Min Jian, Hui Jiang, Xin Jin, Guoqing Li, Jingxiang Li, Yingrui Li, Xiao Liu, Yao Lu, Xuedi Ma, Shuaishuai Tai, Meifang Tang, Bo Wang, Guangbiao Wang, Honglong Wu, Renhua Wu, Ye Yin, Wenwei Zhang, Jiao Zhao, Meiru Zhao, Xiaole Zheng, Hans Lachlan, Lin Fang, Qibin Li, Zhenyu Li, Haoxiang Lin, Binghang Liu, Ruibang Luo, Haojing Shao, Bingqiang Wang, Yinlong Xie, Chen Ye, Chang Yu, Hancheng Zheng, Hongmei Zhu, Hongyu Cai, Hongzhi Cao, Yeyang Su, Zhongming Tian, Huanming Yang, Ling Yang, Jiayong Zhu, Zhiming Cai, Jian Wang, Marcus W. Albrecht, Tatiana A. Borodina, Adam Auton, Seungtai C. Yoon, Jayon Lihm, Vladimir Makarov, Hanjun Jin, Wook Kim, Ki Cheol Kim, Srikanth Gottipati, Danielle Jones, David N. Cooper, Edward V. Ball, Peter D. Stenson, Bret Barnes, Scott Kahn, Kai Ye, Mark A. Batzer, Miriam K. Konkel, Jerilyn A. Walker, Daniel G. MacArthur, Monkol Lek, Mark D. Shriver, Carlos D. Bustamante, Simon Gravel, Eimear E. Kenny, Jeffrey M. Kidd, Phil Lacroute, Brian K. Maples, Andres Moreno-Estrada, Fouad Zakharia, Brenna Henn, Karla Sandoval, Jake K. Byrnes, Eran Halperin, Yael Baran, David W. Craig, Alexis Christoforides, Tyler Izatt, Ahmet A. Kurdoglu, Shripad A. Sinari, Nils Homer, Kevin Squire, Jonathan Sebat, Vineet Bafna, Kenny Ye, Esteban G. Burchard, Ryan D. Hernandez, Christopher R. Gignoux, David Haussler, Sol J. Katzman, W. James Kent, Bryan Howie, Andres Ruiz-Linares, Emmanouil T. Dermitzakis, Tuuli Lappalainen, Scott E. Devine, Xinyue Liu, Ankit Maroo, Luke J. Tallon, Jeffrey A. Rosenfeld, Leslie P. Michelson, Andrea Angius, Francesco Cucca, Serena Sanna, Abigail Bigham, Chris Jones, Fred Reinier, Yun Li, Robert Lyons, David Schlessinger, Philip Awadalla, Alan Hodgkinson, Taras K. Oleksyk, Juan C. Martinez-Cruzado, Yunxin Fu, Xiaoming Liu, Momiao Xiong, Lynn Jorde, David Witherspoon, Jinchuan Xing, Brian L. Browning, Iman Hajirasouliha, Ken Chen, Cornelis A. Albers, Mark B. Gerstein, Alexej Abyzov, Jieming Chen, Yao Fu, Lukas Habegger, Arif O. Harmanci, Xinmeng Jasmine Mu, Cristina Sisu, Suganthi Balasubramanian, Mike Jin, Ekta Khurana, Declan Clarke, Jacob J. Michaelson, Chris OSullivan, Kathleen C. Barnes, Neda Gharani, Lorraine H. Toji, Norman Gerry, Jane S. Kaye, Alastair Kent, Rasika Mathias, Pilar N. Ossorio, Michael Parker, Charles N. Rotimi, Charmaine D. Royal, Sarah Tishkoff, Marc Via, Walter Bodmer, Gabriel Bedoya, Gao Yang, Chu Jia You, Andres Garcia-Montero, Alberto Orfao, Julie Dutil, Lisa D. Brooks, Adam L. Felsenfeld, Jean E. McEwen, Nicholas C. Clemm, Mark S. Guyer, Jane L. Peterson, Audrey Duncanson, Michael Dunn, Leena Peltonen

Research output: Contribution to journalArticle

132 Citations (Scopus)

Abstract

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.

Original languageEnglish (US)
Article number3934
JournalNature communications
Volume5
DOIs
StatePublished - Jun 13 2014

Fingerprint

genome
Haplotypes
polymorphism
nucleotides
Genes
Polymorphism
Genome
Genotype
Nucleotides
Single Nucleotide Polymorphism
Scaffolds
Genome-Wide Association Study
Association reactions
sequencing
chromosomes
Microarrays
Chromosomes
Medical Genetics
low frequencies
estimates

