TogoVar datasets (GRCh37)
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-SNP | SNP-Chip | Japanese | ✔ | ✔ | 183,884 | 1,249,724 | 3 datasets |
| JGA-WES | WES | Japanese | ✔ | ✔ | 125 | 4,679,025 | 7 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 frequency datasets
| Variant dataset name | Analysis method | Target population | Healthy subjects | Affected subjects | Sample size | Number of alleles (# of sites) | Author | Version/Last updated |
|---|---|---|---|---|---|---|---|---|
| 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 | 554,400 | 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 | v20200831 |
Note: 8.3KJPN consists of SNVs (Autosome, chrX(PAR1+PAR2+XTR) and chrMT) and INDELs (Autosome and chrX(PAR1+PAR2+XTR)).
Non-variant frequency datasets
| Dataset name | Version/Last update | Description | Author |
|---|---|---|---|
| ClinVar | 2024/10/03 | Clinical significance of variants | NCBI |
| Colil | Obtained by API | Information on citation relationships in life sciences literature | DBCLS |
| GRCh37.p13 | 2013/06/28 | Human genome reference sequence | GRC |
| GWAS Catalog | 2024/10/15 | Catalog of human genome-wide association studies | NHGRI-EBI |
| HGNC symbol report | 2024/08/27 | Approved human gene nomenclature and associated gene information | HGNC |
| LitVar | Obtained by API | Information on papers in which the names of variants appear | NCBI |
| MedGen | 2024/10/15 | Information related to human medical genetics, such as attributes of conditions with a genetic contribution | NCBI |
| MGeND | 2024/03/08 | Clinical significance of variants collected from the Japanese population | NCGM |
| PubMed | 2024/10/14 | Information on papers | NCBI |
| PubTator Central | 2024/01/04 | Information on papers in which the names of variants appear | NCBI |
Note: TogoVar obtained ClinVar variants from the VCF filethat contains only variants for which GRCh37 positions were determined.
Tools for data processing
| Name | Ver. | Description | Author |
|---|---|---|---|
| bcftools | 1.20 | Split multiallelic sites into biallelic variants, exclude reference mismatches, and normalize them | Genome Research Ltd. |
| BioReT | ‐ | Identify germline short variants (SNPs and Indels) in WES from JGA to produce a joint callset in VCF format | Amelieff |
| Variant Effect Predictor (VEP) | Ensembl release 112 | Add annotations like gene names, consequences or deleterious predictions (AlphaMissense, SIFT and Polyphen) to variants | EMBL-EBI |