title: Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population.
abstract: Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip.
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of Korea.
authors.forename: Tae-Joon
authors.initials: TJ
authors.lastname: Park
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of Korea.
authors.forename: Lyong
authors.initials: L
authors.lastname: Heo
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of Korea.
authors.forename: Sanghoon
authors.initials: S
authors.lastname: Moon
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of Korea.
authors.forename: Young Jin
authors.initials: YJ
authors.lastname: Kim
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of Korea.
authors.forename: Ji Hee
authors.initials: JH
authors.lastname: Oh
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of Korea.
authors.forename: Sohee
authors.initials: S
authors.lastname: Han
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of Korea.
authors.forename: Bong-Jo
authors.initials: BJ
authors.lastname: Kim
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