image: The image above is an example of a search operated on 'TogoVar' using as a key the position of a variant in the genome. If your research on a patient group revealed that many of them have G to A variation at position 127254587 on chromosome 7, you type '7:127254587' in the search box. Variants on the specified position appear on the result area, the second one being the variant you wanted (G to A). Association with type 2 diabetes is suggested via ClinVar in the right-most column. The bar chart in the middle shows variant frequencies in various databases, and detailed figures are displayed by bringing the cursor over the chart. The data shows the frequency of this variant is about 100 times higher in Japanese population (JGA, 3.5KJPN, HGVD) than in ExAC, which is based mainly on Caucasian population. view more
Credit: Japan Science and Technology Agency
Japanese medical genome researchers had long been suffering from the lack of publicly available information about allele frequencies of Japanese genome variants/variations which is necessary to determine disease-associated genome variants/variations in the Japanese population. Although two allelic variant frequency data based on approximately 3,500 and 1,200 genome data respectively have recently been released by Japanese cohort studies, the researchers trying to interpret their variant data still need to visit many different websites in addition to comparing these two websites: ExAC (Exome Aggregation Consortium) or gnomAD (Genome Aggregation Database) to check populational differences, ClinVar to find medical implication if any, and numerous websites of scientific publications for preceding studies.
In addition to the trouble of consulting many resources, researchers face other serious problems when comparing variant data from different databases. One is the variant position differences between various versions of the genomic assembly. Another is the different description of insertion/deletion among data formats. Researchers are spending considerable time struggling to integrate data from different databases, not only for one variant but for many.
"TogoVar" gives a solution to this situation. It is an integrated database for genome variants/variations in Japanese population ("Togo" is a Japanese word meaning "integration"). If you have any information about a variant such as disease name, gene name or position in genome, "TogoVar" retrieves detailed information about the variant including allelic frequency (count) in various databases, variant type, clinical condition and significance, genomic context, transcript information, and related publications. Researchers can access all these details with a click without worrying about inconsistency of description. Variant databases used for "TogoVar" are: ExAC from Broad Institute, 3.5KJPN (ToMMo), HGVD (Kyoto Univ.), JGA-NGS, and JGA-SNP. ExAC has more than sixty thousand exome data acquired from all over the world, while the latter four are Japanese oriented (see table 1 for detail). JGA-NGS and JGA-SNP are databases of variant frequency calculated from deposited genome data in "NBDC Human Database, which is a Japanese human genome data repository operated jointly by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST) and DDBJ center. If you are interested in conducting a further research using original individual genome data, you can apply for the use of controlled-access data in NBDC Human Database.
"TogoVar" aims to be a Japanese genome information infrastructure and contribute to the development of genomic medical science, which would lead to advancement of personalized (precision) medicine including genetic counseling. We are planning to enhance it by adding gene expression data associated with variants as well as incorporating more calculated data from NBDC Human Database, making it more useful for researchers.
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"TogoVar" is one of the results of research collaborations between NBDC of JST and Database Center for Life Science (DBCLS) of Research Organization of Information and Systems (ROIS).
TogoVar URL: https://togovar.biosciencedbc.jp