The first Korean human genome SJK abstract

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The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.

 

Ahn SM, Kim TH, Lee SH, Kim DH, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, Kim S, Reja R, Jho S, Kim CG, Cha JY, Kim KH, Lee B, Bhak Jong*, and Kim Seong-Jin*.

 

1 Lee Gil Ya Cancer and Diabetes Institute;
2 Korean BioInformation Center (KOBIC);
3 Soongsil University;
4 National Center for Standard Reference Data;
5 Gachon University Gil Hospital;
6 Gachon University of Medicine and Science

Genome Research. 2009 Sep;19(9):1622-9. Epub 2009 May 26.

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.

Data

The data are available from BioFtp.org at (ftp://bioftp.org/BiO/Store/Genome/)

 

http://genome.cshlp.org/content/early/2009/05/26/gr.092197.109

 

Accepted May 22, 2009. 
 

SRA sequence from NCBI: http://www.ncbi.nlm.nih.gov/sra/?term=SRA008175


PDF file of the paper

 

  • Received February 3, 2009.
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