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 variants
(# of sites)		 Author Version/Last updated
ClinVar - Mixed ✔ — 674,792 NCBI 2020/06/04
Exome Aggregation Consortium (ExAC) WES Mixed ✔ ✔ 60,706 10,195,872
(9,362,319)		 Broad Institute Release 1 (2017/02/27)
Human Genetic Variation Database (HGVD) WES Japanese ✔ 1,208 554,461
(501,556)		 Kyoto University Version 2.30
(2017/08/02)
ToMMo 4.7KJPN Allele Frequency Panel(4.7KJPN) WGS Japanese ✔ 4,773 74,494,394
(70,101,710)		 Tohoku Medical Megabank Organization v20190826

Note 1: TogoVar contains ClinVar variants only in the VCF file, GRCh37 positions of which were determined.
Note 2 : 4.7KJPN consists of SNVs (Autosome, chrX(PAR1+PAR2+XTR) and chrMT) and INDELs (Autosome and chrX(PAR1+PAR2+XTR)). See Summary of ToMMo 4.7KJPN.

Non-variant datasets

Dataset name Version/Last update Description Author
Colil 2019/01/25 Information on citation relationships in life sciences literature DBCLS
GRCh37.p13 2013/06/28 Human genome reference sequence GRC
HGNC symbol report 2020/03/30 Approved human gene nomenclature and associated gene information HGNC
LitVar Obtained by API Information on papers in which the names of variants appear NCBI
PubTatorCentral 2020/05/09 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 100 Add annotations like gene names or consequences to variants EMBL-EBI