A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans.
To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.
Jeon
Jae Pil
JP
Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea.
Shim
Sung Mi
SM
Jung
Jong Sun
JS
Nam
Hye Young
HY
Lee
Hye Jin
HJ
Oh
Berm Seok
BS
Kim
Kuchan
K
Kim
Hyung Lae
HL
Han
Bok Ghee
BG
D044466:Asian People / Q000235:genetics*; D056915:DNA Copy Number Variations; D005828:Genetics, Population; D015894:Genome, Human; D006801:Humans; D020641:Polymorphism, Single Nucleotide