DNA Data Bank of Japan (DDBJ) Center of the National Institute of Genetics (Mishima, Japan) and National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (Tokyo, Japan) have operated Japanese Genotype-phenotype Archive since October 2013 to serve as one of public domain repositories providing authorized-access to individual-level human phenotype and genotype data.

    The International Nucleotide Sequence Database Collaboration (INSDC) advisors’ letter was published in Nature and Science which reminded scientists to submit sequence data to unrestricted-access INSDC, and human phenotype and genotype data requiring authorized-access to other repositories that are not part of the INSDC, such as the NCBI's Database of Genotypes and Phenotypes (dbGaP), the EMBL-EBI's European Genome-phenome Archive (EGA) or the DDBJ's Japanese Genotype-phenotype Archive (JGA). JGA is also listed in the recommended data repositories of the Scientific Data journal.

    Information about available studies can be accessed freely on the NBDC and the NBDC websites. As of 8 June 2016, 28 studies are available at JGA. DDBJ Center and NBDC continue to develop JGA to support sharing of human phenotype and genotype data and accelerate biomedical research.

Background:

    To exploit personal genomic data while respecting the privacy and consent of study participants, it is essential to establish a public domain repository for data management and a policy for data usage. In the US, the National Institutes of Health (NIH) has established guidelines for sharing human subject data. Likewise, NBDC in Japan has established guidelines for sharing human subject data. The Data Access Committee (DAC) at NBDC reviews and makes decisions about data submission to JGA and usage requests from researchers.

    JGA accepts data that are de-identified at least twice by submitters. Acceptable data types are raw data from array-based and next-generation sequencing platforms, clinical images, and phenotype data associated with data samples. Processed and analyzed data such as alignments, assemblies and variations are also acceptable. Upon submission, the JGA team will archive the original data files in encrypted form in the database. Information in JGA is organized in a hierarchical JGA data model based on that of EGA. JGA assigns stable, unique identifiers prefixed by ‘JGA’ to studies and subsets of information from those studies. Once data usage has been granted by DAC at NBDC, datasets with access permission can be downloaded with secure downloading software.