Introduction to the Korean Reference Genome Database (KRGDB)

Jung Kwangsu, Cho Seongbeom
Division of Biomedical Informatics, Center for Genome Science, KNIH, KCDC

Background: Since 2012, the Center for Genome Science of Korea of the National Institute of Health has conducted the whole genome sequencing project for 1,722 Korean individuals. The project investigated and analyzed 622 samples until 2014 (the first phase), and 1,100 samples until 2016 (the second phase). The main aim of the Korean Reference Genome (KRG) project is to provide a comprehensive map of Korean genomic variants for future studies regarding disease association and population genetics.
Current status: Approximately genomic variant loci of 32 million in the first phases and 36 million in the second phase have been identified using SAM tools’ variant calling with 30X depth coverage. A large proportion of the variant loci were newly detected through those projects. The database does not only contain information on single nucleotide variants (SNVs) and insertion/deletion (INDELs) but also Reference gene and Ensenble gene information panels, genome diversity, selection tendency, variant density, functional annotations for exotic variants, and the encyclopedia of DNA elements (ENCODE) region variants. The results can be found in our web-based genome variant database (KRGDB: http://152.99.75.168/KRGDB/). The KRGDB uses MySQL database and Apache-Tomcat web-server adopted with Java Server Page (JSP).
Future perspective: Serving as a quick reference understanding genomic variants in Korean, the KRG database is expected to provide a pool of East Asian reference genome variants to promote the understanding of the genomic diversities in the human species.

Keywords: Korean Genomic Variant Database, Korean Reference Genome, Single Nucleotide Variant, INDEL, Next Generation Sequencing