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/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0015.v1.freq.v1 | Frequencies of known autosomal SNPs whose minor allele frequencies are more than 5% in 1070 participants. | Unrestricted-access | 2014/10/14 |
| JGAS000159 | 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 | Unrestricted-access | 2018/01/11 |
*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 JGAS000159 (Controlled-access [Type I]) to Unrestricted-access (hum0015.v3.3.5kjpnv2.v1) from 2019/01/11.
MOLECULAR DATA
| 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) | 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 Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 339 MB |
| Comments (Policies) | NBDC policy |
| 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) | 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 Dataset ID | JGAD000237 |
| Total Data Volume | 2 GB (vcf [ref: GRCh37/hg19]) |
| Comments (Policies) | NBDC policy |
hum0015.v3.3.5kjpnv2.v1 (Exactly the same data as JGAS000159)
| 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) | 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 Dataset 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) |
| 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: https://www.megabank.tohoku.ac.jp/english/
Funds / Grants (Research Project Number):
| Name | Title | Project 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
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals | doi:10.1038/ncomms9018 | hum0015.v1.freq.v1 |
| 2 | 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome | doi: 10.1038/s41439-019-0059-5 | hum0015.v3.3.5kjpnv2.v1 |