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Delaneau, O., Marchini, J., McVeanh, G. A., Donnelly, P., Lunter, G., Marchini, J. L., ... Peltonen, L. (2014). Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature communications, 5, [3934]. https://doi.org/10.1038/ncomms4934
Delaneau, Olivier ; Marchini, Jonathan ; McVeanh, Gil A. ; Donnelly, Peter ; Lunter, Gerton ; Marchini, Jonathan L. ; Myers, Simon ; Gupta-Hinch, Anjali ; Iqbal, Zamin ; Mathieson, Iain ; Rimmer, Andy ; Xifara, Dionysia K. ; Kerasidou, Angeliki ; Churchhouse, Claire ; Altshuler, David M. ; Gabriel, Stacey B. ; Lander, Eric S. ; Gupta, Namrata ; Daly, Mark J. ; DePristo, Mark A. ; Banks, Eric ; Bhatia, Gaurav ; Carneiro, Mauricio O. ; Del Angel, Guillermo ; Genovese, Giulio ; Handsaker, Robert E. ; Hartl, Chris ; McCarroll, Steven A. ; Nemesh, James C. ; Poplin, Ryan E. ; Schaffner, Stephen F. ; Shakir, Khalid ; Sabeti, Pardis C. ; Grossman, Sharon R. ; Tabrizi, Shervin ; Tariyal, Ridhi ; Li, Heng ; Reich, David ; Durbin, Richard M. ; Hurles, Matthew E. ; Balasubramaniam, Senduran ; Burton, John ; Danecek, Petr ; Keane, Thomas M. ; Kolb-Kokocinski, Anja ; McCarthy, Shane ; Stalker, James ; Quail, Michael ; Ayub, Qasim ; Chen, Yuan ; Coffey, Alison J. ; Colonna, Vincenza ; Huang, Ni ; Jostins, Luke ; Scally, Aylwyn ; Walter, Klaudia ; Xue, Yali ; Zhang, Yujun ; Blackburne, Ben ; Lindsay, Sarah J. ; Ning, Zemin ; Frankish, Adam ; Harrow, Jennifer ; Chris, Tyler S. ; Abecasis, Gonalo R. ; Kang, Hyun Min ; Anderson, Paul ; Blackwell, Tom ; Busonero, Fabio ; Fuchsberger, Christian ; Jun, Goo ; Maschio, Andrea ; Porcu, Eleonora ; Sidore, Carlo ; Tan, Adrian ; Trost, Mary Kate ; Bentley, David R. ; Grocock, Russell ; Humphray, Sean ; James, Terena ; Kingsbury, Zoya ; Bauer, Markus ; Cheetham, R. Keira ; Cox, Tony ; Eberle, Michael ; Murray, Lisa ; Shaw, Richard ; Chakravarti, Aravinda ; Clark, Andrew G. ; Keinan, Alon ; Rodriguez-Flores, Juan L. ; De LaVega, Francisco M. ; Degenhardt, Jeremiah ; Eichler, Evan E. ; Flicek, Paul ; Clarke, Laura ; Leinonen, Rasko ; Smith, Richard E. ; Zheng-Bradley, Xiangqun ; Beal, Kathryn ; Cunningham, Fiona ; Herrero, Javier ; McLaren, William M. ; Ritchie, Graham R.S. ; Barker, Jonathan ; Kelman, Gavin ; Kulesha, Eugene ; Radhakrishnan, Rajesh ; Roa, Asier ; Smirnov, Dmitriy ; Streeter, Ian ; Toneva, Iliana ; Gibbs, Richard A. ; Dinh, Huyen ; Kovar, Christie ; Lee, Sandra ; Lewis, Lora ; Muzny, Donna ; Reid, Jeff ; Wang, Min ; Yu, Fuli ; Bainbridge, Matthew ; Challis, Danny ; Evani, Uday S. ; Lu, James ; Nagaswamy, Uma ; Sabo, Aniko ; Wang, Yi ; Yu, Jin ; Fowler, Gerald ; Hale, Walker ; Kalra, Divya ; Green, Eric D. ; Knoppers, Bartha M. ; Korbel, Jan O. ; Rausch, Tobias ; Sttz, Adrian M. ; Lee, Charles ; Griffin, Lauren ; Hsieh, Chih Heng ; Mills, Ryan E. ; Von Grotthuss, Marcin ; Zhang, Chengsheng ; Shi, Xinghua ; Lehrach, Hans ; Sudbrak, Ralf ; Amstislavskiy, Vyacheslav S. ; Lienhard, Matthias ; Mertes, Florian ; Sultan, Marc ; Timmermann, Bernd ; Yaspo, Marie Laure ; Herwig, Sudbrak Ralf ; Mardis, Elaine R. ; Wilson, Richard K. ; Fulton, Lucinda ; Fulton, Robert ; Weinstock, George M. ; Chinwalla, Asif ; Ding, Li ; Dooling, David ; Koboldt, Daniel C. ; McLellan, Michael D. ; Wallis, John W. ; Wendl, Michael C. ; Zhang, Qunyuan ; Marth, Gabor T. ; Garrison, Erik P. ; Kural, Deniz ; Lee, Wan Ping ; Leong, Wen Fung ; Ward, Alistair N. ; Wu, Jiantao ; Zhang, Mengyao ; Nickerson, Deborah A. ; Alkan, Can ; Hormozdiari, Fereydoun ; Ko, Arthur ; Sudmant, Peter H. ; Schmidt, Jeanette P. ; Davies, Christopher J. ; Gollub, Jeremy ; Webster, Teresa ; Wong, Brant ; Zhan, Yiping ; Sherry, Stephen T. ; Xiao, Chunlin ; Church, Deanna ; Ananiev, Victor ; Belaia, Zinaida ; Beloslyudtsev, Dimitriy ; Bouk, Nathan ; Chen, Chao ; Cohen, Robert ; Cook, Charles ; Garner, John ; Hefferon, Timothy ; Kimelman, Mikhail ; Liu, Chunlei ; Lopez, John ; Meric, Peter ; Ostapchuk, Yuri ; Phan, Lon ; Ponomarov, Sergiy ; Schneider, Valerie ; Shekhtman, Eugene ; Sirotkin, Karl ; Slotta, Douglas ; Zhang, Hua ; Wang, Jun ; Fang, Xiaodong ; Guo, Xiaosen ; Jian, Min ; Jiang, Hui ; Jin, Xin ; Li, Guoqing ; Li, Jingxiang ; Li, Yingrui ; Liu, Xiao ; Lu, Yao ; Ma, Xuedi ; Tai, Shuaishuai ; Tang, Meifang ; Wang, Bo ; Wang, Guangbiao ; Wu, Honglong ; Wu, Renhua ; Yin, Ye ; Zhang, Wenwei ; Zhao, Jiao ; Zhao, Meiru ; Zheng, Xiaole ; Lachlan, Hans ; Fang, Lin ; Li, Qibin ; Li, Zhenyu ; Lin, Haoxiang ; Liu, Binghang ; Luo, Ruibang ; Shao, Haojing ; Wang, Bingqiang ; Xie, Yinlong ; Ye, Chen ; Yu, Chang ; Zheng, Hancheng ; Zhu, Hongmei ; Cai, Hongyu ; Cao, Hongzhi ; Su, Yeyang ; Tian, Zhongming ; Yang, Huanming ; Yang, Ling ; Zhu, Jiayong ; Cai, Zhiming ; Wang, Jian ; Albrecht, Marcus W. ; Borodina, Tatiana A. ; Auton, Adam ; Yoon, Seungtai C. ; Lihm, Jayon ; Makarov, Vladimir ; Jin, Hanjun ; Kim, Wook ; Kim, Ki Cheol ; Gottipati, Srikanth ; Jones, Danielle ; Cooper, David N. ; Ball, Edward V. ; Stenson, Peter D. ; Barnes, Bret ; Kahn, Scott ; Ye, Kai ; Batzer, Mark A. ; Konkel, Miriam K. ; Walker, Jerilyn A. ; MacArthur, Daniel G. ; Lek, Monkol ; Shriver, Mark D. ; Bustamante, Carlos D. ; Gravel, Simon ; Kenny, Eimear E. ; Kidd, Jeffrey M. ; Lacroute, Phil ; Maples, Brian K. ; Moreno-Estrada, Andres ; Zakharia, Fouad ; Henn, Brenna ; Sandoval, Karla ; Byrnes, Jake K. ; Halperin, Eran ; Baran, Yael ; Craig, David W. ; Christoforides, Alexis ; Izatt, Tyler ; Kurdoglu, Ahmet A. ; Sinari, Shripad A. ; Homer, Nils ; Squire, Kevin ; Sebat, Jonathan ; Bafna, Vineet ; Ye, Kenny ; Burchard, Esteban G. ; Hernandez, Ryan D. ; Gignoux, Christopher R. ; Haussler, David ; Katzman, Sol J. ; Kent, W. James ; Howie, Bryan ; Ruiz-Linares, Andres ; Dermitzakis, Emmanouil T. ; Lappalainen, Tuuli ; Devine, Scott E. ; Liu, Xinyue ; Maroo, Ankit ; Tallon, Luke J. ; Rosenfeld, Jeffrey A. ; Michelson, Leslie P. ; Angius, Andrea ; Cucca, Francesco ; Sanna, Serena ; Bigham, Abigail ; Jones, Chris ; Reinier, Fred ; Li, Yun ; Lyons, Robert ; Schlessinger, David ; Awadalla, Philip ; Hodgkinson, Alan ; Oleksyk, Taras K. ; Martinez-Cruzado, Juan C. ; Fu, Yunxin ; Liu, Xiaoming ; Xiong, Momiao ; Jorde, Lynn ; Witherspoon, David ; Xing, Jinchuan ; Browning, Brian L. ; Hajirasouliha, Iman ; Chen, Ken ; Albers, Cornelis A. ; Gerstein, Mark B. ; Abyzov, Alexej ; Chen, Jieming ; Fu, Yao ; Habegger, Lukas ; Harmanci, Arif O. ; Mu, Xinmeng Jasmine ; Sisu, Cristina ; Balasubramanian, Suganthi ; Jin, Mike ; Khurana, Ekta ; Clarke, Declan ; Michaelson, Jacob J. ; OSullivan, Chris ; Barnes, Kathleen C. ; Gharani, Neda ; Toji, Lorraine H. ; Gerry, Norman ; Kaye, Jane S. ; Kent, Alastair ; Mathias, Rasika ; Ossorio, Pilar N. ; Parker, Michael ; Rotimi, Charles N. ; Royal, Charmaine D. ; Tishkoff, Sarah ; Via, Marc ; Bodmer, Walter ; Bedoya, Gabriel ; Yang, Gao ; You, Chu Jia ; Garcia-Montero, Andres ; Orfao, Alberto ; Dutil, Julie ; Brooks, Lisa D. ; Felsenfeld, Adam L. ; McEwen, Jean E. ; Clemm, Nicholas C. ; Guyer, Mark S. ; Peterson, Jane L. ; Duncanson, Audrey ; Dunn, Michael ; Peltonen, Leena. / Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. In: Nature communications. 2014 ; Vol. 5.
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title = "Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel",
abstract = "A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.",
author = "Olivier Delaneau and Jonathan Marchini and McVeanh, {Gil A.} and Peter Donnelly and Gerton Lunter and Marchini, {Jonathan L.} and Simon Myers and Anjali Gupta-Hinch and Zamin Iqbal and Iain Mathieson and Andy Rimmer and Xifara, {Dionysia K.} and Angeliki Kerasidou and Claire Churchhouse and Altshuler, {David M.} and Gabriel, {Stacey B.} and Lander, {Eric S.} and Namrata Gupta and Daly, {Mark J.} and DePristo, {Mark A.} and Eric Banks and Gaurav Bhatia and Carneiro, {Mauricio O.} and {Del Angel}, Guillermo and Giulio Genovese and Handsaker, {Robert E.} and Chris Hartl and McCarroll, {Steven A.} and Nemesh, {James C.} and Poplin, {Ryan E.} and Schaffner, {Stephen F.} and Khalid Shakir and Sabeti, {Pardis C.} and Grossman, {Sharon R.} and Shervin Tabrizi and Ridhi Tariyal and Heng Li and David Reich and Durbin, {Richard M.} and Hurles, {Matthew E.} and Senduran Balasubramaniam and John Burton and Petr Danecek and Keane, {Thomas M.} and Anja Kolb-Kokocinski and Shane McCarthy and James Stalker and Michael Quail and Qasim Ayub and Yuan Chen and Coffey, {Alison J.} and Vincenza Colonna and Ni Huang and Luke Jostins and Aylwyn Scally and Klaudia Walter and Yali Xue and Yujun Zhang and Ben Blackburne and Lindsay, {Sarah J.} and Zemin Ning and Adam Frankish and Jennifer Harrow and Chris, {Tyler S.} and Abecasis, {Gonalo R.} and Kang, {Hyun Min} and Paul Anderson and Tom Blackwell and Fabio Busonero and Christian Fuchsberger and Goo Jun and Andrea Maschio and Eleonora Porcu and Carlo Sidore and Adrian Tan and Trost, {Mary Kate} and Bentley, {David R.} and Russell Grocock and Sean Humphray and Terena James and Zoya Kingsbury and Markus Bauer and Cheetham, {R. Keira} and Tony Cox and Michael Eberle and Lisa Murray and Richard Shaw and Aravinda Chakravarti and Clark, {Andrew G.} and Alon Keinan and Rodriguez-Flores, {Juan L.} and {De LaVega}, {Francisco M.} and Jeremiah Degenhardt and Eichler, {Evan E.} and Paul Flicek and Laura Clarke and Rasko Leinonen and Smith, {Richard E.} and Xiangqun Zheng-Bradley and Kathryn Beal and Fiona Cunningham and Javier Herrero and McLaren, {William M.} and Ritchie, {Graham R.S.} and Jonathan Barker and Gavin Kelman and Eugene Kulesha and Rajesh Radhakrishnan and Asier Roa and Dmitriy Smirnov and Ian Streeter and Iliana Toneva and Gibbs, {Richard A.} and Huyen Dinh and Christie Kovar and Sandra Lee and Lora Lewis and Donna Muzny and Jeff Reid and Min Wang and Fuli Yu and Matthew Bainbridge and Danny Challis and Evani, {Uday S.} and James Lu and Uma Nagaswamy and Aniko Sabo and Yi Wang and Jin Yu and Gerald Fowler and Walker Hale and Divya Kalra and Green, {Eric D.} and Knoppers, {Bartha M.