NBDC Research ID: hum0015.v3

 

SUMMARY

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

 

Data Set IDType of DataCriteriaRelease Date
hum0015.v1.freq.v1 Frequencies of known autosomal SNPs whose minor allele frequencies are more than 5% in 1070 participants. Un-restricted Access 2014/10/14
JGAS00000000159 Allele frequencies of SNVs/Indels on autosomal chromosomes, X-chromosome, and mitochondrial DNA in 3552 participants Controlled Access (Type I) 2018/12/27
hum0015.v3.3.5kjpnv2.v1 Allele frequencies of SNVs/Indels on autosomal chromosomes, X-chromosome, and mitochondrial DNA in 3552 participants Un-restricted Access 2018/01/11

*Release Note 

*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

* The data provider changed the access level of JGAS00000000159 (Controlled Access [Type I]) to Un-restricted Access (hum0015.v3.3.5kjpnv2.v1) from 2019/01/11.

 

MOLECULAR DATA

hum0015.v1.freq.v1

Participants/Materials 1070 healthy Japanese individuals living in Miyagi prefecture
Targets WGS
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 Ultrasonic fragmentation (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

hum0015.v1.freq.v1

(Click the Data Set ID to download the file)

Total Data Volume 339 MB
Comments (Policies) NBDC policy

 

JGAS00000000159 (The access level was changed to "Un-restricted Access". Please have a look at hum0015.v3.3.5kjpnv2.v1.)

Participants/Materials 3552 individuals from the general populations in Japan
Targets WGS
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 Ultrasonic fragmentation (Covaris LE220)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 162 bp or 259 bp
QC Methods quantitative MiSeq (doi: 10.1016/j.ab.2014.08.015)
Mapping Methods -
Mapping Quality -
Coverage(Depth) 162PE: 27.2x, 259PE: 21.3x
Variation Detection Methods -
Marker Number

About 50,500,000 SNVs/Indels on autosomes

About 2,000,000 SNVs/Indels on X-chromosome

About 2,500 SNVs on mitochondrial DNA

Japanese Genotype-phenotype Archive Data set ID JGAD00000000237
Total Data Volume 2 GB (vcf [ref: GRCh37/hg19])
Comments (Policies) NBDC policy

 

hum0015.v3.3.5kjpnv2.v1 (Exactly the same data as JGAS00000000159)

Participants/Materials 3552 individuals from the general populations in Japan
Targets WGS
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 Ultrasonic fragmentation (Covaris LE220)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 162 bp or 259 bp
QC Methods quantitative MiSeq (doi: 10.1016/j.ab.2014.08.015)
Mapping Methods -
Mapping Quality -
Coverage(Depth) 162PE: 27.2x, 259PE: 21.3x
Variation Detection Methods -
Marker Number

About 50,500,000 SNVs/Indels on autosomes

About 2,000,000 SNVs/Indels on X-chromosome

About 2,500 SNVs on mitochondrial DNA

NBDC Data Set ID

hum0015.v3.3.5kjpnv2.v1

    -Allele frequencies of SNVs (autosomes)

    -Allele frequencies of SNVs (X-chromosome [PAR1+PAR2])

    -Allele frequencies of SNVs (X-chromosome [PAR1+XTR+PAR2])

    -Allele frequencies of SNVs (mitochondrial DNA)

    -Allele frequencies of Indels (autosomes)

    -Allele frequencies of Indels (X-chromosome [PAR1+PAR2])

    -Allele frequencies of Indels (X-chromosome [PAR1+XTR+PAR2])

(Click each data name to download the file)

metadata

Total Data Volume 2 GB (vcf [ref: GRCh37/hg19])
Comments (Policies) NBDC policy

 

DATA PROVIDER

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 - -
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

 

PUBLICATIONS

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
2