NBDC Research ID: hum0015.v1
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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 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 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. |
Un-restricted Access | 2014/10/14 |
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) | 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 |
(Click the Data Set ID to download the file) |
| Total Data Volume | 339 MB |
| Comments (Policies) |
*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
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):
| Name | Title | Project Number |
|---|---|---|
|
Ministry of Education, Culture, Sports, Science and TechnologyJapan |
- |
- |
PUBLICATIONS
| Title | DOI | Data 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 |
