TogoVar datasets (GRCh38)

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 nameAnalysis methodLiftover GRCh37Target populationHealthy subjectsAffected subjectsSample sizeNumber of allelesIncluded controlled-access datasets
GEM Japan Whole Genome Aggregation (GEM-J WGA) PanelWGS✔Japanese✔7,60994,961,1546 datasets
JGA-NGSWES✔Japanese✔✔1254,624,124
7 datasets
JGA-SNPSNP-Chip✔Japanese✔✔183,8841,244,8383 datasets
National Center Biobank Network (NCBN)WGS✔Mixed✔JPN:9,290 1KGP:2,504215,729,032No 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 nameAnalysis methodLiftover GRCh37Target populationHealthy subjectsAffected subjectsSample sizeNumber of allelesAuthorVersion/Last updated
Genome Aggregation Database (gnomAD) exomesWESMixed✔✔730,947183,558,769Broad Institutev4.0
Genome Aggregation Database (gnomAD) genomesWGSMixed✔✔76,215759,336,320Broad Institutev4.0
ToMMo 54KJPN Allele Frequency Panel(54KJPN)WGSJapanese✔54,302262,200,990Tohoku Medical Megabank Organizationv20230626

Note: 54KJPN consists of SNVs (Autosome, chrX(PAR1+PAR2+XTR) and chrMT) and INDELs (Autosome and chrX(PAR1+PAR2+XTR)).

Non-variant datasets

Dataset nameVersion/Last updateDescriptionAuthor
ClinVar2024/01/08Clinical significance of variantsNCBI
ColilObtained by APIInformation on citation relationships in life sciences literatureDBCLS
GRCh38.p132019/03/01Human genome reference sequenceGRC
GWAS Catalog2024/05/28Catalog of human genome-wide association studiesNHGRI-EBI
HGNC symbol report2024/05/28Approved human gene nomenclature and associated gene informationHGNC
LitVarObtained by APIInformation on papers in which the names of variants appearNCBI
PubMed2024/04/26Information on papersNCBI
PubTator Central2024/01/04Information on papers in which the names of variants appearNCBI

Note: TogoVar obtained ClinVar variants from the VCF filethat contains only variants for which GRCh38 positions were determined.

Tools for data processing

NameVer.DescriptionAuthor
bcftoolsSplit multiallelic sites into biallelic variantsGenome Research Ltd.
BioReT‐Execute programs for variant discovery from NGS data in proper orderAmelieff
Variant Effect Predictor (VEP)Ensembl release 110Add annotations like gene names, consequences or deleterious predictions (AlphaMissense, SIFT and Polyphen) to variantsEMBL-EBI