HGVD: Human Genetic Variation Database update 2026 with sequencing of 4344 genetically diverse Japanese individuals.

HGVD v3.1 expanded the Human Genetic Variation Database for Japanese individuals by integrating 1209 exomes and WGS from 3135 people, enabling aggregate variant statistics for 4344 individuals.

• Why it matters: Population-scale genome resources remain biased toward European ancestry, limiting variant interpretation in underrepresented populations such as Japanese and East Asian groups.
• What they did: The update adds coordinated JBrowse-based browsers for GRCh37/hg19, GRCh38/hg38, and T2T-CHM13, with non-GRCh37 tracks generated by liftOver from the GRCh37 call set. It also provides eQTL from 300 individuals on hg19 and a structural-variant release plus a pathSTR portal for 68 tandem-repeat loci using STRdust on Oxford Nanopore long reads from 1019 remapped 1000 Genomes Project individuals.
• The result: HGVD v3.1 supports population-matched interpretation of rare pathogenic and pharmacogenomic variants, comparison of repeat-expansion alleles with long-read reference distributions, and structural-variant-aware reference construction for precision medicine in Japan and East Asian populations.