NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants

被引：33

作者：

Yoo, Seong-Keun ^{[1
,2
]}

Kim, Chang-Uk ^{[2
,3
]}

Kim, Hie Lim ^{[4
,5
]}

Kim, Sungjae ^{[2
,3
]}

Shin, Jong-Yeon ^{[2
]}

Kim, Namcheol ^{[2
]}

Yang, Joshua Sung Woo ^{[2
]}

Lo, Kwok-Wai ^{[6
,7
]}

Cho, Belong ^{[8
]}

Matsuda, Fumihiko ^{[9
]}

Schuster, Stephan C. ^{[5
,10
]}

Kim, Changhoon ^{[2
]}

Kim, Jong-Il ^{[3
,11
]}

Seo, Jeong-Sun ^{[1
,2
,3
,11
,12
]}

机构：

[1] Seoul Natl Univ, Bundang Hosp, Precis Med Ctr, 172 Dolma Ro, Seongnam 13605, Gyeonggi Do, South Korea

[2] Macrogen Inc, Precis Med Inst, Seongnam, South Korea

[3] Seoul Natl Univ, Dept Biomed Sci, Grad Sch, Seoul, South Korea

[4] Nanyang Technol Univ, Asian Sch Environm, Singapore, Singapore

[5] Nanyang Technol Univ, Singapore Ctr Environm Life Sci Engn, Singapore, Singapore

[6] Chinese Univ Hong Kong, Dept Anat & Cellular Pathol, Hong Kong, Peoples R China

[7] Chinese Univ Hong Kong, State Key Lab Translat Oncol, Hong Kong, Peoples R China

[8] Seoul Natl Univ Hosp, Dept Family Med, Seoul, South Korea

[9] Kyoto Univ, Ctr Genom Med, Grad Sch Med, Kyoto, Japan

[10] Nanyang Technol Univ, Sch Biol Sci, Singapore, Singapore

[11] Seoul Natl Univ, Genom Med Inst, Med Res Ctr, Seoul, South Korea

[12] Seoul Natl Univ, Gong Wu Genom Med Inst, Bundang Hosp, Seongnam, South Korea

来源：

GENOME MEDICINE | 2019年 / 11卷 / 01期

关键词：

Whole-genome sequencing; Reference panel; Genotype imputation; Northeast Asians; East Asians; SEQUENCE; ASSOCIATION; DIVERSITY; DATABASE; DNA; HAPLOTYPES; GUIDELINES; DISCOVERY; FRAMEWORK; GENETICS;

D O I：

10.1186/s13073-019-0677-z

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Here, we present the Northeast Asian Reference Database (NARD), including whole-genome sequencing data of 1779 individuals from Korea, Mongolia, Japan, China, and Hong Kong. NARD provides the genetic diversity of Korean (n = 850) and Mongolian (n = 384) ancestries that were not present in the 1000 Genomes Project Phase 3 (1KGP3). We combined and re-phased the genotypes from NARD and 1KGP3 to construct a union set of haplotypes. This approach established a robust imputation reference panel for Northeast Asians, which yields the greatest imputation accuracy of rare and low-frequency variants compared with the existing panels. NARD imputation panel is available at .

