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

Delaneau O.; Marchini J.; McVeanh G.A.; Donnelly P.; Lunter G.; Marchini J.L.; Myers, S.; Gupta-Hinch, A.; Iqbal, Z.; Mathieson I.; Rimmer, A.; Xifara, D.K.; Kerasidou, A.; Churchhouse, C.; Altshuler, D.M.; Gabriel, S.B.; Lander, E.S.; Gupta, N.; Daly, M.J.; DePristo, M.A.; Banks, E.; Bhatia G.; Carneiro, M.O.; Del Angel G.; Genovese G.; Handsaker, R.E.; Hartl, C.; McCarroll, S.A.; Nemesh J.C.; Poplin, R.E.; Schaffner, S.F.; Shakir, K.; Sabeti P.C.; Grossman, S.R.; Tabrizi, S.; Tariyal, R.; Li H.; Reich, D.; Durbin, R.M.; Hurles, M.E.; Balasubramaniam, S.; Burton J.; Danecek P.; Keane, T.M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker J.; Quail, M.; Ayub Q.; Chen, Y.; Coffey, A.J.; Colonna V.; Huang, N.; Jostins L.; Scally, A.; Walter, K.; Xue, Y.; Zhang, Y.; Blackburne, B.; Lindsay, S.J.; Ning, Z.; Frankish, A.; Harrow J.; Chris, T.-S.; Abecasis G.R.; Kang H.M.; Anderson P.; Blackwell, T.; Busonero F.; Fuchsberger, C.; Jun G.; Maschio, A.; Porcu, E.; Sidore, C.; Tan, A.; Trost, M.K.; Bentley, D.R.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Bauer, M.; Cheetham, R.K.; Cox, T.; Eberle, M.; Murray L.; Shaw, R.; Chakravarti, A.; Clark, A.G.; Keinan, A.; Rodriguez-Flores J.L.; De LaVega F.M.; Degenhardt J.; Eichler, E.E.; Flicek P.; Clarke L.; Leinonen, R.; Smith, R.E.; Zheng-Bradley X.; Beal, K.; Cunningham F.; Herrero J.; McLaren W.M.; Ritchie G.R.S.; Barker J.; Kelman G.; Kulesha, E.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Streeter I.; Toneva I.; Gibbs, R.A.; Dinh H.; Kovar, C.; Lee, S.; Lewis L.; Muzny, D.; Reid J.; Wang, M.; Yu F.; Bainbridge, M.; Challis, D.; Evani, U.S.; Lu J.; Nagaswamy, U.; Sabo, A.; Wang, Y.; Yu J.; Fowler G.; Hale W.; Kalra, D.; Green, E.D.; Knoppers, B.M.; Korbel J.O.; Rausch, T.; Sttz, A.M.; Lee, C.; Griffin L.; Hsieh, C.-H.; Mills, R.E.; Von Grotthuss, M.; Zhang, C.; Shi X.; Lehrach H.; Sudbrak, R.; Amstislavskiy V.S.; Lienhard, M.; Mertes F.; Sultan, M.; Timmermann, B.; Yaspo, M.L.; Herwig, S.R.; Mardis, E.R.; Wilson, R.K.; Fulton L.; Fulton, R.; Weinstock G.M.; Chinwalla, A.; Ding L.; Dooling, D.; Koboldt, D.C.; McLellan, M.D.; Wallis J.W.; Wendl, M.C.; Zhang Q.; Marth G.T.; Garrison, E.P.; Kural, D.; Lee W.-P.; Leong W.F.; Ward, A.N.; Wu J.; Zhang, M.; Nickerson, D.A.; Alkan, C.; Hormozdiari F.; Ko, A.; Sudmant P.H.; Schmidt J.P.; Davies, C.J.; Gollub J.; Webster, T.; Wong, B.; Zhan, Y.; Sherry, S.T.; 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.; 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.; Albrecht, M.W.; Borodina, T.A.; Auton, A.; Yoon, S.C.; Lihm J.; Makarov V.; Jin H.; Kim W.; Kim, K.C.; Gottipati, S.; Jones, D.; Cooper, D.N.; Ball, E.V.; Stenson P.D.; Barnes, B.; Kahn, S.; Ye, K.; Batzer, M.A.; Konkel, M.K.; Walker J.A.; MacArthur, D.G.; Lek, M.; Shriver, M.D.; Bustamante, C.D.; Gravel, S.; Kenny, E.E.; Kidd J.M.; Lacroute P.; Maples, B.K.; Moreno-Estrada, A.; Zakharia F.; Henn, B.; Sandoval, K.; Byrnes J.K.; Halperin, E.; Baran, Y.; Craig, D.W.; Christoforides, A.; Izatt, T.; Kurdoglu, A.A.; Sinari, S.A.; Homer, N.; Squire, K.; Sebat J.; Bafna V.; Burchard, E.G.; Hernandez, R.D.; Gignoux, C.R.; Haussler, D.; Katzman, S.J.; Kent W.J.; Howie, B.; Ruiz-Linares, A.; Dermitzakis, E.T.; Lappalainen, T.; Devine, S.E.; Maroo, A.; Tallon L.J.; Rosenfeld J.A.; Michelson L.P.; Angius, A.; Cucca F.; Sanna, S.; Bigham, A.; Jones, C.; Reinier