JGA-WGS dataset
Summary
The JGA-WGS dataset is a frequency dataset that aggregates variants detected by reanalyzing individual-level whole genome sequence data in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA). All JGA data for which an approval for creating secondary data has been obtained are aggregated. To view allele frequencies and genotype counts per dataset, you need an account to access the controlled-access data in the NBDC Human Database. For account registration, please see Data Use (NBDC Human Database).
- Version/Last update: 2024/12/3
- Sample size: 78
- Number of detected variants (alternate alleles): 20,822,413
Terms of use
Rights of Data Users
The rights of data users shall conform to "5-2-1. Open Data" in "5-2. Rights of Data Users" listed in the NBDC Human Data Sharing Guidelines.
- The data user can freely present the result of the study for which data from the NBDC Human Database are used.
- The data user can freely acquire intellectual property rights based on the result of the study for which data from the NBDC Human Database are used.
Responsibilities of Data Users
Terms of "5-3-1. Open Data" in "5-3. Responsibilities of Data Users" listed in the NBDC Human Data Sharing Guidelines shall apply with modification to the responsibilities of data users. As for redistribution of data, terms for controlled-access data shall apply because this dataset was generated by processing controlled-access data.
- In using data, the user must take responsibility for and make judgments concerning the quality, content, and scientific validity of the data.
- The data user must comply with the following rules.
- The use of data is limited to the study being undertaken.
- Identification of individuals is prohibited
- Redistribution of data is prohibited.
- The data user must add the following citation while using the data in public (e.g. publishing an article).
Variant dataset aggregated from NGS data in NBDC Human Database/JGA[Internet]. Kashiwa: Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems; [2024] - . JGA-WGS dataset; [cited YYYY Mmm DD]. Available from: https://grch37.togovar.org/doc/datasets/jga_wgs
Data analysis method
- Explanation: Whole genome sequencing analysis data (germline)
- Workflow Source Code (jga-analysis): https://github.com/ddbj/jga-analysis
Included controlled-access datasets
By specifying the JGAID, you can apply for data use to the NBDC Human database.
| JGAID | Human DB ID | Study title | Participants | Sample size | Data provider |
|---|---|---|---|---|---|
| JGAD000670 | hum0068 | Cancer genomics for elucidation of molecular mechanisms of carcinogenecis and progression in lung cancer | WGS data of the matched control (germline) | 21 | Takashi Kono |
| JGAD000687 | hum0201 | Collection and transfer of human tumor samples and research using genomic information | WGS data of the matched control (germline) | 14 | Toshiro Sato |
| JGAD000688 | hum0161 | Genome sequencing analysis for hepatoblastoma | WGS data of the matched control (germline) | 33 | Hidewaki Nakagawa |
| JGAD000689 | hum0159 | Genome sequencing analysis for colorectal cancer | WGS data of the matched control (germline) | 10 | Hidewaki Nakagawa |
| Total | 78 | ||||