KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses

Jungeun Kim, Jessica A. Weber, Sungwoong Jho, Jinho Jang, Jehoon Jun, Yun Sung Cho, Hak Min Kim, Hyunho Kim, Yumi Kim, Oksung Chung, Chang Geun Kim, Hyejin Lee, Byung Chul Kim, Kyudong Han, Insong Koh, Kyun Shik Chae, Semin Lee, Jeremy S. Edwards, Jong Bhak

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. 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 in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. 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 when prioritizing disease-causing variants. 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.

Original languageEnglish
Article number5677
JournalScientific reports
Volume8
Issue number1
DOIs
StatePublished - 2018 Dec 1

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    Kim, J., Weber, J. A., Jho, S., Jang, J., Jun, J., Cho, Y. S., Kim, H. M., Kim, H., Kim, Y., Chung, O., Kim, C. G., Lee, H., Kim, B. C., Han, K., Koh, I., Chae, K. S., Lee, S., Edwards, J. S., & Bhak, J. (2018). KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses. Scientific reports, 8(1), [5677]. https://doi.org/10.1038/s41598-018-23837-x