F.; Lyons, R.; Schlessinger, D.; Awadalla P.; Hodgkinson, A.; Oleksyk, T.K.; Martinez-Cruzado J.C.; Fu, Y.; Xiong, M.; Jorde L.; Witherspoon, D.; Xing J.; Browning, B.L.; Hajirasouliha I.; Chen, K.; Albers, C.A.; Gerstein, M.B.; Abyzov, A.; Chen J.; Habegger L.; Harmanci, A.O.; Mu X.J.; Sisu, C.; Balasubramanian, S.; Jin, M.; Khurana, E.; Clarke, D.; Michaelson J.J.; OSullivan, C.; Barnes, K.C.; Gharani, N.; Toji L.H.; Gerry, N.; Kaye J.S.; Kent, A.; Mathias, R.; Ossorio P.N.; Parker, M.; Rotimi, C.N.; Royal, C.D.; Tishkoff, S.; Via, M.; Bodmer W.; Bedoya G.; Yang G.; You, C.J.; Garcia-Montero, A.; Orfao, A.; Dutil J.; Brooks L.D.; Felsenfeld, A.L.; McEwen J.E.; Clemm, N.C.; Guyer, M.S.; Peterson J.L.; Duncanson, A.; Dunn, M.; Peltonen L.

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

dc.citation.volumeNumber	5	en_US
dc.contributor.author	Delaneau O.	en_US
dc.contributor.author	Marchini J.	en_US
dc.contributor.author	McVeanh G.A.	en_US
dc.contributor.author	Donnelly P.	en_US
dc.contributor.author	Lunter G.	en_US
dc.contributor.author	Marchini J.L.	en_US
dc.contributor.author	Myers, S.	en_US
dc.contributor.author	Gupta-Hinch, A.	en_US
dc.contributor.author	Iqbal, Z.	en_US
dc.contributor.author	Mathieson I.	en_US
dc.contributor.author	Rimmer, A.	en_US
dc.contributor.author	Xifara, D.K.	en_US
dc.contributor.author	Kerasidou, A.	en_US
dc.contributor.author	Churchhouse, C.	en_US
dc.contributor.author	Altshuler, D.M.	en_US
dc.contributor.author	Gabriel, S.B.	en_US
dc.contributor.author	Lander, E.S.	en_US
dc.contributor.author	Gupta, N.	en_US
dc.contributor.author	Daly, M.J.	en_US
dc.contributor.author	DePristo, M.A.	en_US
dc.contributor.author	Banks, E.	en_US
dc.contributor.author	Bhatia G.	en_US
dc.contributor.author	Carneiro, M.O.	en_US
dc.contributor.author	Del Angel G.	en_US
dc.contributor.author	Genovese G.	en_US
dc.contributor.author	Handsaker, R.E.	en_US
dc.contributor.author	Hartl, C.	en_US
dc.contributor.author	McCarroll, S.A.	en_US
dc.contributor.author	Nemesh J.C.	en_US
dc.contributor.author	Poplin, R.E.	en_US
dc.contributor.author	Schaffner, S.F.	en_US
dc.contributor.author	Shakir, K.	en_US
dc.contributor.author	Sabeti P.C.	en_US
dc.contributor.author	Grossman, S.R.	en_US
dc.contributor.author	Tabrizi, S.	en_US
dc.contributor.author	Tariyal, R.	en_US
dc.contributor.author	Li H.	en_US
dc.contributor.author	Reich, D.	en_US
dc.contributor.author	Durbin, R.M.	en_US
dc.contributor.author	Hurles, M.E.	en_US
dc.contributor.author	Balasubramaniam, S.	en_US
dc.contributor.author	Burton J.	en_US
dc.contributor.author	Danecek P.	en_US
dc.contributor.author	Keane, T.M.	en_US
dc.contributor.author	Kolb-Kokocinski, A.	en_US
dc.contributor.author	McCarthy, S.	en_US
dc.contributor.author	Stalker J.	en_US
dc.contributor.author	Quail, M.	en_US
dc.contributor.author	Ayub Q.	en_US
dc.contributor.author	Chen, Y.	en_US
dc.contributor.author	Coffey, A.J.	en_US
dc.contributor.author	Colonna V.	en_US
dc.contributor.author	Huang, N.	en_US
dc.contributor.author	Jostins L.	en_US
dc.contributor.author	Scally, A.	en_US
dc.contributor.author	Walter, K.	en_US
dc.contributor.author	Xue, Y.	en_US
dc.contributor.author	Zhang, Y.	en_US
dc.contributor.author	Blackburne, B.	en_US
dc.contributor.author	Lindsay, S.J.	en_US
dc.contributor.author	Ning, Z.	en_US
dc.contributor.author	Frankish, A.	en_US
dc.contributor.author	Harrow J.	en_US
dc.contributor.author	Chris, T.-S.	en_US
