Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.
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.
Park
Hansoo
H
Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea.
Kim
Jong-Il
JI
Ju
Young Seok
YS
Gokcumen
Omer
O
Mills
Ryan E
RE
Kim
Sheehyun
S
Lee
Seungbok
S
Suh
Dongwhan
D
Hong
Dongwan
D
Kang
Hyunseok Peter
HP
Yoo
Yun Joo
YJ
Shin
Jong-Yeon
JY
Kim
Hyun-Jin
HJ
Yavartanoo
Maryam
M
Chang
Young Wha
YW
Ha
Jung-Sook
JS
Chong
Wilson
W
Hwang
Ga-Ram
GR
Darvishi
Katayoon
K
Kim
Hyeran
H
Yang
Song Ju
SJ
Yang
Kap-Seok
KS
Kim
Hyungtae
H
Hurles
Matthew E
ME
Scherer
Stephen W
SW
Carter
Nigel P
NP
Tyler-Smith
Chris
C
Lee
Charles
C
Seo
Jeong-Sun
JS
D000465:Algorithms; D044466:Asian People; D002681:China; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D018628:Gene Dosage; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D007564:Japan; D007723:Korea; D008986:Mongolia; D009693:Nucleic Acid Hybridization; D017422:Sequence Analysis, DNA / Q000379:methods*