} and Korbel, {Jan O.} and Tobias Rausch and Sttz, {Adrian M.} and Charles Lee and Lauren Griffin and Hsieh, {Chih Heng} and Mills, {Ryan E.} and {Von Grotthuss}, Marcin and Chengsheng Zhang and Xinghua Shi and Hans Lehrach and Ralf Sudbrak and Amstislavskiy, {Vyacheslav S.} and Matthias Lienhard and Florian Mertes and Marc Sultan and Bernd Timmermann and Yaspo, {Marie Laure} and Herwig, {Sudbrak Ralf} and Mardis, {Elaine R.} and Wilson, {Richard K.} and Lucinda Fulton and Robert Fulton and Weinstock, {George M.} and Asif Chinwalla and Li Ding and David Dooling and Koboldt, {Daniel C.} and McLellan, {Michael D.} and Wallis, {John W.} and Wendl, {Michael C.} and Qunyuan Zhang and Marth, {Gabor T.} and Garrison, {Erik P.} and Deniz Kural and Lee, {Wan Ping} and Leong, {Wen Fung} and Ward, {Alistair N.} and Jiantao Wu and Mengyao Zhang and Nickerson, {Deborah A.} and Can Alkan and Fereydoun Hormozdiari and Arthur Ko and Sudmant, {Peter H.} and Schmidt, {Jeanette P.} and Davies, {Christopher J.} and Jeremy Gollub and Teresa Webster and Brant Wong and Yiping Zhan and Sherry, {Stephen T.} and Chunlin Xiao and Deanna Church and Victor Ananiev and Zinaida Belaia and Dimitriy Beloslyudtsev and Nathan Bouk and Chao Chen and Robert Cohen and Charles Cook and John Garner and Timothy Hefferon and Mikhail Kimelman and Chunlei Liu and John Lopez and Peter Meric and Yuri Ostapchuk and Lon Phan and Sergiy Ponomarov and Valerie Schneider and Eugene Shekhtman and Karl Sirotkin and Douglas Slotta and Hua Zhang and Jun Wang and Xiaodong Fang and Xiaosen Guo and Min Jian and Hui Jiang and Xin Jin and Guoqing Li and Jingxiang Li and Yingrui Li and Xiao Liu and Yao Lu and Xuedi Ma and Shuaishuai Tai and Meifang Tang and Bo Wang and Guangbiao Wang and Honglong Wu and Renhua Wu and Ye Yin and Wenwei Zhang and Jiao Zhao and Meiru Zhao and Xiaole Zheng and Hans Lachlan and Lin Fang and Qibin Li and Zhenyu Li and Haoxiang Lin and Binghang Liu and Ruibang Luo and Haojing Shao and Bingqiang Wang and Yinlong Xie and Chen Ye and Chang Yu and Hancheng Zheng and Hongmei Zhu and Hongyu Cai and Hongzhi Cao and Yeyang Su and Zhongming Tian and Huanming Yang and Ling Yang and Jiayong Zhu and Zhiming Cai and Jian Wang and Albrecht, {Marcus W.} and Borodina, {Tatiana A.} and Adam Auton and Yoon, {Seungtai C.} and Jayon Lihm and Vladimir Makarov and Hanjun Jin and Wook Kim and Kim, {Ki Cheol} and Srikanth Gottipati and Danielle Jones and Cooper, {David N.} and Ball, {Edward V.} and Stenson, {Peter D.} and Bret Barnes and Scott Kahn and Kai Ye and Batzer, {Mark A.} and Konkel, {Miriam K.} and Walker, {Jerilyn A.} and MacArthur, {Daniel G.} and Monkol Lek and Shriver, {Mark D.} and Bustamante, {Carlos D.} and Simon Gravel and Kenny, {Eimear E.} and Kidd, {Jeffrey M.} and Phil Lacroute and Maples, {Brian K.} and Andres Moreno-Estrada and Fouad Zakharia and Brenna Henn and Karla Sandoval and Byrnes, {Jake K.} and Eran Halperin and Yael Baran and Craig, {David W.} and Alexis Christoforides and Tyler Izatt and Kurdoglu, {Ahmet A.} and Sinari, {Shripad A.} and Nils Homer and Kevin Squire and Jonathan Sebat and Vineet Bafna and Kenny Ye and Burchard, {Esteban G.} and Hernandez, {Ryan D.} and Gignoux, {Christopher R.} and David Haussler and Katzman, {Sol J.} and Kent, {W. James} and Bryan Howie and Andres Ruiz-Linares and Dermitzakis, {Emmanouil T.} and Tuuli Lappalainen and Devine, {Scott E.} and Xinyue Liu and Ankit Maroo and Tallon, {Luke J.} and Rosenfeld, {Jeffrey A.} and Michelson, {Leslie P.} and Andrea Angius and Francesco Cucca and Serena Sanna and Abigail Bigham and Chris Jones and Fred Reinier and Yun Li and Robert Lyons and David Schlessinger and Philip Awadalla and Alan Hodgkinson and Oleksyk, {Taras K.} and Martinez-Cruzado, {Juan C.} and Yunxin Fu and Xiaoming Liu and Momiao Xiong and Lynn Jorde and David Witherspoon and Jinchuan Xing and Browning, {Brian L.} and Iman Hajirasouliha and Ken Chen and Albers, {Cornelis A.} and Gerstein, {Mark B.} and Alexej Abyzov and Jieming Chen and Yao Fu and Lukas Habegger and Harmanci, {Arif O.} and Mu, {Xinmeng Jasmine} and Cristina Sisu and Suganthi Balasubramanian and Mike Jin and Ekta Khurana and Declan Clarke and Michaelson, {Jacob J.} and Chris OSullivan and Barnes, {Kathleen C.} and Neda Gharani and Toji, {Lorraine H.} and Norman Gerry and Kaye, {Jane S.} and Alastair Kent and Rasika Mathias and Ossorio, {Pilar N.} and Michael Parker and Rotimi, {Charles N.} and Royal, {Charmaine D.} and Sarah Tishkoff and Marc Via and Walter Bodmer and Gabriel Bedoya and Gao Yang and You, {Chu Jia} and Andres Garcia-Montero and Alberto Orfao and Julie Dutil and Brooks, {Lisa D.} and Felsenfeld, {Adam L.} and McEwen, {Jean E.} and Clemm, {Nicholas C.} and Guyer, {Mark S.} and Peterson, {Jane L.} and Audrey Duncanson and Michael Dunn and Leena Peltonen",
year = "2014",
month = "6",
day = "13",
doi = "10.1038/ncomms4934",
language = "English (US)",
volume = "5",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",

