TogoVar datasets
Variant frequencies for which you can apply for use of individual-level data∗1 to the NBDC human databases∗2
Click the links at the Included controlled-access datasets to apply for use of individual-level data
| Variant dataset name | Analysis method | Target population | Healthy subjects | Affected subjects | Sample size | Number of variants (# of sites) | Included controlled-access datasets |
|---|---|---|---|---|---|---|---|
| GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel | WGS | Japanese | ✔ | 7,609 | 95,863,463 (90,280,248) | 6 datasets | |
| JGA-NGS | WES | Japanese | ✔ | ✔ | 125 | 4,679,025 | 7 datasets |
| JGA-SNP | SNP-Chip | Japanese | ✔ | ✔ | 183,884 | 1,249,724 | 3 datasets |
∗1：fastq/bam/cel files and/or lists of genotype data etc.
∗2：Japanese Genotype-phenotype Archive (JGA) / AMED Genome group sharing Database (AGD)
Other variant datasets
| Variant dataset name | Analysis method | Target population | Healthy subjects | Affected subjects | Sample size | Number of alleles (# of sites) | Author | Version/Last updated |
|---|---|---|---|---|---|---|---|---|
| ClinVar | - | Mixed | ✔ | — | 788,993 | NCBI | 2021 | |
| Genome Aggregation Database (gnomAD) exomes | WES | Mixed | ✔ | ✔ | 125,748 | 17,209,972 | Broad Institute | v2.1.1 |
| Genome Aggregation Database (gnomAD) genomes | WGS | Mixed | ✔ | ✔ | 15,708 | 261,942,336 | Broad Institute | v2.1.1 |
| Human Genetic Variation Database (HGVD) | WES | Japanese | ✔ | 1,208 | 554,461 (501,556) | Kyoto University | Version 2.30 (2017/08/02) | |
| ToMMo 8.3KJPN Allele Frequency Panel(8.3KJPN) | WGS | Japanese | ✔ | 8,380 | 95,085,851 (79,359,228) | Tohoku Medical Megabank Organization | v202109 |
Note 1: TogoVar contains ClinVar variants only in the VCF file, GRCh37 positions of which were determined.
Note 2 : 8.3KJPN consists of SNVs (Autosome, chrX(PAR1+PAR2+XTR) and chrMT) and INDELs (Autosome and chrX(PAR1+PAR2+XTR)). See Summary of ToMMo 8.3KJPN.
Non-variant datasets
| Dataset name | Version/Last update | Description | Author |
|---|---|---|---|
| Colil | Obtained by API | Information on citation relationships in life sciences literature | DBCLS |
| GRCh37.p13 | 2013/06/28 | Human genome reference sequence | GRC |
| HGNC symbol report | 2021 | Approved human gene nomenclature and associated gene information | HGNC |
| LitVar | Obtained by API | Information on papers in which the names of variants appear | NCBI |
| PubTator Central | 2021 | Information on papers in which the names of variants appear | NCBI |
| TogoGenome | ‐ | Comprehensive information on genomes | DBCLS |
Tools for data processing
| Name | Ver. | Description | Author |
|---|---|---|---|
| bcftools | Normalize indels and split multiallelic sites into biallelic variants | Genome Research Ltd. | |
| BioReT | ‐ | Execute programs for variant discovery from NGS data in proper order | Amelieff |
| Variant Effect Predictor (VEP) | Ensembl release 104 | Addannotations like gene names or consequences to variants | EMBL-EBI |