A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans

• Published in: Experimental & molecular medicine Vol. 41; no. 9; pp. 618 - 628
• Main Authors: Jeon, Jae-Pil, Shim, Sung-Mi, Jung, Jongsun, Nam, Hye-Young, Lee, Hye-Jin, Oh, Bermseok, Kimm, Kuchan, Kim, Hyung-Lae, Han, Bok-Ghee
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.09.2009; Springer Nature B.V; Korean Society of Medical Biochemistry and Molecular Biology; 생화학분자생물학회
• Subjects: Asian Continental Ancestry Group - genetics; Biomedical and Life Sciences; Biomedicine; DNA Copy Number Variations; Genetics, Population; Genome, Human; Humans; Medical Biochemistry; Molecular Medicine; Original; Polymorphism, Single Nucleotide; Stem Cells; 생화학; single nucleotide; genetic variation; haplotypes; polymorphism; gene dosage; Korea
• ISSN: 1226-3613; 2092-6413; 2092-6413
• DOI: 10.3858/emm.2009.41.9.068

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 ≥ 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 ≥ 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.