}

Delaneau, O, Marchini, J, McVeanh, GA, Donnelly, P, Lunter, G, Marchini, JL, Myers, S, Gupta-Hinch, A, Iqbal, Z, Mathieson, I, Rimmer, A, Xifara, DK, Kerasidou, A, Churchhouse, C, Altshuler, DM, Gabriel, SB, Lander, ES, Gupta, N, Daly, MJ, DePristo, MA, Banks, E, Bhatia, G, Carneiro, MO, Del Angel, G, Genovese, G, Handsaker, RE, Hartl, C, McCarroll, SA, Nemesh, JC, Poplin, RE, Schaffner, SF, Shakir, K, Sabeti, PC, Grossman, SR, Tabrizi, S, Tariyal, R, Li, H, Reich, D, Durbin, RM, Hurles, ME, Balasubramaniam, S, Burton, J, Danecek, P, Keane, TM, Kolb-Kokocinski, A, McCarthy, S, Stalker, J, Quail, M, Ayub, Q, Chen, Y, Coffey, AJ, Colonna, V, Huang, N, Jostins, L, Scally, A, Walter, K, Xue, Y, Zhang, Y, Blackburne, B, Lindsay, SJ, Ning, Z, Frankish, A, Harrow, J, Chris, TS, Abecasis, GR, Kang, HM, Anderson, P, Blackwell, T, Busonero, F, Fuchsberger, C, Jun, G, Maschio, A, Porcu, E, Sidore, C, Tan, A, Trost, MK, Bentley, DR, Grocock, R, Humphray, S, James, T, Kingsbury, Z, Bauer, M, Cheetham, RK, Cox, T, Eberle, M, Murray, L, Shaw, R, Chakravarti, A, Clark, AG, Keinan, A, Rodriguez-Flores, JL, De LaVega, FM, Degenhardt, J, Eichler, EE, Flicek, P, Clarke, L, Leinonen, R, Smith, RE, Zheng-Bradley, X, Beal, K, Cunningham, F, Herrero, J, McLaren, WM, Ritchie, GRS, Barker, J, Kelman, G, Kulesha, E, Radhakrishnan, R, Roa, A, Smirnov, D, Streeter, I, Toneva, I, Gibbs, RA, Dinh, H, Kovar, C, Lee, S, Lewis, L, Muzny, D, Reid, J, Wang, M, Yu, F, Bainbridge, M, Challis, D, Evani, US, Lu, J, Nagaswamy, U, Sabo, A, Wang, Y, Yu, J, Fowler, G, Hale, W, Kalra, D, Green, ED, Knoppers, BM, Korbel, JO, Rausch, T, Sttz, AM, Lee, C, Griffin, L, Hsieh, CH, Mills, RE, Von Grotthuss, M, Zhang, C, Shi, X, Lehrach, H, Sudbrak, R, Amstislavskiy, VS, Lienhard, M, Mertes, F, Sultan, M, Timmermann, B, Yaspo, ML, Herwig, SR, Mardis, ER, Wilson, RK, Fulton, L, Fulton, R, Weinstock, GM, Chinwalla, A, Ding, L, Dooling, D, Koboldt, DC, McLellan, MD, Wallis, JW, Wendl, MC, Zhang, Q, Marth, GT, Garrison, EP, Kural, D, Lee, WP, Leong, WF, Ward, AN, Wu, J, Zhang, M, Nickerson, DA, Alkan, C, Hormozdiari, F, Ko, A, Sudmant, PH, Schmidt, JP, Davies, CJ, Gollub, J, Webster, T, Wong, B, Zhan, Y, Sherry, ST, Xiao, C, Church, D, Ananiev, V, Belaia, Z, Beloslyudtsev, D, Bouk, N, Chen, C, Cohen, R, Cook, C, Garner, J, Hefferon, T, Kimelman, M, Liu, C, Lopez, J, Meric, P, Ostapchuk, Y, Phan, L, Ponomarov, S, Schneider, V, Shekhtman, E, Sirotkin, K, Slotta, D, Zhang, H, Wang, J, Fang, X, Guo, X, Jian, M, Jiang, H, Jin, X, Li, G, Li, J, Li, Y, Liu, X, Lu, Y, Ma, X, Tai, S, Tang, M, Wang, B, Wang, G, Wu, H, Wu, R, Yin, Y, Zhang, W, Zhao, J, Zhao, M, Zheng, X, Lachlan, H, Fang, L, Li, Q, Li, Z, Lin, H, Liu, B, Luo, R, Shao, H, Wang, B, Xie, Y, Ye, C, Yu, C, Zheng, H, Zhu, H, Cai, H, Cao, H, Su, Y, Tian, Z, Yang, H, Yang, L, Zhu, J, Cai, Z, Wang, J, Albrecht, MW, Borodina, TA, Auton, A, Yoon, SC, Lihm, J, Makarov, V, Jin, H, Kim, W, Kim, KC, Gottipati, S, Jones, D, Cooper, DN, Ball, EV, Stenson, PD, Barnes, B, Kahn, S, Ye, K, Batzer, MA, Konkel, MK, Walker, JA, MacArthur, DG, Lek, M, Shriver, MD, Bustamante, CD, Gravel, S, Kenny, EE, Kidd, JM, Lacroute, P, Maples, BK, Moreno-Estrada, A, Zakharia, F, Henn, B, Sandoval, K, Byrnes, JK, Halperin, E, Baran, Y, Craig, DW, Christoforides, A, Izatt, T, Kurdoglu, AA, Sinari, SA, Homer, N, Squire, K, Sebat, J, Bafna, V, Ye, K, Burchard, EG, Hernandez, RD, Gignoux, CR, Haussler, D, Katzman, SJ, Kent, WJ, Howie, B, Ruiz-Linares, A, Dermitzakis, ET, Lappalainen, T, Devine, SE, Liu, X, Maroo, A, Tallon, LJ, Rosenfeld, JA, Michelson, LP, Angius, A, Cucca, F, Sanna, S, Bigham, A, Jones, C, Reinier, F, Li, Y, Lyons, R, Schlessinger, D, Awadalla, P, Hodgkinson, A, Oleksyk, TK, Martinez-Cruzado, JC, Fu, Y, Liu, X, Xiong, M, Jorde, L, Witherspoon, D, Xing, J, Browning, BL, Hajirasouliha, I, Chen, K, Albers, CA, Gerstein, MB, Abyzov, A, Chen, J, Fu, Y, Habegger, L, Harmanci, AO, Mu, XJ, Sisu, C, Balasubramanian, S, Jin, M, Khurana, E, Clarke, D, Michaelson, JJ, OSullivan, C, Barnes, KC, Gharani, N, Toji, LH, Gerry, N, Kaye, JS, Kent, A, Mathias, R, Ossorio, PN, Parker, M, Rotimi, CN, Royal, CD, Tishkoff, S, Via, M, Bodmer, W, Bedoya, G, Yang, G, You, CJ, Garcia-Montero, A, Orfao, A, Dutil, J, Brooks, LD, Felsenfeld, AL, McEwen, JE, Clemm, NC, Guyer, MS, Peterson, JL, Duncanson, A, Dunn, M & Peltonen, L 2014, 'Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel', Nature communications, vol. 5, 3934. https://doi.org/10.1038/ncomms4934

