JGA-NGS dataset

Summary

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 no variants with 5 alternative alleles or less are included.

  • Version/Last update: 2018/06/01
  • Sample size: 125
  • Number of detected variants: 13,338,968
  • Number of variants after the exclusion: 4,679,025

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.

  1. The data user can freely present the result of the study for which data from the NBDC Human Database are used.
  2. 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.

  1. In using data, the user must take responsibility for and make judgments concerning the quality, content, and scientific validity of the data.
  2. 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.
  3. 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]. Tokyo: Japan Science and Technology Agency (Japan), National Bioscience Database Center; [2018] - . JGA-NGS dataset; [cited YYYY Mmm DD]. Available from: https://togovar.biosciencedbc.jp/doc/datasets/jga_ngs

Data analysis method

See How JGA dataset was created.

Included controlled-access datasets

By specifying the JGAID, you can apply for data use to the NBDC Human database.

JGAIDHuman DB IDStudy titleParticipantsSample
size
Data provider
JGAD00000000004hum0006Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significanceastrocytomas6Nobuhito Saito
(P-DIRECT)
JGAD00000000106hum0006Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significanceoligodendrogliomas16Nobuhito Saito
(P-DIRECT)
JGAD00000000112hum0006Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significancegliomas17Nobuhito Saito
(P-DIRECT)
JGAD00000000014hum0021Genetic Analysis in Psychiatric DisordersHealthy Monozygotic Twins6Tadafumi Kato
(Genome Science)
JGAD00000000036hum0035Genome wide analysis of gene mutations in solid tumorssolid tumors23Junko Takita
(P-DIRECT)
JGAD00000000038hum0040Epigenomic analysis of the human placentahuman placenta and maternal blood48Takahiro Arima
IHEC)
JGAD00000000060hum0066Identification of non­coding RNAs involved in the recurrence or spread of cancer and the elucidation of their mechanismsColon cancer9Koshi Mimori
Total125