NBDC Research ID: hum0015.v1

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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 for 1070 individuals were pooled, and allele frequencies were calculated. We selected autosomal SNPs (minor allele frequency >5%) that matched known SNPs in dbSNP138.

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.

URL: http://ijgvd.megabank.tohoku.ac.jp/


Data Set IDType of DataCriteriaRelease Date

Frequencies of known autosomal SNPs whose minor allele frequencies are more than 5% in 1070 participants.

Un-restricted Access 2014/10/14

*Release Note 




Participants/Materials 1070 healthy Japanese individuals living in Miyagi prefecture


Target Loci for Capture Methods


Platform Illumina [Hiseq 2500]
Library Source gDNA extracted from peripheral blood cells
Cell Lines -
Library Construction (kit name) Illumina TruSeq DNA PCR-Free HT sample prep kit
Fragmentation Methods Sonication (Covaris LE220)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) -
QC Methods -
Mapping Methods -
Mapping Quality -
Coverage(Depth) 32.4 x
Variation Detection Methods -
Marker Number 4,301,546 SNPs (hg19)
NBDC Data Set ID


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Total Data Volume 339 MB
Comments (Policies)

NBDC policy

*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more



Principal Investigator: Masayuki Yamamoto

Affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University

Project / Group Name: Tohoku Medical Megabank Organization

URL: http://www.megabank.tohoku.ac.jp/

Funds / Grants (Research Project Number):

NameTitleProject Number

Ministry of Education, Culture, Sports, Science and TechnologyJapan





TitleDOIData Set ID
1 Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals doi:10.1038/ncomms9018 hum0015.v1.freq.v1