引用

页数：10

共 46 条

[1] NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants
Seong-Keun Yoo
Chang-Uk Kim
Hie Lim Kim
Sungjae Kim
Jong-Yeon Shin
Namcheol Kim
Joshua Sung Woo Yang
Kwok-Wai Lo
Belong Cho
Fumihiko Matsuda
Stephan C. Schuster
Changhoon Kim
Jong-Il Kim
Jeong-Sun Seo
Genome Medicine, 11
[2] Improved Imputation Accuracy of Rare and Low-Frequency Genetic Variants Using Population-Specific High-Coverage Whole-Genome Sequencing Data Based Imputation Reference Panel
Mitt, Mario
Kals, Mart
Parn, Kalle
Gabriel, Stacey B.
Lander, Eric S.
Palotie, Aarno
Ripatti, Samuli
Morris, Andrew P.
Metspalu, Andres
Esko, Tonu
Magi, Reedik
Palta, Priit
HUMAN HEREDITY, 2016, 81 (04) : 235 - 235
[3] Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel
Mario Mitt
Mart Kals
Kalle Pärn
Stacey B Gabriel
Eric S Lander
Aarno Palotie
Samuli Ripatti
Andrew P Morris
Andres Metspalu
Tõnu Esko
Reedik Mägi
Priit Palta
European Journal of Human Genetics, 2017, 25 : 869 - 876
[4] Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel
Mitt, Mario
Kals, Mart
Parn, Kalle
Gabriel, Stacey B.
Lander, Eric S.
Palotie, Aarno
Ripatti, Samuli
Morris, Andrew P.
Metspalu, Andres
Esko, Tonu
Magi, Reedik
Palta, Priit
EUROPEAN JOURNAL OF HUMAN GENETICS, 2017, 25 (07) : 869 - 876
[5] Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
Huang, Jie
Howie, Bryan
McCarthy, Shane
Memari, Yasin
Walter, Klaudia
Min, Josine L.
Danecek, Petr
Malerba, Giovanni
Trabetti, Elisabetta
Zheng, Hou-Feng
Gambaro, Giovanni
Richards, J. Brent
Durbin, Richard
Timpson, Nicholas J.
Marchini, Jonathan
Soranzo, Nicole
NATURE COMMUNICATIONS, 2015, 6
[6] Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
Jie Huang
Bryan Howie
Shane McCarthy
Yasin Memari
Klaudia Walter
Josine L. Min
Petr Danecek
Giovanni Malerba
Elisabetta Trabetti
Hou-Feng Zheng
Giovanni Gambaro
J. Brent Richards
Richard Durbin
Nicholas J. Timpson
Jonathan Marchini
Nicole Soranzo
Nature Communications, 6
[7] Contribution of rare and low-frequency whole-genome sequence variants to complex traits variation in dairy cattle
Zhang, Qianqian
Calus, Mario P. L.
Guldbrandtsen, Bernt
Lund, Mogens Sando
Sahana, Goutam
GENETICS SELECTION EVOLUTION, 2017, 49
[8] Contribution of rare and low-frequency whole-genome sequence variants to complex traits variation in dairy cattle
Qianqian Zhang
Mario P. L. Calus
Bernt Guldbrandtsen
Mogens Sandø Lund
Goutam Sahana
Genetics Selection Evolution, 49
[9] Estimating frequency of pathogenic variants in a Japanese population by using the whole-genome reference panel of ToMMo
Yamaguchi-Kabata, Yumi
Yasuda, Jun
Tanabe, Osamu
Suzuki, Yoichi
Kawame, Hiroshi
Fuse, Nobuo
Nagasaki, Masao
Kawai, Yosuke
Kojima, Kaname
Katsuoka, Fumiki
Saito, Sakae
Danjoh, Inaho
Motoike, Ikuko N.
Yamashita, Riu
Koshiba, Seizo
Saigusa, Daisuke
Tamiya, Gen
Kure, Shigeo
Yaegashi, Nobuo
Kawaguchi, Yoshio
Nagami, Fuji
Kuriyama, Shinichi
Sugawara, Junichi
Minegishi, Naoko
Hozawa, Atsushi
Ogishima, Soichi
Kiyomoto, Hideyasu
Takai-Igarashi, Takako
Kinoshita, Kengo
Yamamoto, Masayuki
HUMAN GENOMICS, 2018, 12
[10] Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'
Deelen, Patrick
Menelaou, Androniki
van Leeuwen, Elisabeth M.
Kanterakis, Alexandros
van Dijk, Freerk
Medina-Gomez, Carolina
Francioli, Laurent C.
Hottenga, Jouke Jan
Karssen, Lennart C.
Estrada, Karol
Kreiner-Moller, Eskil
Rivadeneira, Fernando
van Setten, Jessica
Gutierrez-Achury, Javier
Westra, Harm-Jan
Franke, Lude
van Enckevort, David
Dijkstra, Martijn
Byelas, Heorhiy
van Duijn, Cornelia M.
de Bakker, Paul I. W.
Wijmenga, Cisca
Swertz, Morris A.
EUROPEAN JOURNAL OF HUMAN GENETICS, 2014, 22 (11) : 1321 - 1326

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