Evidence map›Paper›PMID 41206389›Full record

ArticleJournal of human genetics2026

Whole-genome sequencing of 3135 individuals representing the genetic diversity of the Japanese population.

Koichiro Higasa, Yoichiro Kamatani, Takahisa Kawaguchi, Shuji Kawaguchi, Saori Sakaue, Ta-Yu Yang, Yukinori Okada, Yukihide Momozawa, Izumi Yamaguchi, Dominic Nelson and 9 more

Abstract read
In one paragraph

Article in Journal of human genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors.

Koichiro HigasaDepartment of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata, Japan. higasa.koi@kmu.ac.jp.
Yoichiro KamataniHuman Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
Takahisa KawaguchiHuman Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
Shuji KawaguchiHuman Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.ORCID http://orcid.org/0000-0002-4045-6518
Saori SakaueLaboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Ta-Yu YangKyoto-McGill International Collaborative Study in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
Yukinori OkadaDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
Yukihide MomozawaLaboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.ORCID http://orcid.org/0000-0001-5638-3504
Izumi YamaguchiHuman Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
Dominic NelsonDepartment of Human Genetics, McGill University, Montreal, Canada, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
Simon GravelDepartment of Human Genetics, McGill University, Montreal, Canada, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
Yoshinori MurakamiDivision of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0002-2826-4396
Ryo YamadaStatistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.ORCID http://orcid.org/0000-0002-1587-630X
Keitaro MatsuoDivision of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Aichi, Japan.ORCID http://orcid.org/0000-0003-1761-6314
Yoshihisa YamanoSt. Marianna University School of Medicine, Kawasaki, Japan.ORCID http://orcid.org/0000-0001-7527-0345
Changhoon KimBioinformatics Institute, Macrogen, Inc., Seoul, Republic of Korea.
Jeong-Sun SeoBioinformatics Institute, Macrogen, Inc., Seoul, Republic of Korea.
Michiaki KuboRIKEN Center for Integrative Medical Sciences, Yokohama, Japan.ORCID http://orcid.org/0000-0002-0095-2322
Fumihiko MatsudaHuman Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan. fumi@genome.med.kyoto-u.ac.jp.

Funding

MEXT | Japan Society for the Promotion of Science (JSPS) JP16K18474MEXT | Japan Society for the Promotion of Science (JSPS) JP17K07255MEXT | Japan Society for the Promotion of Science (JSPS) JP17KT0125MEXT | Japan Society for the Promotion of Science (JSPS) JP19H03209MEXT | Japan Society for the Promotion of Science (JSPS) JP19K07349MEXT | Japan Society for the Promotion of Science (JSPS) JP21H03548
6 · The paper itself

Abstract

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.

Indexed as

Genetic VariationGenome, HumanWhole Genome SequencingEast Asian PeopleGene FrequencyGenetics, PopulationHaplotypesHumansJapanPolymorphism, Single Nucleotide

Identifiers

PMID41206389
PMCPMC13021519

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.