dc.contributor.author	Abecasis G.R.	en_US
dc.contributor.author	Kang H.M.	en_US
dc.contributor.author	Anderson P.	en_US
dc.contributor.author	Blackwell, T.	en_US
dc.contributor.author	Busonero F.	en_US
dc.contributor.author	Fuchsberger, C.	en_US
dc.contributor.author	Jun G.	en_US
dc.contributor.author	Maschio, A.	en_US
dc.contributor.author	Porcu, E.	en_US
dc.contributor.author	Sidore, C.	en_US
dc.contributor.author	Tan, A.	en_US
dc.contributor.author	Trost, M.K.	en_US
dc.contributor.author	Bentley, D.R.	en_US
dc.contributor.author	Grocock, R.	en_US
dc.contributor.author	Humphray, S.	en_US
dc.contributor.author	James, T.	en_US
dc.contributor.author	Kingsbury, Z.	en_US
dc.contributor.author	Bauer, M.	en_US
dc.contributor.author	Cheetham, R.K.	en_US
dc.contributor.author	Cox, T.	en_US
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dc.contributor.author	Flicek P.	en_US
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dc.contributor.author	Smith, R.E.	en_US
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dc.contributor.author	Beal, K.	en_US
dc.contributor.author	Cunningham F.	en_US
dc.contributor.author	Herrero J.	en_US
dc.contributor.author	McLaren W.M.	en_US
dc.contributor.author	Ritchie G.R.S.	en_US
dc.contributor.author	Barker J.	en_US
dc.contributor.author	Kelman G.	en_US
dc.contributor.author	Kulesha, E.	en_US
dc.contributor.author	Radhakrishnan, R.	en_US
dc.contributor.author	Roa, A.	en_US
dc.contributor.author	Smirnov, D.	en_US
dc.contributor.author	Streeter I.	en_US
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dc.contributor.author	Gibbs, R.A.	en_US
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dc.contributor.author	Kovar, C.	en_US
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dc.contributor.author	Wang, M.	en_US
dc.contributor.author	Yu F.	en_US
dc.contributor.author	Bainbridge, M.	en_US
dc.contributor.author	Challis, D.	en_US
dc.contributor.author	Evani, U.S.	en_US
dc.contributor.author	Lu J.	en_US
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dc.contributor.author	Korbel J.O.	en_US
dc.contributor.author	Rausch, T.	en_US
dc.contributor.author	Sttz, A.M.	en_US
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dc.contributor.author	Griffin L.	en_US
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dc.contributor.author	Mills, R.E.	en_US
dc.contributor.author	Von Grotthuss, M.	en_US
dc.contributor.author	Zhang, C.	en_US
dc.contributor.author	Shi X.	en_US
dc.contributor.author	Lehrach H.	en_US
dc.contributor.author	Sudbrak, R.	en_US
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dc.contributor.author	Lienhard, M.	en_US
dc.contributor.author	Mertes F.	en_US
dc.contributor.author	Sultan, M.	en_US
dc.contributor.author	Timmermann, B.	en_US
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dc.contributor.author	Herwig, S.R.	en_US
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dc.contributor.author	Wilson, R.K.	en_US
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dc.contributor.author	Dooling, D.	en_US
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dc.contributor.author	Awadalla P.	en_US
dc.contributor.author	Hodgkinson, A.	en_US
dc.contributor.author	Oleksyk, T.K.	en_US
dc.contributor.author	Martinez-Cruzado J.C.	en_US
dc.contributor.author	Fu, Y.	en_US
dc.contributor.author	Liu X.	en_US
dc.contributor.author	Xiong, M.	en_US
dc.contributor.author	Jorde L.	en_US
dc.contributor.author	Witherspoon, D.	en_US
