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

被引：31

作者：

Duan, Qing ^{[1
]}

Liu, Eric Yi ^{[2
]}

Auer, Paul L. ^{[3
]}

Zhang, Guosheng ^{[1
]}

Lange, Ethan M. ^{[1
,4
]}

Jun, Goo ^{[5
,6
]}

Bizon, Chris ^{[7
]}

Jiao, Shuo ^{[3
]}

Buyske, Steven ^{[8
,9
]}

Franceschini, Nora ^{[10
]}

Carlson, Chris S. ^{[3
]}

Hsu, Li ^{[3
]}

Reiner, Alex P. ^{[3
]}

Peters, Ulrike ^{[3
,11
]}

Haessler, Jeffrey ^{[3
]}

Curtis, Keith ^{[3
]}

Wassel, Christina L. ^{[12
]}

Robinson, Jennifer G. ^{[13
]}

Martin, Lisa W. ^{[14
]}

Haiman, Christopher A. ^{[15
]}

Le Marchand, Loic ^{[16
]}

Matise, Tara C. ^{[9
]}

Hindorff, Lucia A. ^{[17
]}

Crawford, Dana C. ^{[18
]}

Assimes, Themistocles L. ^{[19
]}

Kang, Hyun Min ^{[5
,6
]}

Heiss, Gerardo ^{[10
]}

Jackson, Rebecca D. ^{[20
]}

Kooperberg, Charles ^{[3
]}

Wilson, James G. ^{[21
]}

Abecasis, Goncalo R. ^{[5
,6
]}

North, Kari E. ^{[10
]}

Nickerson, Deborah A. ^{[22
]}

Lange, Leslie A. ^{[1
]}

Li, Yun ^{[1
,2
,4
]}

机构：

[1] Univ N Carolina, Dept Genet, Chapel Hill, NC 27599 USA

[2] Univ N Carolina, Dept Comp Sci, Chapel Hill, NC 27599 USA

[3] Fred Hutchinson Canc Res Ctr, Div Publ Hlth Sci, Seattle, WA 98109 USA

[4] Univ N Carolina, Dept Biostat, Chapel Hill, NC 27599 USA

[5] Univ Michigan, Sch Publ Hlth, Dept Biostat, Ann Arbor, MI 48109 USA

[6] Univ Michigan, Sch Publ Hlth, Ctr Stat Genet, Ann Arbor, MI 48109 USA

[7] Univ N Carolina, Renaissance Comp Inst, Chapel Hill, NC 27599 USA

[8] Rutgers State Univ, Dept Stat, Piscataway, NJ 08854 USA

[9] Rutgers State Univ, Dept Genet, Piscataway, NJ 08854 USA

[10] Univ N Carolina, Dept Epidemiol, Chapel Hill, NC 27599 USA

[11] Univ Washington, Dept Epidemiol, Seattle, WA 98195 USA

[12] Univ Pittsburgh, Grad Sch Publ Hlth, Div Epidemiol, Pittsburgh, PA 15261 USA

[13] Univ Iowa, Dept Epidemiol & Med, Iowa City, IA 52242 USA

[14] George Washington Univ, Sch Med & Hlth Sci, Div Cardiol, Washington, DC 20037 USA

[15] Univ So Calif, Kenneth Norris Jr Comprehens Canc Ctr, Keck Sch Med, Dept Prevent Med, Los Angeles, CA 90033 USA

[16] Univ Hawaii, Ctr Canc, Program Epidemiol, Honolulu, HI 96813 USA

[17] NHGRI, Div Genom Med, NIH, Bethesda, MD 20892 USA

[18] Vanderbilt Univ, Ctr Human Genet Res, Dept Mol Physiol & Biophys, Nashville, TN 37232 USA

[19] Stanford Univ, Sch Med, Dept Med, Stanford, CA 94305 USA

[20] Ohio State Univ, Div Endocrinol Diabet & Metab, Columbus, OH 43210 USA

[21] Univ Mississippi, Med Ctr, Dept Physiol & Biophys, Jackson, MS 39216 USA

[22] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

来源：

BIOINFORMATICS | 2013年 / 29卷 / 21期

基金：

美国国家卫生研究院;

关键词：

GENOTYPE IMPUTATION; RARE VARIANT; DESIGN; ATHEROSCLEROSIS; ASSOCIATIONS; HAPLOTYPES; DEEP; LOCI; TOOL;

D O I：

10.1093/bioinformatics/btt477

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 51%. 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.

引用

页码：2744 / 2749

页数：6

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