Discovery of Common Asian Copy Number Variants Using Integrated High-resolution Array CGH and Massively Parallel DNA Sequencing

Overview

Journal Nat Genet

Specialty Genetics

Date 2010 Apr 6

PMID 20364138

Citations 120

Authors

Hansoo Park

Jong-Il Kim

Young Seok Ju

Omer Gokcumen

Ryan E Mills

Sheehyun Kim

Seungbok Lee

Dongwhan Suh

Dongwan Hong

Hyunseok Peter Kang

Yun Joo Yoo

Jong-Yeon Shin

Hyun-Jin Kim

Maryam Yavartanoo

Young Wha Chang

Jung-Sook Ha

Wilson Chong

Ga-Ram Hwang

Katayoon Darvishi

Hyeran Kim

Song Ju Yang

Kap-Seok Yang

Hyungtae Kim

Matthew E Hurles

Stephen W Scherer

Nigel P Carter

Chris Tyler-Smith

Charles Lee

Jeong-Sun Seo

Affiliations

Soon will be listed here.

Abstract

Copy number variants (CNVs) account for the majority of human genomic diversity in terms of base coverage. Here, we have developed and applied a new method to combine high-resolution array comparative genomic hybridization (CGH) data with whole-genome DNA sequencing data to obtain a comprehensive catalog of common CNVs in Asian individuals. The genomes of 30 individuals from three Asian populations (Korean, Chinese and Japanese) were interrogated with an ultra-high-resolution array CGH platform containing 24 million probes. Whole-genome sequencing data from a reference genome (NA10851, with 28.3x coverage) and two Asian genomes (AK1, with 27.8x coverage and AK2, with 32.0x coverage) were used to transform the relative copy number information obtained from array CGH experiments into absolute copy number values. We discovered 5,177 CNVs, of which 3,547 were putative Asian-specific CNVs. These common CNVs in Asian populations will be a useful resource for subsequent genetic studies in these populations, and the new method of calling absolute CNVs will be essential for applying CNV data to personalized medicine.

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