Genomic copy number variations in three Southeast Asian populations.
Research on the role of copy number variations (CNVs) in the genetic risk of diseases in Asian populations has been hampered by a relative lack of reference CNV maps for Asian populations outside the East Asians. In this article, we report the population characteristics of CNVs in Chinese, Malay, and Asian Indian populations in Singapore. Using the Illumina Human 1M Beadchip array, we identify 1,174 CNV loci in these populations that corroborated with findings when the same samples were typed on the Affymetrix 6.0 platform. We identify 441 novel loci not previously reported in the Database of Genomic Variations (DGV). We observe a considerable number of loci that span all three populations and were previously unreported, as well as population-specific loci that are quite common in the respective populations. From this we observe the distribution of CNVs in the Asian Indian population to be considerably different from the Chinese and Malay populations. About half of the deletion loci and three-quarters of duplication loci overlap UCSC genes. Tens of loci show population differentiation and overlap with genes previously known to be associated with genetic risk of diseases. One of these loci is the CYP2A6 deletion, previously linked to reduced susceptibility to lung cancer.
Ku
Chee-Seng
CS
Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
Pawitan
Yudi
Y
Sim
Xueling
X
Ong
Rick T H
RT
Seielstad
Mark
M
Lee
Edmund J D
EJ
Teo
Yik-Ying
YY
Chia
Kee-Seng
KS
Salim
Agus
A
D001189:Aryl Hydrocarbon Hydroxylases / Q000235:genetics; D044466:Asian People / Q000208:ethnology / Q000235:genetics*; D002874:Chromosome Mapping; D065637:Cytochrome P-450 CYP2A6; D017353:Gene Deletion; D018628:Gene Dosage / Q000235:genetics*; D020440:Gene Duplication; D020022:Genetic Predisposition to Disease / Q000208:ethnology / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D007194:India / Q000208:ethnology; D008175:Lung Neoplasms / Q000235:genetics; D008296:Malaysia / Q000208:ethnology; D025341:Principal Component Analysis; D012846:Singapore
D001189:Aryl Hydrocarbon Hydroxylases; C585710:CYP2A6 protein, human; D065637:Cytochrome P-450 CYP2A6