期刊
GENE
卷 540, 期 1, 页码 104-109出版社
ELSEVIER SCIENCE BV
DOI: 10.1016/j.gene.2014.01.069
关键词
Illumina HumanExome array; Expanding GWAS; Genotyping rare SNPs; Coding variants
资金
- NIH [1 R01MH093500, 1 U01 MH092758, 5 UL1 RR025774, R21 AI085374, 5 U01 DA024417, 5 R01 HL089655, 5 R01 DA030976, 5 R01 AG035020, 1 R01 MH093500, 2 U19 AI063603, 2 U19 AG023122, 5 P01 AG027734, 1 R21 DA033813]
- Marine Corps and Navy Bureau of Medicine and Surgery (BUMED)
- Johnson and Johnson
- Veteran's Administration
- Viterbi Foundation
- Stand-Up-to-Cancer organization
- Price Foundation
- Scripps Genomic Medicine
- VA Health Services Research and Development (VAHSRD)
- VA Clinical Research and Development (VA CSRD)
- NIMH [R01MH093500]
- VA Center of Excellence for Stress and Mental Health (CESAMH)
There is considerable debate about the most efficient way to interrogate rare coding variants in association studies. The options include direct genotyping of specific known coding variants in genes or, alternatively, sequencing across the entire exome to capture known as well as novel variants. Each strategy has advantages and disadvantages, but the availability of cost-efficient exome arrays has made the former appealing. Here we consider the utility of a direct genotyping chip, the Illumina HumanExome array (HE), by evaluating its content based on: 1. functionality: and 2. amenability to imputation. We explored these issues by genotyping a large, ethnically diverse cohort on the HumanOmniExpressExome array (HOEE) which combines the HE with content from the GWAS array (HOE). We find that the use of the HE is likely to be a cost-effective way of expanding GWAS, but does have some drawbacks that deserve consideration when planning studies. (C) 2014 Elsevier B.V. All rights reserved.
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