RT Journal Article
SR Electronic
T1 KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 187096
DO 10.1101/187096
A1 Jungeun Kim
A1 Jessica A. Weber
A1 Sungwoong Jho
A1 Jinho Jang
A1 JeHoon Jun
A1 Yun Sung Cho
A1 Hak-Min Kim
A1 Hyunho Kim
A1 Yumi Kim
A1 OkSung Chung
A1 Chang Geun Kim
A1 HyeJin Lee
A1 Byung Chul Kim
A1 Kyudong Han
A1 InSong Koh
A1 Kyun Shik Chae
A1 Semin Lee
A1 Jeremy S. Edwards
A1 Jong Bhak
YR 2017
UL http://biorxiv.org/content/early/2017/09/12/187096.abstract
AB High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations. Herein, we report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals with an average coverage depth of 31×. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project data when prioritizing disease-causing variants. CNV analyses revealed gene losses related to bone mineral densities and duplicated genes involved in brain development and fat reduction. Finally, KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.