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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
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Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Research ID

hum0015-v3Release info

Latest

Research title

Construction of the Whole-genome Reference Panel of 3552 Japanese Individuals

Research overview

Aims
Construction of the whole-genome reference panel of Japanese individuals by deep whole-genome sequencing
Methods
DNA was extracted from the blood samples of the subjects. We conducted whole-genome sequencing by using HiSeq 2500. After genotype calling for each individual, genotype frequencies were pooled, and allele frequencies were calculated.
Participants/materials
Selected 1070 individuals from the adult (age ≥ 20) cohort participants who gave the informed consent at the places for health survey in Miyagi prefecture, by removing relatives.
3552 individuals from the general populations in Japan. This population includes 1) 3342 individuals who participated in Tohoku Medical Megabank Project and were recruited in Miyagi and Iwate prefectures, 2) 181 individuals recruited in National Hospital Organization Nagasaki Medical Center, 3) 29 individuals who participated in Nagahama Study.
URL

Datasets

CartDataset IDType of dataAnalysis methodAccess criteriaDate published
NHA000002Frequencies of known autosomal SNPs whose minor allele frequencies are more than 5% in 1070 participants.
  • WGS
Unrestricted-access2014-10-14
JGAD000237Allele frequencies of SNVs/Indels on autosomal chromosomes, X-chromosome, and mitochondrial DNA in 3552 participants
  • WGS
Controlled-access (Type I)2020-09-28
NHA000077Allele frequencies of SNVs/Indels on autosomal chromosomes, X-chromosome, and mitochondrial DNA in 3552 participants
  • WGS
Unrestricted-access2019-01-11

Data provider

Principal investigator
Masayuki Yamamoto
Affiliation
Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University

Research projects

NameURL
Tohoku Medical Megabank Organization

Grants

NameTitleProject number
Japan Agency for Medical Research and Development (AMED)
Tohoku Medical Megabank Project (Tohoku University) Special Account of the Great East Japan Earthquake Disaster Recovery
  • JP18km0105001
Japan Agency for Medical Research and Development (AMED)
Tohoku Medical Megabank Project (Tohoku University) General Accounting
  • JP18km0105002
Japan Agency for Medical Research and Development (AMED)
Tohoku Medical Megabank Project (Iwate Medical University) Special Account of the Great East Japan Earthquake Disaster Recovery
  • JP18km0105003
Japan Agency for Medical Research and Development (AMED)
Tohoku Medical Megabank Project (Iwate Medical University) General Accounting
  • JP18km0105004
Ministry of Education, Culture, Sports, Science and TechnologyJapan
N/A
N/A

Related publications

TitleDOIDataset ID
Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
https://doi.org/10.1038/ncomms9018 (opens in a new tab)
3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome
https://doi.org/10.1038/s41439-019-0059-5 (opens in a new tab)

Controlled access users

No use of the controlled access data has been recorded.