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. / Delaneau, Olivier; Marchini, Jonathan; McVeanh, Gil A.; Donnelly, Peter; Lunter, Gerton; Marchini, Jonathan L.; Myers, Simon; Gupta-Hinch, Anjali; Iqbal, Zamin; Mathieson, Iain; Rimmer, Andy; Xifara, Dionysia K.; Kerasidou, Angeliki; Churchhouse, Claire; Altshuler, David M.; Gabriel, Stacey B.; Lander, Eric S.; Gupta, Namrata; Daly, Mark J.; DePristo, Mark A.; Banks, Eric; Bhatia, Gaurav; Carneiro, Mauricio O.; Del Angel, Guillermo; Genovese, Giulio; Handsaker, Robert E.; Hartl, Chris; McCarroll, Steven A.; Nemesh, James C.; Poplin, Ryan E.; Schaffner, Stephen F.; Shakir, Khalid; Sabeti, Pardis C.; Grossman, Sharon R.; Tabrizi, Shervin; Tariyal, Ridhi; Li, Heng; Reich, David; Durbin, Richard M.; Hurles, Matthew E.; Balasubramaniam, Senduran; Burton, John; Danecek, Petr; Keane, Thomas M.; Kolb-Kokocinski, Anja; McCarthy, Shane; Stalker, James; Quail, Michael; Ayub, Qasim; Chen, Yuan; Coffey, Alison J.; Colonna, Vincenza; Huang, Ni; Jostins, Luke; Scally, Aylwyn; Walter, Klaudia; Xue, Yali; Zhang, Yujun; Blackburne, Ben; Lindsay, Sarah J.; Ning, Zemin; Frankish, Adam; Harrow, Jennifer; Chris, Tyler S.; Abecasis, Gonalo R.; Kang, Hyun Min; Anderson, Paul; Blackwell, Tom; Busonero, Fabio; Fuchsberger, Christian; Jun, Goo; Maschio, Andrea; Porcu, Eleonora; Sidore, Carlo; Tan, Adrian; Trost, Mary Kate; Bentley, David R.; Grocock, Russell; Humphray, Sean; James, Terena; Kingsbury, Zoya; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; Murray, Lisa; Shaw, Richard; Chakravarti, Aravinda; Clark, Andrew G.; Keinan, Alon; Rodriguez-Flores, Juan L.; De LaVega, Francisco M.; Degenhardt, Jeremiah; Eichler, Evan E.; Flicek, Paul; Clarke, Laura; Leinonen, Rasko; Smith, Richard E.; Zheng-Bradley, Xiangqun; Beal, Kathryn; Cunningham, Fiona; Herrero, Javier; McLaren, William M.; Ritchie, Graham R.S.; Barker, Jonathan; Kelman, Gavin; Kulesha, Eugene; Radhakrishnan, Rajesh; Roa, Asier; Smirnov, Dmitriy; Streeter, Ian; Toneva, Iliana; Gibbs, Richard A.; Dinh, Huyen; Kovar, Christie; Lee, Sandra; Lewis, Lora; Muzny, Donna; Reid, Jeff; Wang, Min; Yu, Fuli; Bainbridge, Matthew; Challis, Danny; Evani, Uday S.; Lu, James; Nagaswamy, Uma; Sabo, Aniko; Wang, Yi; Yu, Jin; Fowler, Gerald; Hale, Walker; Kalra, Divya; Green, Eric D.; Knoppers, Bartha M.; Korbel, Jan O.; Rausch, Tobias; Sttz, Adrian M.; Lee, Charles; Griffin, Lauren; Hsieh, Chih Heng; Mills, Ryan E.; Von Grotthuss, Marcin; Zhang, Chengsheng; Shi, Xinghua; Lehrach, Hans; Sudbrak, Ralf; Amstislavskiy, Vyacheslav S.; Lienhard, Matthias; Mertes, Florian; Sultan, Marc; Timmermann, Bernd; Yaspo, Marie Laure; Herwig, Sudbrak Ralf; Mardis, Elaine R.; Wilson, Richard K.; Fulton, Lucinda; Fulton, Robert; Weinstock, George M.; Chinwalla, Asif; Ding, Li; Dooling, David; Koboldt, Daniel C.; McLellan, Michael D.; Wallis, John W.; Wendl, Michael C.; Zhang, Qunyuan; Marth, Gabor T.; Garrison, Erik P.; Kural, Deniz; Lee, Wan Ping; Leong, Wen Fung; Ward, Alistair N.; Wu, Jiantao; Zhang, Mengyao; Nickerson, Deborah A.; Alkan, Can; Hormozdiari, Fereydoun; Ko, Arthur; Sudmant, Peter H.; Schmidt, Jeanette P.; Davies, Christopher J.; Gollub, Jeremy; Webster, Teresa; Wong, Brant; Zhan, Yiping; Sherry, Stephen T.; Xiao, Chunlin; Church, Deanna; Ananiev, Victor; Belaia, Zinaida; Beloslyudtsev, Dimitriy; Bouk, Nathan; Chen, Chao; Cohen, Robert; Cook, Charles; Garner, John; Hefferon, Timothy; Kimelman, Mikhail; Liu, Chunlei; Lopez, John; Meric, Peter; Ostapchuk, Yuri; Phan, Lon; Ponomarov, Sergiy; Schneider, Valerie; Shekhtman, Eugene; Sirotkin, Karl; Slotta, Douglas; Zhang, Hua; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Jian, Min; Jiang, Hui; Jin, Xin; Li, Guoqing; Li, Jingxiang; Li, Yingrui; Liu, Xiao; Lu, Yao; Ma, Xuedi; Tai, Shuaishuai; Tang, Meifang; Wang, Bo; Wang, Guangbiao; Wu, Honglong; Wu, Renhua; Yin, Ye; Zhang, Wenwei; Zhao, Jiao; Zhao, Meiru; Zheng, Xiaole; Lachlan, Hans; Fang, Lin; Li, Qibin; Li, Zhenyu; Lin, Haoxiang; Liu, Binghang; Luo, Ruibang; Shao, Haojing; Wang, Bingqiang; Xie, Yinlong; Ye, Chen; Yu, Chang; Zheng, Hancheng; Zhu, Hongmei; Cai, Hongyu; Cao, Hongzhi; Su, Yeyang; Tian, Zhongming; Yang, Huanming; Yang, Ling; Zhu, Jiayong; Cai, Zhiming; Wang, Jian; Albrecht, Marcus W.; Borodina, Tatiana A.; Auton, Adam; Yoon, Seungtai C.; Lihm, Jayon; Makarov, Vladimir; Jin, Hanjun; Kim, Wook; Kim, Ki Cheol; Gottipati, Srikanth; Jones, Danielle; Cooper, David N.; Ball, Edward V.; Stenson, Peter D.; Barnes, Bret; Kahn, Scott; Ye, Kai; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; MacArthur, Daniel G.; Lek, Monkol; Shriver, Mark D.; Bustamante, Carlos D.; Gravel, Simon; Kenny, Eimear E.; Kidd, Jeffrey M.; Lacroute, Phil; Maples, Brian K.; Moreno-Estrada, Andres; Zakharia, Fouad; Henn, Brenna; Sandoval, Karla; Byrnes, Jake K.; Halperin, Eran; Baran, Yael; Craig, David W.; Christoforides, Alexis; Izatt, Tyler; Kurdoglu, Ahmet A.; Sinari, Shripad A.; Homer, Nils; Squire, Kevin; Sebat, Jonathan; Bafna, Vineet; Ye, Kenny; Burchard, Esteban G.; Hernandez, Ryan D.; Gignoux, Christopher R.; Haussler, David; Katzman, Sol J.; Kent, W. James; Howie, Bryan; Ruiz-Linares, Andres; Dermitzakis, Emmanouil T.; Lappalainen, Tuuli; Devine, Scott E.; Liu, Xinyue; Maroo, Ankit; Tallon, Luke J.; Rosenfeld, Jeffrey A.; Michelson, Leslie P.; Angius, Andrea; Cucca, Francesco; Sanna, Serena; Bigham, Abigail; Jones, Chris; Reinier, Fred; Li, Yun; Lyons, Robert; Schlessinger, David; Awadalla, Philip; Hodgkinson, Alan; Oleksyk, Taras K.; Martinez-Cruzado, Juan C.; Fu, Yunxin; Liu, Xiaoming; Xiong, Momiao; Jorde, Lynn; Witherspoon, David; Xing, Jinchuan; Browning, Brian L.; Hajirasouliha, Iman; Chen, Ken; Albers, Cornelis A.; Gerstein, Mark B.; Abyzov, Alexej; Chen, Jieming; Fu, Yao; Habegger, Lukas; Harmanci, Arif O.; Mu, Xinmeng Jasmine; Sisu, Cristina; Balasubramanian, Suganthi; Jin, Mike; Khurana, Ekta; Clarke, Declan; Michaelson, Jacob J.; OSullivan, Chris; Barnes, Kathleen C.; Gharani, Neda; Toji, Lorraine H.; Gerry, Norman; Kaye, Jane S.; Kent, Alastair; Mathias, Rasika; Ossorio, Pilar N.; Parker, Michael; Rotimi, Charles N.; Royal, Charmaine D.; Tishkoff, Sarah; Via, Marc; Bodmer, Walter; Bedoya, Gabriel; Yang, Gao; You, Chu Jia; Garcia-Montero, Andres; Orfao, Alberto; Dutil, Julie; Brooks, Lisa D.; Felsenfeld, Adam L.; McEwen, Jean E.; Clemm, Nicholas C.; Guyer, Mark S.; Peterson, Jane L.; Duncanson, Audrey; Dunn, Michael; Peltonen, Leena.

