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
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
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DOI：
10.1016/j.ygeno.2011.08.007
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发表时间：
2011-12-01
期刊：
影响因子：
4.4
通讯作者：
Risch, Neil
中科院分区：
文献类型：
--
作者：
Hoffmann, Thomas J.;Zhan, Yiping;Risch, Neil
四个定制的Axiom基因分型阵列被设计用于Kaiser Permanente基因、环境和健康研究计划的100，000名参与者的全基因组关联（GWA）研究。先前描述了针对欧洲种族/民族的个体优化的阵列。在这里，我们详细介绍了三个额外的微阵列优化东亚，非洲裔美国人和拉丁美洲人的种族/民族的个人的发展。对于这些阵列，我们减少了高性能SNP的冗余以增加SNP容量。使用贪婪成对SNP选择设计东亚阵列。然而，基于填补覆盖率从目标集中去除SNP比成对标记更有效。因此，我们开发了一种新的混合SNP选择方法，用于非洲裔美国人和拉丁美洲人阵列，利用贪婪的成对SNP选择轮次，然后从由插补覆盖的SNP的目标集合中去除。该阵列提供了极好的全基因组覆盖，是大规模GWA研究的宝贵补充。(C)2011 Elsevier Inc. All rights reserved.
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.