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dc.contributor.authorDelaneau O.en_US
dc.contributor.authorMarchini J.en_US
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dc.contributor.authorBrooks L.D.en_US
dc.contributor.authorFelsenfeld, A.L.en_US
dc.contributor.authorMcEwen J.E.en_US
dc.contributor.authorClemm, N.C.en_US
dc.contributor.authorGuyer, M.S.en_US
dc.contributor.authorPeterson J.L.en_US
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dc.date.accessioned2016-02-08T10:52:06Z
dc.date.available2016-02-08T10:52:06Z
dc.date.issued2014en_US
dc.identifier.issn20411723
dc.identifier.urihttp://hdl.handle.net/11693/25902
dc.description.abstractA 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.language.isoEnglishen_US
dc.source.titleNature Communicationsen_US
dc.relation.isversionofhttp://dx.doi.org/10.1038/ncomms4934en_US
dc.subjectalleleen_US
dc.subjectgenetic analysisen_US
dc.subjectgenomeen_US
dc.subjectgenotypeen_US
dc.subjectpolymorphismen_US
dc.subjectaccuracyen_US
dc.subjectalleleen_US
dc.subjectarticleen_US
dc.subjectchromosomeen_US
dc.subjectchromosome 20en_US
dc.subjectgene frequencyen_US
dc.subjectgene sequenceen_US
dc.subjectgenetic associationen_US
dc.subjectgenomeen_US
dc.subjectgenotypeen_US
dc.subjecthaplotypeen_US
dc.subjecthumanen_US
dc.subjectindel mutationen_US
dc.subjectmicroarray analysisen_US
dc.subjectreference databaseen_US
dc.subjectsingle nucleotide polymorphismen_US
dc.titleIntegrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panelen_US
dc.typeArticleen_US
dc.departmentDepartment of Computer Engineeringen_US
dc.citation.volumeNumber5en_US
dc.identifier.doi10.1038/ncomms4934en_US
dc.publisherNature Publishing Groupen_US


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