Whole-genome sequencing of 3135 individuals representing the genetic diversity of the Japanese population
Whole-genome sequence information currently available for large-scale sequencing studies is biased toward European descent populations. Such bias causes difficulties in identifying disease-associated genetic variations in non-European populations, including the Japanese. Here, to comprehensively identify genetic variants, we sequenced 3135 individuals representing the genetic diversity of the Japanese population. Of the 44,757,785 identified variants, 31.0% exhibiting a minor allele frequency of <1% were novel. Using these variants, we constructed a reference haplotype and graph-structured reference sequence to facilitate accurate imputation and variant characterization. Our findings suggest that integrating genetic variations from ethnically diverse populations into the prevailing catalogs is essential to achieve precision medicine for all populations.
Authors
- Yukihide Momozawa (ORCID: https://orcid.org/0000-0001-5638-3504)
- Takahisa Kawaguchi (ORCID: https://orcid.org/0000-0001-7781-7404)
- Ryo Yamada (ORCID: https://orcid.org/0000-0002-1587-630X)
- Yoichiro Kamatani (ORCID: https://orcid.org/0000-0001-8748-5597)
- Dominic Nelson (ORCID: https://orcid.org/0000-0003-2496-8588)
- Yukinori Okada (ORCID: https://orcid.org/0000-0002-0311-8472)
- Fumihiko Matsuda (ORCID: https://orcid.org/0000-0003-4557-4553)
- Jeong‐Sun Seo (ORCID: https://orcid.org/0000-0002-5818-5533)
- Shuji Kawaguchi (ORCID: https://orcid.org/0000-0002-4045-6518)
- Izumi Yamaguchi (ORCID: https://orcid.org/0000-0003-0890-0145)
- Saori Sakaue (ORCID: https://orcid.org/0000-0003-3618-9717)
- Keitaro Matsuo (ORCID: https://orcid.org/0000-0003-1761-6314)
- Yoshihisa Yamano (ORCID: https://orcid.org/0000-0001-7527-0345)
- Koichiro Higasa (ORCID: https://orcid.org/0000-0003-4049-8256)
- Michiaki Kubo (ORCID: https://orcid.org/0000-0002-0095-2322)
- Yoshinori Murakami (ORCID: https://orcid.org/0000-0002-2826-4396)
- Changhoon Kim (ORCID: https://orcid.org/0000-0003-1087-0424)
- Ta‐Yu Yang (ORCID: https://orcid.org/0000-0002-5379-5340)
- Simon Gravel
Institutions
- Kansai Medical University (JP)
- St. Marianna University School of Medicine (JP)
- Kyoto University (JP)
- Seoul National University Bundang Hospital (KR)
- McGill Genome Centre (CA)
- Macrogen (South Korea) (KR)
- Aichi Cancer Center (JP)
- Kyoto International University (JP)
- McGill University and Génome Québec Innovation Centre (CA)
- RIKEN Center for Integrative Medical Sciences (JP)
- The University of Tokyo (JP)
- The University of Osaka (JP)
Publication Details
- Journal
- Journal of Human Genetics
- Published
- 2025-11-08
- DOI
- https://doi.org/10.1038/s10038-025-01430-1
- Citations
- 1
- Primary Topic
- Genetic Associations and Epidemiology
- Type
- article
- Field-Weighted Citation Impact
- 1.82
Funders
- Japan Agency for Medical Research and Development
- Japan Society for the Promotion of Science