title: 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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratory of Genomic Diversity, Department of Life Science, Sogang University, Seoul, Republic of Korea.
authors.forename: Joon Seol
authors.initials: JS
authors.lastname: Bae
authors.forename: Hyun Sub
authors.initials: HS
authors.lastname: Cheong
authors.forename: Byung Lae
authors.initials: BL
authors.lastname: Park
authors.forename: Lyoung Hyo
authors.initials: LH
authors.lastname: Kim
authors.forename: Chang Soo
authors.initials: CS
authors.lastname: Han
authors.forename: Tae Joon
authors.initials: TJ
authors.lastname: Park
authors.forename: Jason Yongha
authors.initials: JY
authors.lastname: Kim
authors.forename: Charisse Flerida A
authors.initials: CF
authors.lastname: Pasaje
authors.forename: Jin Sol
authors.initials: JS
authors.lastname: Lee
authors.forename: Hyoung Doo
authors.initials: HD
authors.lastname: Shin
mesh_terms: D000328:Adult; D000368:Aged; D044466:Asian People / Q000235:genetics; D002460:Cell Line; D002869:Chromosome Aberrations; D015894:Genome, Human / Q000235:genetics*; D056914:Genomic Structural Variation / Q000235:genetics*; D005838:Genotype; D006801:Humans; D019656:Loss of Heterozygosity / Q000235:genetics; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics