RT Journal Article
SR Electronic
T1 Whole-genome reference panel of 1,781 Northeast Asians improves imputation accuracy of rare and low-frequency variants
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 600353
DO 10.1101/600353
A1 Seong-Keun Yoo
A1 Chang-Uk Kim
A1 Hie Lim Kim
A1 Sungjae Kim
A1 Jong-Yeon Shin
A1 Namcheol Kim
A1 Joshua SungWoo Yang
A1 Kwok-Wai Lo
A1 Belong Cho
A1 Fumihiko Matsuda
A1 Stephan C. Schuster
A1 Changhoon Kim
A1 Jong-Il Kim
A1 Jeong-Sun Seo
YR 2019
UL http://biorxiv.org/content/early/2019/04/22/600353.abstract
AB Genotype imputation using the reference panel is a cost-effective strategy to fill millions of missing genotypes for the purpose of various genetic analyses. Here, we present the Northeast Asian Reference Database (NARD), including whole-genome sequencing data of 1,781 individuals from Korea, Mongolia, Japan, China, and Hong Kong. NARD provides the genetic diversities of Korean (n=850) and Mongolian (n=386) 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 the Northeast Asian populations, which yields the greatest imputation accuracy of rare and low-frequency variants compared with the existing panels. Also, we illustrate that NARD can potentially improve disease variant discovery by reducing pathogenic candidates. Overall, this study provides a decent reference panel for the genetic studies in Northeast Asia.