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

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.