Copy number variations in East-Asian population and their evolutionary and functional implications.
Recent discovery of the copy number variation (CNV) in normal individuals has widened our understanding of genomic variation. However, most of the reported CNVs have been identified in Caucasians, which may not be directly applicable to people of different ethnicities. To profile CNV in East-Asian population, we screened CNVs in 3578 healthy, unrelated Korean individuals, using the Affymetrix Genome-Wide Human SNP array 5.0. We identified 144,207 CNVs using a pooled data set of 100 randomly chosen Korean females as a reference. The average number of CNVs per genome was 40.3, which is higher than that of CNVs previously reported using lower resolution platforms. The median size of CNVs was 18.9 kb (range 0.2-5406 kb). Copy number losses were 4.7 times more frequent than copy number gains. CNV regions (CNVRs) were defined by merging overlapping CNVs identified in two or more samples. In total, 4003 CNVRs were defined encompassing 241.9 Mb accounting for approximately 8% of the human genome. A total of 2077 CNVRs (51.9%) were potentially novel. Known CNVRs were larger and more frequent than novel CNVRs. Sixteen percent of the CNVRs were observed in > or =1% of study subjects and 24% overlapped with the OMIM genes. A total of 476 (11.9%) CNVRs were associated with segmental duplications. CNVS/CNVRs identified in this study will be valuable resources for studying human genome diversity and its association with disease.
Yim
Seon-Hee
SH
Integrated Research Center for Genome Polymorphism, Seoul St Mary's Hospital, School of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul 137-701, Korea.
Kim
Tae-Min
TM
Hu
Hae-Jin
HJ
Kim
Ji-Hong
JH
Kim
Bong-Jo
BJ
Lee
Jong-Young
JY
Han
Bok-Ghee
BG
Shin
Seung-Hun
SH
Jung
Seung-Hyun
SH
Chung
Yeun-Jun
YJ
D044466:Asian People / Q000235:genetics*; D001483:Base Sequence; D002877:Chromosomes, Human / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005202:Asia, Eastern / Q000208:ethnology; D005260:Female; D005787:Gene Frequency / Q000235:genetics; D005796:Genes; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D008297:Male; D018626:Retroelements / Q000235:genetics
D018626:Retroelements