DNA Data Bank of Japan (DDBJ) Center of National Institute of Genetics (Mishima, Japan) and National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (Tokyo, Japan) have operated the Japanese Genotype-phenotype Archive since October 2013 to serve as one of centralized repositories providing authorized access to individual-level human phenotype and genotype data.
International Nucleotide Sequence Database Collaboration (INSDC) advisors' letter was published in Nature and Science which reminds scientists to submit unrestricted-access sequence data to INSDC, and human phenotype and genotype data requiring restricted-access to other repositories that are not part of INSDC, such as NCBI's Database of Genotypes and Phenotypes (dbGaP), EMBL-EBI's European Genome-phenome Archive (EGA) or DDBJ's Japanese Genotype-phenotype Archive (JGA). JGA is also listed in the recommended data repositories of Scientific Data journal.
DDBJ Center and NBDC continue to improve JGA as internationally-recognized repository to promote human data sharing and to accelerate biomedical research world-wide.
To exploit personal genomic data while respecting the privacy and informed consents of study participants, it is essential to establish a centralized repository for data management and a policy for data usage. In the US, the National Institutes of Health (NIH) have established guidelines for sharing human subject data. Likewise, NBDC in Japan established guidelines for sharing human-derived data. Data submission to JGA and usage requests from researchers are reviewed by the Data Access Committee (DAC) at NBDC.
JGA accepts data that are de-identified by submitters. Acceptable data types include 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 granted by DAC, approved datasets can be downloaded with secure downloading software.