Genome-Wide Profiling of Structural Genomic Variations in Korean HapMap Individuals 英文参考文献.docVIP

Genome-WideProfilingofStructuralGenomicVariations inKoreanHapMapIndividuals JoonSeolBae1,HyunSubCheong2,ByungLaePark2,LyoungHyoKim2,ChangSooHan2,TaeJoon Park1,JasonYonghaKim1,CharisseFleridaA.Pasaje1,JinSolLee1,HyoungDooShin1,2* 1LaboratoryofGenomicDiversity,DepartmentofLifeScience,SogangUniversity,Seoul,RepublicofKorea,2DepartmentofGeneticEpidemiology,SNPGenetics,Inc., Seoul,RepublicofKorea Abstract Background: Structural genomic variation study, along with microarray technology development has provided many genomicresourcesrelatedwitharchitectureofhumangenome,andledtothefactthathumangenomestructureisalot morecomplicatedthanpreviouslythought. Methodology/PrincipalFindings:InthecaseofInternationalHapMapProject,Epstein-Barrvariousimmortalizedcelllines werepreferablyusedoverbloodinordertogetalargernumberofgenomicDNA.However,genomicaberrationstemming fromimmortalizationprocess,biasedrepresentationofthedonortissue,andcultureprocessmayinfluencetheaccuracyof SNPgenotypes.Inordertoidentifychromosomeaberrationsincludinglossofheterozygosity(LOH),large-scaleandsmall- scalecopynumbervariations,weusedIlluminaHumanHap500BeadChip(555,352markers)onKoreanHapMapindividuals (n=90)toobtainLogRratioandBallelefrequencyinformation,andthenutilizedthedatawithvariousprogramsincluding Illumina ChromoZone, cnvParition and PennCNV. As a result, we identified 28 LOHs (.3mb) and 35 large-scale CNVs (.1mb), 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 signalintensity andB allele frequency simultaneously for identification of small-scale CNVs (,1mb) 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 reportedCNVsinDGV,andquantitativePCR. Conclusion/Significance:Inthisstudy,wedescribetheresultoftheidentifiedchromosomeaberrationsinKorea