title: The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.
abstract: We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human reference genome. We identified 420,083 novel single nucleotide polymorphisms (SNPs) that are not in the dbSNP database. Despite a close similarity, significant differences were observed between the Chinese genome (YH), the only other Asian genome available, and SJK: (1) 39.87% (1,371,239 out of 3,439,107) SNPs were SJK-specific (49.51% against Venter's, 46.94% against Watson's, and 44.17% against the Yoruba genomes); (2) 99.5% (22,495 out of 22,605) of short indels (< 4 bp) discovered on the same loci had the same size and type as YH; and (3) 11.3% (331 out of 2920) deletion structural variants were SJK-specific. Even after attempting to map unmapped reads of SJK to unanchored NCBI scaffolds, HGSV, and available personal genomes, there were still 5.77% SJK reads that could not be mapped. All these findings indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant. Hence, constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.
authors.affiliation: Lee Gil Ya Cancer and Diabetes Institute, Gachon University of Medicine and Science, Incheon 406-799, Korea.
authors.forename: Sung-Min
authors.initials: SM
authors.lastname: Ahn
authors.forename: Tae-Hyung
authors.initials: TH
authors.lastname: Kim
authors.forename: Sunghoon
authors.initials: S
authors.lastname: Lee
authors.forename: Deokhoon
authors.initials: D
authors.lastname: Kim
authors.forename: Ho
authors.initials: H
authors.lastname: Ghang
authors.forename: Dae-Soo
authors.initials: DS
authors.lastname: Kim
authors.forename: Byoung-Chul
authors.initials: BC
authors.lastname: Kim
authors.forename: Sang-Yoon
authors.initials: SY
authors.lastname: Kim
authors.forename: Woo-Yeon
authors.initials: WY
authors.lastname: Kim
authors.forename: Chulhong
authors.initials: C
authors.lastname: Kim
authors.forename: Daeui
authors.initials: D
authors.lastname: Park
authors.forename: Yong Seok
authors.initials: YS
authors.lastname: Lee
authors.forename: Sangsoo
authors.initials: S
authors.lastname: Kim
authors.forename: Rohit
authors.initials: R
authors.lastname: Reja
authors.forename: Sungwoong
authors.initials: S
authors.lastname: Jho
authors.forename: Chang Geun
authors.initials: CG
authors.lastname: Kim
authors.forename: Ji-Young
authors.initials: JY
authors.lastname: Cha
authors.forename: Kyung-Hee
authors.initials: KH
authors.lastname: Kim
authors.forename: Bonghee
authors.initials: B
authors.lastname: Lee
authors.forename: Jong
authors.initials: J
authors.lastname: Bhak
authors.forename: Seong-Jin
authors.initials: SJ
authors.lastname: Kim
mesh_terms: D044466:Asian People / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D005260:Female; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics / Q000379:methods; D006801:Humans; D054643:INDEL Mutation; D007723:Korea; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods*