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Genomic copy number variations in three Southeast Asian populations

Authors

  • Chee-Seng Ku,

    1. Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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  • Yudi Pawitan,

    1. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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  • Xueling Sim,

    1. Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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  • Rick T.H. Ong,

    1. Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    2. Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
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  • Mark Seielstad,

    1. Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
    2. Institute for Human Genetics and Department of Laboratory Medicine, University of California, San Francisco, California
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  • Edmund J.D. Lee,

    1. Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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  • Yik-Ying Teo,

    1. Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    2. Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
    3. Department of Statistics and Applied Probability, National University of Singapore, Singapore
    4. Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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  • Kee-Seng Chia,

    1. Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    2. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    3. Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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  • Agus Salim

    Corresponding author
    1. Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    2. Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    • Centre for Molecular Epidemiology, Department of Epidemiology and Public Health (MD3), Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore 117597
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  • Communicated by Pui-Yan Kwok

Abstract

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. Hum Mutat 31:1–7, 2010. © 2010 Wiley-Liss, Inc.

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