Title

Imputation of coding variants in African Americans: Better performance using data from the exome sequencing project

Authors

Qing Duan, The Ohio State University
Eric Yi Liu, The University of North Carolina at Chapel Hill
Paul L. Auer, Fred Hutchinson Cancer Research Center
Guosheng Zhang, The Ohio State University
Ethan M. Lange, The Ohio State University
Goo Jun, University of Michigan, Ann Arbor
Chris Bizon, The University of North Carolina at Chapel Hill
Shuo Jiao, Fred Hutchinson Cancer Research Center
Steven Buyske, Rutgers University–New Brunswick
Nora Franceschini, The University of North Carolina at Chapel Hill
Chris S. Carlson, Fred Hutchinson Cancer Research Center
Li Hsu, Fred Hutchinson Cancer Research Center
Alex P. Reiner, Fred Hutchinson Cancer Research Center
Ulrike Peters, Fred Hutchinson Cancer Research Center
Jeffrey Haessler, Fred Hutchinson Cancer Research Center
Keith Curtis, Fred Hutchinson Cancer Research Center
Christina L. Wassel, University of Pittsburgh
Jennifer G. Robinson, University of Iowa
Lisa W. Martin, School of Medicine and Health Sciences
Christopher A. Haiman, Keck School of Medicine of USC
Loic Le Marchand, University Hawaii Cancer Research Center
Tara C. Matise, Rutgers University–New Brunswick
Lucia A. Hindorff, National Human Genome Research Institute (NHGRI)
Dana C. Crawford, Vanderbilt University Medical Center
Themistocles L. Assimes, Stanford University School of Medicine
Hyun Min Kang, University of Michigan, Ann Arbor
Gerardo Heiss, The University of North Carolina at Chapel Hill
Rebecca D. Jackson, The Ohio State University
Charles Kooperberg, Fred Hutchinson Cancer Research Center
James G. Wilson, University of Mississippi Medical Center
Gonçalo R. Abecasis, University of Michigan, Ann Arbor
Kari E. North, The University of North Carolina at Chapel Hill

Document Type

Journal Article

Publication Date

11-1-2013

Journal

Bioinformatics

Volume

29

Issue

21

DOI

10.1093/bioinformatics/btt477

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. © 2013 The Author 2013.

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