International Journal of Genomics, 2015, 01, 1─6

Practical genotype calling approach of Human Exome BeadChip for exome array-based genome-wide association study in Korean population

Tae-Joon Park, L Heo, S Moon, Y Kim, J Oh, S Han, B Kim

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

• ISBN or ISSN: 2314-436X

• 본 연구는 질병관리본부 연구개발과제(과제번호 2014-NI73001-00) 연구비를 지원받아 수행되었습니다.
• This research was supported by a fund(code 2014-NI73001-00) by Research of Korea Centers for Disease Control and Prevention.