Copy number variations (CNVs) identified in Korean individuals

Tae-Wook Kang,Siwoo Lee,Seon-Young Kim,Yeo-Jin Jeon,Jong Yeol Kim,Eunsu Jang,Hee-Jin Kim,Yong Sung Kim,Jong-Lyul Park,Jeong-Hwan Kim

doi:10.1186/1471-2164-9-492

Tae-Wook Kang, Siwoo Lee + Show 8 more

Open Access

https://doi.org/10.1186/1471-2164-9-492

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Abstract

BackgroundCopy number variations (CNVs) are deletions, insertions, duplications, and more complex variations ranging from 1 kb to sub-microscopic sizes. Recent advances in array technologies have enabled researchers to identify a number of CNVs from normal individuals. However, the identification of new CNVs has not yet reached saturation, and more CNVs from diverse populations remain to be discovered.ResultsWe identified 65 copy number variation regions (CNVRs) in 116 normal Korean individuals by analyzing Affymetrix 250 K Nsp whole-genome SNP data. Ten of these CNVRs were novel and not present in the Database of Genomic Variants (DGV). To increase the specificity of CNV detection, three algorithms, CNAG, dChip and GEMCA, were applied to the data set, and only those regions recognized at least by two algorithms were identified as CNVs. Most CNVRs identified in the Korean population were rare (<1%), occurring just once among the 116 individuals. When CNVs from the Korean population were compared with CNVs from the three HapMap ethnic groups, African, European, and Asian; our Korean population showed the highest degree of overlap with the Asian population, as expected. However, the overlap was less than 40%, implying that more CNVs remain to be discovered from the Asian population as well as from other populations. Genes in the novel CNVRs from the Korean population were enriched for genes involved in regulation and development processes.ConclusionCNVs are recently-recognized structural variations among individuals, and more CNVs need to be identified from diverse populations. Until now, CNVs from Asian populations have been studied less than those from European or American populations. In this regard, our study of CNVs from the Korean population will contribute to the full cataloguing of structural variation among diverse human populations.

Highlights

Copy number variations (CNVs) are deletions, insertions, duplications, and more complex variations ranging from 1 kb to sub-microscopic sizes
We identified a total of 65 copy number variation regions (CNVRs), among which 10 CNVRs (15.4%) were novel and not present in the Database of Genomic Variants
More than 15.4% of the identified CNVs in the Korean population would be novel if we consider a recent study, which showed that most CNV loci are smaller than currently recorded in the Database of Genomic Variants [28]

Summary

Introduction

Copy number variations (CNVs) are deletions, insertions, duplications, and more complex variations ranging from 1 kb to sub-microscopic sizes. Copy number variations (CNVs), a new type of genomic variation that has recently received considerable attention, are deletions, insertions, duplications, and more complex variations ranging from 1 kb to submicroscopic sizes [1,2,3,4]. Since Sebat et al [6] and Iafrate et al [7] first reported large-scale CNVs among normal human individuals in 2004, and since many researchers have identified novel CNVs using diverse technical and computational approaches [8,9,10,11,12,13,14,15,16,17] These reported CNVs are collected and maintained in a curated database, the database of genomic variants http://projects.tcag.ca/variation/, which contains more than 15,000 CNVs obtained from 48 publications as of April, 2008. The global map of CNVs from the 270 normal individuals in the HapMap collection is an important advance in the field, yet genomes from more individuals from diverse populations should be studied to achieve a full cataloging of human CNVs [11]

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