Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm

被引：123

作者：

Hoffmann, Thomas J. ^{[1
,5
]}

Zhan, Yiping ^{[2
]}

Kvale, Mark N. ^{[1
]}

Hesselson, Stephanie E. ^{[1
]}

Gollub, Jeremy ^{[2
]}

Iribarren, Carlos ^{[3
]}

Lu, Yontao ^{[2
]}

Mei, Gangwu ^{[2
]}

Purdy, Matthew M. ^{[2
]}

Quesenberry, Charles ^{[3
]}

Rowell, Sarah ^{[3
]}

Shapero, Michael H. ^{[2
]}

Smethurst, David ^{[3
]}

Somkin, Carol P. ^{[3
]}

Van den Eeden, Stephen K. ^{[3
]}

Walter, Larry ^{[3
]}

Webster, Teresa ^{[2
]}

Whitmer, Rachel A. ^{[3
]}

Finn, Andrea ^{[2
]}

Schaefer, Catherine ^{[3
]}

Kwok, Pui-Yan ^{[1
,4
]}

Risch, Neil ^{[1
,3
,5
]}

机构：

[1] Univ Calif San Francisco, Inst Human Genet, San Francisco, CA 94143 USA

[2] Affymetrix Inc, Santa Clara, CA USA

[3] Kaiser Permanente No Calif Div Res, Oakland, CA USA

[4] Univ Calif San Francisco, Cardiovasc Res Inst, San Francisco, CA 94143 USA

[5] Univ Calif San Francisco, Dept Epidemiol & Biostat, San Francisco, CA 94143 USA

来源：

GENOMICS | 2011年 / 98卷 / 06期

基金：

美国国家卫生研究院;

关键词：

Microarray; Genome-wide association study; Coverage; Imputation; Single nucleotide polymorphism; Throughput; GENOME-WIDE ASSOCIATION; HUMAN-POPULATIONS; COMMON; ADMIXTURE; GENETICS; DISEASES; LOCI; MAP;

D O I：

10.1016/j.ygeno.2011.08.007

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Four custom Axiom genotyping arrays were designed for a genome-wide association (GWA) study of 100,000 participants from the Kaiser Permanente Research Program on Genes, Environment and Health. The array optimized for individuals of European race/ethnicity was previously described. Here we detail the development of three additional microarrays optimized for individuals of East Asian, African American, and Latino race/ethnicity. For these arrays, we decreased redundancy of high-performing SNPs to increase SNP capacity. The East Asian array was designed using greedy pairwise SNP selection. However, removing SNPs from the target set based on imputation coverage is more efficient than pairwise tagging. Therefore, we developed a novel hybrid SNP selection method for the African American and Latino arrays utilizing rounds of greedy pairwise SNP selection, followed by removal from the target set of SNPs covered by imputation. The arrays provide excellent genome-wide coverage and are valuable additions for large-scale GWA studies. (C) 2011 Elsevier Inc. All rights reserved.

引用

页码：422 / 430

页数：9

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