The second Korean human genome AK1 abstract
A highly annotated whole-genome sequence of a Korean individual
Jong-Il Kim1,2,4,5,11, Young Seok Ju1,2,11, Hansoo Park1,5, Sheehyun Kim4, Seonwook Lee4, Jae-Hyuk Yi1, Joann Mudge6, Neil A. Miller6, Dongwan Hong1, Callum J. Bell6, Hye-Sun Kim4, In-Soon Chung4, Woo-Chung Lee4, Ji-Sun Lee4, Seung-Hyun Seo5, Ji-Young Yun5, Hyun Nyun Woo4, Heewook Lee4, Dongwhan Suh1,2,3, Seungbok Lee1,2,3, Hyun-Jin Kim1,3, Maryam Yavartanoo1,2, Minhye Kwak1,2, Ying Zheng1,2, Mi Kyeong Lee5, Hyunjun Park1, Jeong Yeon Kim1, Omer Gokcumen7, Ryan E. Mills7, Alexander Wait Zaranek8, Joseph Thakuria8, Xiaodi Wu8, Ryan W. Kim6, Jim J. Huntley9, Shujun Luo9, Gary P. Schroth9, Thomas D. Wu10, HyeRan Kim4, Kap-Seok Yang4, Woong-Yang Park1,2,3, Hyungtae Kim4, George M. Church8, Charles Lee7, Stephen F. Kingsmore6 & Jeong-Sun Seo1,2,3,4,5
1.Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul 110-799, Korea
2.Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine,
3.Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 110-799, Korea
4.Macrogen Inc., Seoul 153-023, Korea
5.Psoma Therapeutics, Inc., Seoul 110-799, Korea
6.National Center for Genome Resources, Santa Fe, New Mexico 87505, USA
7.Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
8.Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
9.Illumina Inc., Hayward, California 94545, USA
10.Department of Bioinformatics, Genentech Inc., South San Francisco, California 94080, USA
11.These authors contributed equally to this work.
Correspondence to: Jeong-Sun Seo1,2,3,4,5 Correspondence and requests for materials should be addressed to J.-S.S. (Email: email@example.com).
Nature 460, 1011-1015 (20 August 2009) | doi:10.1038/nature08211; Received 6 March 2009; Accepted 18 June 2009; Published online 8 July 2009
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Top of pageAbstractRecent advances in sequencing technologies have initiated an era of personal genome sequences. To date, human genome sequences have been reported for individuals with ancestry in three distinct geographical regions: a Yoruba African, two individuals of northwest European origin, and a person from China1, 2, 3, 4. Here we provide a highly annotated, whole-genome sequence for a Korean individual, known as AK1. The genome of AK1 was determined by an exacting, combined approach that included whole-genome shotgun sequencing (27.8× coverage), targeted bacterial artificial chromosome sequencing, and high-resolution comparative genomic hybridization using custom microarrays featuring more than 24 million probes. Alignment to the NCBI reference, a composite of several ethnic clades5, 6, disclosed nearly 3.45 million single nucleotide polymorphisms (SNPs), including 10,162 non-synonymous SNPs, and 170,202 deletion or insertion polymorphisms (indels). SNP and indel densities were strongly correlated genome-wide. Applying very conservative criteria yielded highly reliable copy number variants for clinical considerations. Potential medical phenotypes were annotated for non-synonymous SNPs, coding domain indels, and structural variants. The integration of several human whole-genome sequences derived from several ethnic groups will assist in understanding genetic ancestry, migration patterns and population bottlenecks.