dc.contributor.author	Xing J.	en_US
dc.contributor.author	Browning, B.L.	en_US
dc.contributor.author	Hajirasouliha I.	en_US
dc.contributor.author	Chen, K.	en_US
dc.contributor.author	Albers, C.A.	en_US
dc.contributor.author	Gerstein, M.B.	en_US
dc.contributor.author	Abyzov, A.	en_US
dc.contributor.author	Chen J.	en_US
dc.contributor.author	Fu, Y.	en_US
dc.contributor.author	Habegger L.	en_US
dc.contributor.author	Harmanci, A.O.	en_US
dc.contributor.author	Mu X.J.	en_US
dc.contributor.author	Sisu, C.	en_US
dc.contributor.author	Balasubramanian, S.	en_US
dc.contributor.author	Jin, M.	en_US
dc.contributor.author	Khurana, E.	en_US
dc.contributor.author	Clarke, D.	en_US
dc.contributor.author	Michaelson J.J.	en_US
dc.contributor.author	OSullivan, C.	en_US
dc.contributor.author	Barnes, K.C.	en_US
dc.contributor.author	Gharani, N.	en_US
dc.contributor.author	Toji L.H.	en_US
dc.contributor.author	Gerry, N.	en_US
dc.contributor.author	Kaye J.S.	en_US
dc.contributor.author	Kent, A.	en_US
dc.contributor.author	Mathias, R.	en_US
dc.contributor.author	Ossorio P.N.	en_US
dc.contributor.author	Parker, M.	en_US
dc.contributor.author	Rotimi, C.N.	en_US
dc.contributor.author	Royal, C.D.	en_US
dc.contributor.author	Tishkoff, S.	en_US
dc.contributor.author	Via, M.	en_US
dc.contributor.author	Bodmer W.	en_US
dc.contributor.author	Bedoya G.	en_US
dc.contributor.author	Yang G.	en_US
dc.contributor.author	You, C.J.	en_US
dc.contributor.author	Garcia-Montero, A.	en_US
dc.contributor.author	Orfao, A.	en_US
dc.contributor.author	Dutil J.	en_US
dc.contributor.author	Brooks L.D.	en_US
dc.contributor.author	Felsenfeld, A.L.	en_US
dc.contributor.author	McEwen J.E.	en_US
dc.contributor.author	Clemm, N.C.	en_US
dc.contributor.author	Guyer, M.S.	en_US
dc.contributor.author	Peterson J.L.	en_US
dc.contributor.author	Duncanson, A.	en_US
dc.contributor.author	Dunn, M.	en_US
dc.contributor.author	Peltonen L.	en_US
dc.date.accessioned	2016-02-08T10:52:06Z
dc.date.available	2016-02-08T10:52:06Z
dc.date.issued	2014	en_US
dc.department	Department of Computer Engineering	en_US
dc.description.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.	en_US
dc.description.provenance	Made available in DSpace on 2016-02-08T10:52:06Z (GMT). No. of bitstreams: 1 bilkent-research-paper.pdf: 70227 bytes, checksum: 26e812c6f5156f83f0e77b261a471b5a (MD5) Previous issue date: 2014	en
dc.identifier.doi	10.1038/ncomms4934	en_US
dc.identifier.issn	20411723
dc.identifier.uri	http://hdl.handle.net/11693/25902
dc.language.iso	English	en_US
dc.publisher	Nature Publishing Group	en_US
dc.relation.isversionof	http://dx.doi.org/10.1038/ncomms4934	en_US
dc.source.title	Nature Communications	en_US
dc.subject	allele	en_US
dc.subject	genetic analysis	en_US
dc.subject	genome	en_US
dc.subject	genotype	en_US
dc.subject	polymorphism	en_US
dc.subject	accuracy	en_US
dc.subject	allele	en_US
dc.subject	article	en_US
dc.subject	chromosome	en_US
dc.subject	chromosome 20	en_US
dc.subject	gene frequency	en_US
dc.subject	gene sequence	en_US
dc.subject	genetic association	en_US
dc.subject	genome	en_US
dc.subject	genotype	en_US
dc.subject	haplotype	en_US
dc.subject	human	en_US
dc.subject	indel mutation	en_US
dc.subject	microarray analysis	en_US
dc.subject	reference database	en_US
dc.subject	single nucleotide polymorphism	en_US
dc.title	Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel	en_US
dc.type	Article	en_US

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