A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population

Jeongeun Lee; Jean Lee; Sungwon Jeon; Jeongha Lee; Insu Jang; Jin Ok Yang; Soojin Park; Byungwook Lee; Jinwook Choi; Byung Ok Choi; Heon Yung Gee; Jaeseong Oh; In Jin Jang; Sanghyuk Lee; Daehyun Baek; Youngil Koh; Sung Soo Yoon; Young Joon Kim; Jong Hee Chae; Woong Yang Park; Jong Hwa Bhak; Murim Choi

doi:10.1038/s12276-022-00871-4

A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population

Jeongeun Lee, Jean Lee, Sungwon Jeon, Jeongha Lee, Insu Jang, Jin Ok Yang, Soojin Park, Byungwook Lee, Jinwook Choi, Byung Ok Choi, Heon Yung Gee, Jaeseong Oh, In Jin Jang, Sanghyuk Lee, Daehyun Baek, Youngil Koh, Sung Soo Yoon, Young Joon Kim, Jong Hee Chae, Woong Yang ParkJong Hwa Bhak, Murim Choi

Department of Life Science

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

Abstract

Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci of ADH1A/1B and UHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website (https://www.kobic.re.kr/kova/). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.

Original language	English
Pages (from-to)	1862-1871
Number of pages	10
Journal	Experimental and Molecular Medicine
Volume	54
Issue number	11
DOIs	https://doi.org/10.1038/s12276-022-00871-4
State	Published - Nov 2022

Bibliographical note

Funding Information:
We thank the Korea Bioinformation Center (KOBIC) K-BDS and Clinical and Omics Data Archive for sharing Korean genome data and Drs. Semin Lee, Jungmin Choi, Joon Yong An, and Choong Won Chung for critical comments. A part of this study was supported by the research programs through the National Research Foundation funded by the Ministry of Science and Technology (2014M3C9A2064686, 2018M3C9A5064708, and 2020M3E5D7086836).

Funding Information:
We thank the Korea Bioinformation Center (KOBIC) K-BDS and Clinical and Omics Data Archive for sharing Korean genome data and Drs. Semin Lee, Jungmin Choi, Joon Yong An, and Choong Won Chung for critical comments. A part of this study was supported by the research programs through the National Research Foundation funded by the Ministry of Science and Technology (2014M3C9A2064686, 2018M3C9A5064708, and 2020M3E5D7086836).

Publisher Copyright:
© 2022, The Author(s).

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10.1038/s12276-022-00871-4

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Lee, J., Lee, J., Jeon, S., Lee, J., Jang, I., Yang, J. O., Park, S., Lee, B., Choi, J., Choi, B. O., Gee, H. Y., Oh, J., Jang, I. J., Lee, S., Baek, D., Koh, Y., Yoon, S. S., Kim, Y. J., Chae, J. H., ... Choi, M. (2022). A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population. Experimental and Molecular Medicine, 54(11), 1862-1871. https://doi.org/10.1038/s12276-022-00871-4

@article{5c8fe3e0284549eba7585feb401beffd,

title = "A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population",

abstract = "Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci of ADH1A/1B and UHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website (https://www.kobic.re.kr/kova/). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.",

author = "Jeongeun Lee and Jean Lee and Sungwon Jeon and Jeongha Lee and Insu Jang and Yang, {Jin Ok} and Soojin Park and Byungwook Lee and Jinwook Choi and Choi, {Byung Ok} and Gee, {Heon Yung} and Jaeseong Oh and Jang, {In Jin} and Sanghyuk Lee and Daehyun Baek and Youngil Koh and Yoon, {Sung Soo} and Kim, {Young Joon} and Chae, {Jong Hee} and Park, {Woong Yang} and Bhak, {Jong Hwa} and Murim Choi",

note = "Funding Information: We thank the Korea Bioinformation Center (KOBIC) K-BDS and Clinical and Omics Data Archive for sharing Korean genome data and Drs. Semin Lee, Jungmin Choi, Joon Yong An, and Choong Won Chung for critical comments. A part of this study was supported by the research programs through the National Research Foundation funded by the Ministry of Science and Technology (2014M3C9A2064686, 2018M3C9A5064708, and 2020M3E5D7086836). Funding Information: We thank the Korea Bioinformation Center (KOBIC) K-BDS and Clinical and Omics Data Archive for sharing Korean genome data and Drs. Semin Lee, Jungmin Choi, Joon Yong An, and Choong Won Chung for critical comments. A part of this study was supported by the research programs through the National Research Foundation funded by the Ministry of Science and Technology (2014M3C9A2064686, 2018M3C9A5064708, and 2020M3E5D7086836). Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = nov,

doi = "10.1038/s12276-022-00871-4",

language = "English",

volume = "54",

pages = "1862--1871",

journal = "Experimental and Molecular Medicine",

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Lee, J, Lee, J, Jeon, S, Lee, J, Jang, I, Yang, JO, Park, S, Lee, B, Choi, J, Choi, BO, Gee, HY, Oh, J, Jang, IJ, Lee, S, Baek, D, Koh, Y, Yoon, SS, Kim, YJ, Chae, JH, Park, WY, Bhak, JH & Choi, M 2022, 'A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population', Experimental and Molecular Medicine, vol. 54, no. 11, pp. 1862-1871. https://doi.org/10.1038/s12276-022-00871-4

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AU - Lee, Jean

AU - Jeon, Sungwon

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AU - Jang, Insu

AU - Yang, Jin Ok

AU - Park, Soojin

AU - Lee, Byungwook

AU - Choi, Jinwook

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AU - Gee, Heon Yung

AU - Oh, Jaeseong

AU - Jang, In Jin

AU - Lee, Sanghyuk

AU - Baek, Daehyun

AU - Koh, Youngil

AU - Yoon, Sung Soo

AU - Kim, Young Joon

AU - Chae, Jong Hee

AU - Park, Woong Yang

AU - Bhak, Jong Hwa

AU - Choi, Murim

N1 - Funding Information: We thank the Korea Bioinformation Center (KOBIC) K-BDS and Clinical and Omics Data Archive for sharing Korean genome data and Drs. Semin Lee, Jungmin Choi, Joon Yong An, and Choong Won Chung for critical comments. A part of this study was supported by the research programs through the National Research Foundation funded by the Ministry of Science and Technology (2014M3C9A2064686, 2018M3C9A5064708, and 2020M3E5D7086836). Funding Information: We thank the Korea Bioinformation Center (KOBIC) K-BDS and Clinical and Omics Data Archive for sharing Korean genome data and Drs. Semin Lee, Jungmin Choi, Joon Yong An, and Choong Won Chung for critical comments. A part of this study was supported by the research programs through the National Research Foundation funded by the Ministry of Science and Technology (2014M3C9A2064686, 2018M3C9A5064708, and 2020M3E5D7086836). Publisher Copyright: © 2022, The Author(s).

PY - 2022/11

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N2 - Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci of ADH1A/1B and UHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website (https://www.kobic.re.kr/kova/). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.

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A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population

Abstract

Bibliographical note

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