Genomics, 2015, 01, 145─149

Combinatorial approach to estimate copy number genotype using whole-exome sequencing data

MiYeong Hwang, Sanghoon Moon, Lyong Heo, Young Jin Kim, Ji Hee Oh, Yeon-Jung Kim, Yun Kyoung Kim, Juyoung Lee, Bok-Ghee Han, Bong-Jo Kim

Abstract

Copy number variations (CNVs) are known risk factors in complex diseases. Array-based approaches have been widely used to detect CNVs, but limitations of array-based CNV detection methods, such as noisy signal and low resolution, have hindered detection of small CNVs. Recently, the development of next-generation sequencing techniques has increased rapidly owing to declines in cost. Particularly, whole-exome sequencing has proved useful for finding causal genes and variants in complex diseases. Because gene copy number may affect expression, CNV genotyping can be very valuable in disease association studies. However, almost all current CNV detection tools consider only two types of CNV genotypes. In this study, we propose a CNV genotype estimation approach using a combination of existing methods. Our approach was comprehensively compared with the customized Agilent array？comparative genomic hybridization. We found that our genotyping approach proved to be accurate, and reproducible, suggesting that it can complement existing CNV genotyping methods.

• ISBN or ISSN: 0888-7543

• 본 연구는 질병관리본부 연구개발과제(과제번호 2012-N73004-00) 연구비를 지원받아 수행되었습니다.
• This research was supported by a fund(code 2012-N73004-00) by Research of Korea Centers for Disease Control and Prevention.