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.

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

Responsibilities of data users shall conform to "5-­3-­1. Open Data" in "5­-3. Responsibilities of Data Users" listed in the NBDC Human Data Sharing Guidelines.

  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

Please visit How JGA dataset was created.

Derivations of aggregated data

JGAID Human DB ID Study title Participants Sample
size
Data provider
JGAD00000000004 hum0006 Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance astrocytomas 6 Nobuhito Saito
(P-DIRECT)
JGAD00000000106 hum0006 Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance oligodendrogliomas 16 Nobuhito Saito
(P-DIRECT)
JGAD00000000112 hum0006 Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance gliomas 17 Nobuhito Saito
(P-DIRECT)
JGAD00000000014 hum0021 Genetic Analysis in Psychiatric Disorders Healthy Monozygotic Twins 6 Tadafumi Kato
(Genome Science)
JGAD00000000036 hum0035 Genome wide analysis of gene mutations in solid tumors solid tumors 23 Junko Takita
(P-DIRECT)
JGAD00000000038 hum0040 Epigenomic analysis of the human placenta human placenta and maternal blood 48 Takahiro Arima
IHEC)
JGAD00000000060 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