History | TogoVar

Datasets: Allele frequencies and genotype counts (by disease and sex) for 45 diseases were added to JGA-SNP as disease-specific information.
- BioBank Japanand RIKENcollected samples and performed genotyping by SNP array for 182,557 individuals.
- The frequency can be displayed by expanding the “Section: Frequency” > “Dataset: "JGA-SNP” > “Population: Total” on each variant report page (e.g., tgv66359566). You can search for variants based on the disease and sex-specific frequencies using the “Alternative allele frequency/count” in the Advanced search.
Datasets: Allele frequencies and genotype counts of 9,290 Japanese were newly added as NCBN dataset(GRCh38 only).
- The National Center BioBank Network (NCBN) collected the samples and conducted whole-genome analysis.
- The Japanese frequencies can be compared with those of the 2,504 individuals from the international 1000 Genomes Project (1KGP). Joint calling was performed for the Japanese and 1KGP samples.
- The frequency can be displayed by expanding the “Section: Frequency” > “Dataset: NCBN” > “Population: Total” on each variant report page (e.g., tgv80918483). You can search for variants based on the population-specific frequencies using the “Alternative allele frequency/count” in the Advanced search.

Simple/Advanced search: Pathogenicity predictions with AlphaMissense (Cheng et al.2023) were added to the missense variants in TogoVar.
Datasets: The Genome Aggregation Database (gnomAD) was updated to version 4.0.

Datasets: ToMMo 14KJPN was updated to ToMMo 54KJPN (ToMMo 54KJPN-SNV/INDEL Allele Frequency Panel (v20230626)).
Advanced search: You can search by TogoVar ID (e.g. tgv47264307) or dbSNP refSNP ID (e.g. rs671).
Downloads: Allele frequencies for all variants are available in VCF format as well as tab-separated format.

Simple/Advanced search: You can download search results in JSON, CSV, or TSV formats.
Advanced search: We added the "Disease" field to the "Add condition" menu. You can now search by disease names from MedGen. The search targets include diseases in the subconcepts of the Mondo disease ontology.

URL: The URL of TogoVar was changed from https://togovar.biosciencedbc.jp to https://togovar.org.
Simple/Advanced search: You can search variants by a location of the GRCh38 reference sequence. Search by a GRCh37 location is still available.
- https://grch38.togovar.org (GRCh38)
- https://grch37.togovar.org (GRCh37)
Downloads: Bulk download of the GRCh38-based variant data was made available in addition to the GRCh37-based one.
- https://grch38.togovar.org/downloads/release/current/grch38/ (GRCh38)
- https://grch37.togovar.org/downloads/release/current/grch37/ (GRCh37)
Misc: The provider of TogoVar was changed from Department of NBDC Program, Japan Science and Technology Agencyto Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems (DBCLS).

Advanced search: Advanced searchwas released.
Gene page/Disease page: Variant information pages related with a gene（e.g.：PAX4) or a disease (e.g.：Acute myeloid leukemia ) was released.
Variant page/Gene page/Disease page: Genome-wide association studies from GWAS Catalogwas added to the variant, gene and disease pages.
TogoVar API: TogoVar API version 0.91was released.

Datasets: ToMMo 4.7KJPN was updated to ToMMo 8.3KJPN (ToMMo 8.3KJPN Allele Frequency Panel).
Datasets: ExAC was updated to gnomAD v2.1.1 (The Genome Aggregation Database).

Keyword search: You can search TogoVar by Human Genome Variation Society (HGVS) description(e.g.ALDH2:c.1510G>A or ALDH2:p.Glu504Lys).

Datasets: The new dataset, GEM-Japan Whole Genome Aggregation (GEM-J WGA), was added. Additionally, ToMMo 3.5KJPN was updated to ToMMo 54KJPN (ToMMo 4.7KJPN Allele Frequency Panel). ClinVar information was also updated.
Usability: You can search the variants on Karyotype image.

Keyword search: You can search TogoVar by an alias name of HGNC Gene Symbol (e.g. PD-1, p53).
Filters: You can specify either all or any of datasets of your choice as a target when searching by an alternative allele frequency.
Filters: You can filter variants by Consequence value, SIFT and/or Polyphen score.
Filters: You can hide and show low quality variants.
Datasets: ToMMo 3.5KJPN was updated to Ver.2 (ToMMo 3.5KJPNv2 Allele Frequency Panel). ClinVar, Variant Effect Predictor (VEP) and Ensembl were updated as well. See Datasets for detail.
Usability: You can choose the data items to display at the Configuration menu.
Usability: The user interface was refined for easier use.