Imputation of coding variants in African Americans: better performance using data from the exome sequencing project.
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ABSTRACT: Summary
Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3-11.4% for coding variants with minor allele frequency <1%. No loss of imputation quality was observed using a panel built from phenotypic extremes. We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2's two-panel combination.Contact
yunli@med.unc.edu.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Duan Q
PROVIDER: S-EPMC3799474 | biostudies-literature | 2013 Nov
REPOSITORIES: biostudies-literature
Publications
Imputation of coding variants in African Americans: better performance using data from the exome sequencing project.
Duan Qing Q Liu Eric Yi EY Auer Paul L PL Zhang Guosheng G Lange Ethan M EM Jun Goo G Bizon Chris C Jiao Shuo S Buyske Steven S Franceschini Nora N Carlson Chris S CS Hsu Li L Reiner Alex P AP Peters Ulrike U Haessler Jeffrey J Curtis Keith K Wassel Christina L CL Robinson Jennifer G JG Martin Lisa W LW Haiman Christopher A CA Le Marchand Loic L Matise Tara C TC Hindorff Lucia A LA Crawford Dana C DC Assimes Themistocles L TL Kang Hyun Min HM Heiss Gerardo G Jackson Rebecca D RD Kooperberg Charles C Wilson James G JG Abecasis Gonçalo R GR North Kari E KE Nickerson Deborah A DA Lange Leslie A LA Li Yun Y
Bioinformatics (Oxford, England) 20130816 21
<h4>Summary</h4>Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3-11.4% for coding variants with minor allele frequency <1%. No loss of imputation quality was observed using a panel b ...[more]
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2015-09-03 | GSE72680 | GEO
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