In: Nature communications, Vol. 5, 3934, 13.06.2014.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

AU - Delaneau, Olivier

AU - Marchini, Jonathan

AU - McVeanh, Gil A.

AU - Donnelly, Peter

AU - Lunter, Gerton

AU - Marchini, Jonathan L.

AU - Myers, Simon

AU - Gupta-Hinch, Anjali

AU - Iqbal, Zamin

AU - Mathieson, Iain

AU - Rimmer, Andy

AU - Xifara, Dionysia K.

AU - Kerasidou, Angeliki

AU - Churchhouse, Claire

AU - Altshuler, David M.

AU - Gabriel, Stacey B.

AU - Lander, Eric S.

AU - Gupta, Namrata

AU - Daly, Mark J.

AU - DePristo, Mark A.

AU - Banks, Eric

AU - Bhatia, Gaurav

AU - Carneiro, Mauricio O.

AU - Del Angel, Guillermo

AU - Genovese, Giulio

AU - Handsaker, Robert E.

AU - Hartl, Chris

AU - McCarroll, Steven A.

AU - Nemesh, James C.

AU - Poplin, Ryan E.

AU - Schaffner, Stephen F.

AU - Shakir, Khalid

AU - Sabeti, Pardis C.

AU - Grossman, Sharon R.

AU - Tabrizi, Shervin

AU - Tariyal, Ridhi

AU - Li, Heng

AU - Reich, David

AU - Durbin, Richard M.

AU - Hurles, Matthew E.

AU - Balasubramaniam, Senduran

AU - Burton, John

AU - Danecek, Petr

AU - Keane, Thomas M.

AU - Kolb-Kokocinski, Anja

AU - McCarthy, Shane

AU - Stalker, James

AU - Quail, Michael

AU - Ayub, Qasim

AU - Chen, Yuan

AU - Coffey, Alison J.

AU - Colonna, Vincenza

AU - Huang, Ni

AU - Jostins, Luke

AU - Scally, Aylwyn

AU - Walter, Klaudia

AU - Xue, Yali

AU - Zhang, Yujun

AU - Blackburne, Ben

AU - Lindsay, Sarah J.

AU - Ning, Zemin

AU - Frankish, Adam

AU - Harrow, Jennifer

AU - Chris, Tyler S.

AU - Abecasis, Gonalo R.

AU - Kang, Hyun Min

AU - Anderson, Paul

AU - Blackwell, Tom

AU - Busonero, Fabio

AU - Fuchsberger, Christian

AU - Jun, Goo

AU - Maschio, Andrea

AU - Porcu, Eleonora

AU - Sidore, Carlo

AU - Tan, Adrian

AU - Trost, Mary Kate

AU - Bentley, David R.

AU - Grocock, Russell

AU - Humphray, Sean

AU - James, Terena

AU - Kingsbury, Zoya

AU - Bauer, Markus

AU - Cheetham, R. Keira

AU - Cox, Tony

AU - Eberle, Michael

AU - Murray, Lisa

AU - Shaw, Richard

AU - Chakravarti, Aravinda

AU - Clark, Andrew G.

AU - Keinan, Alon

AU - Rodriguez-Flores, Juan L.

AU - De LaVega, Francisco M.

AU - Degenhardt, Jeremiah

AU - Eichler, Evan E.

AU - Flicek, Paul

AU - Clarke, Laura

AU - Leinonen, Rasko

AU - Smith, Richard E.

AU - Zheng-Bradley, Xiangqun

AU - Beal, Kathryn

AU - Cunningham, Fiona

AU - Herrero, Javier

AU - McLaren, William M.

AU - Ritchie, Graham R.S.

AU - Barker, Jonathan

AU - Kelman, Gavin

AU - Kulesha, Eugene

AU - Radhakrishnan, Rajesh

AU - Roa, Asier

AU - Smirnov, Dmitriy

AU - Streeter, Ian

AU - Toneva, Iliana

AU - Gibbs, Richard A.

AU - Dinh, Huyen

AU - Kovar, Christie

AU - Lee, Sandra

AU - Lewis, Lora

AU - Muzny, Donna

AU - Reid, Jeff

AU - Wang, Min

AU - Yu, Fuli

AU - Bainbridge, Matthew

AU - Challis, Danny

AU - Evani, Uday S.

AU - Lu, James

AU - Nagaswamy, Uma

AU - Sabo, Aniko

AU - Wang, Yi

AU - Yu, Jin

AU - Fowler, Gerald

AU - Hale, Walker

AU - Kalra, Divya

AU - Green, Eric D.

AU - Knoppers, Bartha M.

AU - Korbel, Jan O.

AU - Rausch, Tobias

AU - Sttz, Adrian M.

AU - Lee, Charles

AU - Griffin, Lauren

AU - Hsieh, Chih Heng

AU - Mills, Ryan E.

AU - Von Grotthuss, Marcin

AU - Zhang, Chengsheng

AU - Shi, Xinghua

AU - Lehrach, Hans

AU - Sudbrak, Ralf

AU - Amstislavskiy, Vyacheslav S.

AU - Lienhard, Matthias

AU - Mertes, Florian

AU - Sultan, Marc

AU - Timmermann, Bernd

AU - Yaspo, Marie Laure

AU - Herwig, Sudbrak Ralf

AU - Mardis, Elaine R.

AU - Wilson, Richard K.

AU - Fulton, Lucinda

AU - Fulton, Robert

AU - Weinstock, George M.

AU - Chinwalla, Asif

AU - Ding, Li

AU - Dooling, David

AU - Koboldt, Daniel C.

AU - McLellan, Michael D.

AU - Wallis, John W.

AU - Wendl, Michael C.

AU - Zhang, Qunyuan

AU - Marth, Gabor T.

AU - Garrison, Erik P.

AU - Kural, Deniz

AU - Lee, Wan Ping

AU - Leong, Wen Fung

AU - Ward, Alistair N.

AU - Wu, Jiantao

AU - Zhang, Mengyao

AU - Nickerson, Deborah A.

AU - Alkan, Can

AU - Hormozdiari, Fereydoun

AU - Ko, Arthur

AU - Sudmant, Peter H.

AU - Schmidt, Jeanette P.

AU - Davies, Christopher J.

AU - Gollub, Jeremy

AU - Webster, Teresa

AU - Wong, Brant

AU - Zhan, Yiping

AU - Sherry, Stephen T.

