Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
Articolo
Data di Pubblicazione:
2014
Citazione:
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, Qib
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. © 2014 Macmillan Publishers Limited. All rights reserved.
Tipologia CRIS:
1.1 Articolo in rivista
Keywords:
Alleles; Gene Frequency; Haplotypes; Humans; Microarray Analysis; Polymorphism, Single Nucleotide; Algorithms; Genome, Human; Genome-Wide Association Study; Chemistry (all); Biochemistry, Genetics and Molecular Biology (all); Physics and Astronomy (all)
Elenco autori:
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; Y
Link alla scheda completa:
Pubblicato in: