JGA-NGS dataset
Summary
The JGA-NGS dataset is a frequency dataset that assembles variants detected by reanalyzing individual-level 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 to be aggregated. Note that variants with alternative allele counts of five or fewer are not included. The GRCh37-based data was lifted over to GRCh38 by usingtransanno.
- Version/Last update: 2018/06/01
- Sample size: 125
- Number of detected variants (alternative alleles): 13,338,968
- Number of variants after the exclusion: 4,679,025
- Number of variants after the liftover from GRCh37 to GRCh38： 4,624,124
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; [2018] - . JGA-NGS dataset; [cited YYYY Mmm DD]. Available from: https://grch38.togovar.org/doc/datasets/jga_ngs
Data analysis method
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 |
|---|---|---|---|---|---|
| JGAD000004 | hum0006 | Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance | astrocytomas | 6 | Nobuhito Saito (P-DIRECT) |
| JGAD000106 | hum0006 | Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance | oligodendrogliomas | 16 | Nobuhito Saito (P-DIRECT) |
| JGAD000112 | hum0006 | Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance | gliomas | 17 | Nobuhito Saito (P-DIRECT) |
| JGAD000014 | hum0021 | Genetic Analysis in Psychiatric Disorders | Healthy Monozygotic Twins | 6 | Tadafumi Kato (Genome Science) |
| JGAD000036 | hum0035 | Genome wide analysis of gene mutations in solid tumors | solid tumors | 23 | Junko Takita (P-DIRECT) |
| JGAD000038 | hum0040 | Epigenomic analysis of the human placenta | human placenta and maternal blood | 48 | Takahiro Arima IHEC) |
| JGAD000060 | hum0066 | Identification of noncoding RNAs involved in the recurrence or spread of cancer and the elucidation of their mechanisms | Colon cancer | 9 | Koshi Mimori |
| Total | 125 | ||||