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SgD-CNV, a database for common and rare copy number variants in three Asian populations

Authors

  • Haiyan Xu,

    1. Centre for Molecular Epidemiology, National University of Singapore, Singapore
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  • Wan-Ting Poh,

    1. Department of Epidemiology and Public Health, National University of Singapore, Singapore
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  • Xueling Sim,

    1. Centre for Molecular Epidemiology, National University of Singapore, Singapore
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  • Rick Twee-Hee Ong,

    1. Centre for Molecular Epidemiology, National University of Singapore, Singapore
    2. Department of Epidemiology and Public Health, National University of Singapore, Singapore
    3. NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
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  • Chen Suo,

    1. Centre for Molecular Epidemiology, National University of Singapore, Singapore
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  • Wan-Ting Tay,

    1. Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
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  • Chiea-Chuen Khor,

    1. Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
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  • Mark Seielstad,

    1. Institute of Human Genetics, University of California, San Francisco, California
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  • Jianjun Liu,

    1. Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
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  • Tin Aung,

    1. Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
    2. Department of Ophthalmology, National University of Singapore, Singapore
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  • E-Shyong Tai,

    1. Department of Epidemiology and Public Health, National University of Singapore, Singapore
    2. Department of Medicine, National University of Singapore, Singapore
    3. Duke-National University of Singapore Graduate Medical School, Singapore
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  • Tien-Yin Wong,

    1. Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
    2. Department of Ophthalmology, National University of Singapore, Singapore
    3. Centre for Eye Research Australia, University of Melbourne, Australia
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  • Kee-Seng Chia,

    1. Centre for Molecular Epidemiology, National University of Singapore, Singapore
    2. Department of Epidemiology and Public Health, National University of Singapore, Singapore
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  • Yik-Ying Teo

    Corresponding author
    1. Centre for Molecular Epidemiology, National University of Singapore, Singapore
    2. Department of Epidemiology and Public Health, National University of Singapore, Singapore
    3. Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
    4. Department of Statistics and Applied Probability, National University of Singapore, Singapore
    • Department of Statistics and Applied Probability, National University of Singapore, Block S16, Level 7, 6 Science Drive 2, Singapore 117546
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  • Communicated by Johan T. den Dunnen

Abstract

Copy number variants (CNVs) extend our understanding of the genetic diversity in humans. However, the distribution and characteristics of CNVs in Asian populations remain largely unexplored, especially for rare CNVs that have emerged as important genetic factors for complex traits. In the present study, we performed an in-depth investigation of common and rare CNVs across 8,148 individuals from the three major Asian ethnic groups: Chinese (n = 1,945), Malays (n = 2,399), and Indians (n = 2,217) in Singapore, making this investigation the most comprehensive genome-wide survey of CNVs outside the European-ancestry populations to date. We detected about 16 CNVs per individual and the ratio of loss to gain events is ∼2:1. The majority of the CNVs are of low frequency (<10%), and 40% are rare (<1%). In each population, ∼20% of the CNVs are not previously catalogued in the Database of Genomic Variants (DGV). Contrary to findings from European studies, the common CNVs (>5%) in our populations are not well tagged by SNPs in Illumina 1M and 610K arrays, and most disease-associated common CNVs previously reported in Caucasians are rare in our populations. We also report noticeable population differentiation in the CNV landscape of these Asian populations, with the greatest diversity seen between the Indians and the Chinese. 32:1341–1349, 2011. ©2011 Wiley Periodicals, Inc.

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