TogoVar: A comprehensive Japanese genetic variation database

Abstract

TogoVar ( https://togovar.org) is a database that integrates allele frequencies derived from Japanese populations and provides annotations for variant interpretation. First, a scheme to reanalyze individual-level genome sequence data deposited in the Japanese Genotype-phenotype Archive (JGA), a controlled-access database, was established to make allele frequencies publicly available. As more Japanese individual-level genome sequence data are deposited in JGA, the sample size employed in TogoVar is expected to increase, contributing to genetic study as reference data for Japanese populations. Second, public datasets of Japanese and non-Japanese populations were integrated into TogoVar to easily compare allele frequencies in Japanese and other populations. Each variant detected in Japanese populations was assigned a TogoVar ID as a permanent identifier. Third, these variants were annotated with molecular consequence, pathogenicity, and literature information for interpreting and prioritizing variants. Here, we introduce the newly developed TogoVar database that compares allele frequencies among Japanese and non-Japanese populations and describes the integrated annotations.

Genomic database: Genetic variation patterns in Japan

A comprehensive database of genome sequence differences found in Japanese individuals is helping researchers uncover the genetic basis of diseases occurring in the Japanese population. Nobutaka Mitsuhashi from the Database Center for Life Science in Chiba, Japan, and colleagues describe the development of TogoVar, a web-based resource that includes genetic data from more than 200,000 Japanese individuals, plus many others of non-Japanese ancestry for comparison. From the millions of tracked DNA differences, many associated with disease, researchers can search for genetic variants of interest and find information on variant frequency, clinical importance, genomic context, related publications, and more. First established in 2018, TogoVar ( https://togovar.org) now provides a one-stop shop for researchers looking to interpret genomic variation data in Japanese populations.