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

doi:10.1186/s13073-019-0677-z

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^*

^*Corresponding author for this work

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

31 Citations (Scopus)

Abstract

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 https://nard.macrogen.com/.

Original language	English
Article number	64
Journal	Genome Medicine
Volume	11
Issue number	1
DOIs	https://doi.org/10.1186/s13073-019-0677-z
Publication status	Published - Oct 22 2019
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2019 The Author(s).

ASJC Scopus Subject Areas

Molecular Medicine
Molecular Biology
Genetics
Genetics(clinical)

Keywords

East Asians
Genotype imputation
Northeast Asians
Reference panel
Whole-genome sequencing

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Cite this

Yoo, S. K., Kim, C. U., Kim, H. L., Kim, S., Shin, J. Y., Kim, N., Yang, J. S. W., Lo, K. W., Cho, B., Matsuda, F., Schuster, S. C., Kim, C., Kim, J. I., & Seo, J. S. (2019). NARD: Whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants. Genome Medicine, 11(1), Article 64. https://doi.org/10.1186/s13073-019-0677-z

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abstract = "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 https://nard.macrogen.com/.",

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doi = "10.1186/s13073-019-0677-z",

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AU - Kim, Chang Uk

AU - Kim, Hie Lim

AU - Kim, Sungjae

AU - Shin, Jong Yeon

AU - Kim, Namcheol

AU - Yang, Joshua Sung Woo

AU - Lo, Kwok Wai

AU - Cho, Belong

AU - Matsuda, Fumihiko

AU - Schuster, Stephan C.

AU - Kim, Changhoon

AU - Kim, Jong Il

AU - Seo, Jeong Sun

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AB - 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 https://nard.macrogen.com/.

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KW - Northeast Asians

KW - Reference panel

KW - Whole-genome sequencing

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

Abstract

Bibliographical note

ASJC Scopus Subject Areas

Keywords

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