Genome-wide profiling of structural genomic variations in Korean HapMap individuals.

Abstract

BACKGROUND: Structural genomic variation study, along with microarray technology development has provided many genomic resources related with architecture of human genome, and led to the fact that human genome structure is a lot more complicated than previously thought. METHODOLOGY/PRINCIPAL FINDINGS: In the case of International HapMap Project, Epstein-Barr various immortalized cell lines were preferably used over blood in order to get a larger number of genomic DNA. However, genomic aberration stemming from immortalization process, biased representation of the donor tissue, and culture process may influence the accuracy of SNP genotypes. In order to identify chromosome aberrations including loss of heterozygosity (LOH), large-scale and small-scale copy number variations, we used Illumina HumanHap500 BeadChip (555,352 markers) on Korean HapMap individuals (n = 90) to obtain Log R ratio and B allele frequency information, and then utilized the data with various programs including Illumina ChromoZone, cnvParition and PennCNV. As a result, we identified 28 LOHs (>3 mb) and 35 large-scale CNVs (>1 mb), with 4 samples having completely duplicated chromosome. In addition, after checking the sample quality (standard deviation of log R ratio <0.30), we selected 79 samples and used both signal intensity and B allele frequency simultaneously for identification of small-scale CNVs (<1 mb) to discover 4,989 small-scale CNVs. Identified CNVs in this study were successfully validated using visual examination of the genoplot images, overlapping analysis with previously reported CNVs in DGV, and quantitative PCR. CONCLUSION/SIGNIFICANCE: In this study, we describe the result of the identified chromosome aberrations in Korean HapMap individuals, and expect that these findings will provide more meaningful information on the human genome.