2024/12/3
- Datasets: Clinical significance from MGeND (Medical Genomics Japan Variant Database) was newly added.
- MGeND is a database of genome variants and their clinical characteristics, collected through the Clinical Genome Information Integration Database Development Project by the Japan Agency for Medical Research and Development (AMED). MGeND contains variant information for diseases such as cancer, rare and intractable diseases, infectious diseases, dementia, and hearing loss, and can be considered the Japanese equivalent of ClinVar.
- The disease names in MGeND have been aligned with the vocabulary defined in MedGen, which is also used in ClinVar, wherever possible.
- Datasets: The JGA-WGS datasetwas newly added (GRCh38 only).
- Gene page: Missense variants are visualized on a 3D protein structure.
- The visualization helps you to assess the potential impact of each missense variant on a protein structure (e.g., BRAF:p.V600E, KRAS:p.G12D).
- You can choose from protein structures registered in Protein Data Bank Japan (PDBj) or those predicted by AlphaFold. Please note that the displayed structures do not account for the effects of the variant.
2024/6/27
- 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.
2024/2/28
2023/11/16
2023/7/14
- 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.
2022/11/1
2022/8/5
2021/12/16
2020/10/22
2020/7/27
2019/7/25
- 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.
2018/6/7
