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
∗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 | Liftover GRCh37 | Target population | Healthy subjects | Affected subjects | Sample size | Number of alleles | Author | Version/Last updated |
---|---|---|---|---|---|---|---|---|---|
ClinVar | – | Mixed | ✔ | — | 1,117,487 | NCBI | 2022/09/01 | ||
Genome Aggregation Database (gnomAD) genomes | WGS | Mixed | ✔ | ✔ | 76,156 | 759,302,267 | Broad Institute | v3.1.2 | |
Human Genetic Variation Database (HGVD) | WES | ✔ | Japanese | ✔ | 1,208 | 549,623 | Kyoto University | Version 2.30 (2017/08/02) |
|
ToMMo 14KJPN Allele Frequency Panel(14KJPN) | WGS | Japanese | ✔ | approx. 14,000 | 133,757,499 | Tohoku Medical Megabank Organization | v20211208r2 |
Note 1: TogoVar contains ClinVar variants only in the VCF file, GRCh38 positions of which were determined.
Note 2 : 14KJPN consists of SNVs (Autosome, chrX(PAR1+PAR2+XTR) and chrMT) and INDELs (Autosome and chrX(PAR1+PAR2+XTR)).
Non-variant datasets
Dataset name | Version/Last update | Description | Author |
---|---|---|---|
Colil | Obtained by API | Information on citation relationships in life sciences literature | DBCLS |
GRCh38.p13 | 2019/3/1 | Human genome reference sequence | GRC |
HGNC symbol report | 2022/9/16 | 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 | 2022/9/20 | Information on papers in which the names of variants appear | NCBI |
TogoGenome | ‐ | Comprehensive information on genomes | DBCLS |
Tools for data processing
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