AU - Xiao, Chunlin

AU - Church, Deanna

AU - Ananiev, Victor

AU - Belaia, Zinaida

AU - Beloslyudtsev, Dimitriy

AU - Bouk, Nathan

AU - Chen, Chao

AU - Cohen, Robert

AU - Cook, Charles

AU - Garner, John

AU - Hefferon, Timothy

AU - Kimelman, Mikhail

AU - Liu, Chunlei

AU - Lopez, John

AU - Meric, Peter

AU - Ostapchuk, Yuri

AU - Phan, Lon

AU - Ponomarov, Sergiy

AU - Schneider, Valerie

AU - Shekhtman, Eugene

AU - Sirotkin, Karl

AU - Slotta, Douglas

AU - Zhang, Hua

AU - Wang, Jun

AU - Fang, Xiaodong

AU - Guo, Xiaosen

AU - Jian, Min

AU - Jiang, Hui

AU - Jin, Xin

AU - Li, Guoqing

AU - Li, Jingxiang

AU - Li, Yingrui

AU - Liu, Xiao

AU - Lu, Yao

AU - Ma, Xuedi

AU - Tai, Shuaishuai

AU - Tang, Meifang

AU - Wang, Bo

AU - Wang, Guangbiao

AU - Wu, Honglong

AU - Wu, Renhua

AU - Yin, Ye

AU - Zhang, Wenwei

AU - Zhao, Jiao

AU - Zhao, Meiru

AU - Zheng, Xiaole

AU - Lachlan, Hans

AU - Fang, Lin

AU - Li, Qibin

AU - Li, Zhenyu

AU - Lin, Haoxiang

AU - Liu, Binghang

AU - Luo, Ruibang

AU - Shao, Haojing

AU - Wang, Bingqiang

AU - Xie, Yinlong

AU - Ye, Chen

AU - Yu, Chang

AU - Zheng, Hancheng

AU - Zhu, Hongmei

AU - Cai, Hongyu

AU - Cao, Hongzhi

AU - Su, Yeyang

AU - Tian, Zhongming

AU - Yang, Huanming

AU - Yang, Ling

AU - Zhu, Jiayong

AU - Cai, Zhiming

AU - Wang, Jian

AU - Albrecht, Marcus W.

AU - Borodina, Tatiana A.

AU - Auton, Adam

AU - Yoon, Seungtai C.

AU - Lihm, Jayon

AU - Makarov, Vladimir

AU - Jin, Hanjun

AU - Kim, Wook

AU - Kim, Ki Cheol

AU - Gottipati, Srikanth

AU - Jones, Danielle

AU - Cooper, David N.

AU - Ball, Edward V.

AU - Stenson, Peter D.

AU - Barnes, Bret

AU - Kahn, Scott

AU - Ye, Kai

AU - Batzer, Mark A.

AU - Konkel, Miriam K.

AU - Walker, Jerilyn A.

AU - MacArthur, Daniel G.

AU - Lek, Monkol

AU - Shriver, Mark D.

AU - Bustamante, Carlos D.

AU - Gravel, Simon

AU - Kenny, Eimear E.

AU - Kidd, Jeffrey M.

AU - Lacroute, Phil

AU - Maples, Brian K.

AU - Moreno-Estrada, Andres

AU - Zakharia, Fouad

AU - Henn, Brenna

AU - Sandoval, Karla

AU - Byrnes, Jake K.

AU - Halperin, Eran

AU - Baran, Yael

AU - Craig, David W.

AU - Christoforides, Alexis

AU - Izatt, Tyler

AU - Kurdoglu, Ahmet A.

AU - Sinari, Shripad A.

AU - Homer, Nils

AU - Squire, Kevin

AU - Sebat, Jonathan

AU - Bafna, Vineet

AU - Ye, Kenny

AU - Burchard, Esteban G.

AU - Hernandez, Ryan D.

AU - Gignoux, Christopher R.

AU - Haussler, David

AU - Katzman, Sol J.

AU - Kent, W. James

AU - Howie, Bryan

AU - Ruiz-Linares, Andres

AU - Dermitzakis, Emmanouil T.

AU - Lappalainen, Tuuli

AU - Devine, Scott E.

AU - Liu, Xinyue

AU - Maroo, Ankit

AU - Tallon, Luke J.

AU - Rosenfeld, Jeffrey A.

AU - Michelson, Leslie P.

AU - Angius, Andrea

AU - Cucca, Francesco

AU - Sanna, Serena

AU - Bigham, Abigail

AU - Jones, Chris

AU - Reinier, Fred

AU - Li, Yun

AU - Lyons, Robert

AU - Schlessinger, David

AU - Awadalla, Philip

AU - Hodgkinson, Alan

AU - Oleksyk, Taras K.

AU - Martinez-Cruzado, Juan C.

AU - Fu, Yunxin

AU - Liu, Xiaoming

AU - Xiong, Momiao

AU - Jorde, Lynn

AU - Witherspoon, David

AU - Xing, Jinchuan

AU - Browning, Brian L.

AU - Hajirasouliha, Iman

AU - Chen, Ken

AU - Albers, Cornelis A.

AU - Gerstein, Mark B.

AU - Abyzov, Alexej

AU - Chen, Jieming

AU - Fu, Yao

AU - Habegger, Lukas

AU - Harmanci, Arif O.

AU - Mu, Xinmeng Jasmine

AU - Sisu, Cristina

AU - Balasubramanian, Suganthi

AU - Jin, Mike

AU - Khurana, Ekta

AU - Clarke, Declan

AU - Michaelson, Jacob J.

AU - OSullivan, Chris

AU - Barnes, Kathleen C.

AU - Gharani, Neda

AU - Toji, Lorraine H.

AU - Gerry, Norman

AU - Kaye, Jane S.

AU - Kent, Alastair

AU - Mathias, Rasika

AU - Ossorio, Pilar N.

AU - Parker, Michael

AU - Rotimi, Charles N.

AU - Royal, Charmaine D.

AU - Tishkoff, Sarah

AU - Via, Marc

AU - Bodmer, Walter

AU - Bedoya, Gabriel

AU - Yang, Gao

AU - You, Chu Jia

AU - Garcia-Montero, Andres

AU - Orfao, Alberto

AU - Dutil, Julie

AU - Brooks, Lisa D.

AU - Felsenfeld, Adam L.

AU - McEwen, Jean E.

AU - Clemm, Nicholas C.

AU - Guyer, Mark S.

AU - Peterson, Jane L.

AU - Duncanson, Audrey

AU - Dunn, Michael

AU - Peltonen, Leena

PY - 2014/6/13

Y1 - 2014/6/13

N2 - A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.

AB - A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.

UR - http://www.scopus.com/inward/record.url?scp=84902504030&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84902504030&partnerID=8YFLogxK

U2 - 10.1038/ncomms4934

DO - 10.1038/ncomms4934

M3 - Article

C2 - 25653097

AN - SCOPUS:84902504030

VL - 5

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 3934

ER -