The GEM-J WGA panel is a variant frequency dataset of a Japanese general population, which was obtained by joint variant calling of whole genome sequence (WGS) data collected from 7,609 individuals across Japan. The WGS data is also available in a controlled access manner. They are the result of a joint research by Tohoku Medical Megabank Organization (ToMMo), Iwate Tohoku Medical Megabank Organization, RIKEN, and the Institute of Medical Science of the University of Tokyo, as part of the GEnome Medical alliance Japan (GEM Japan) project promoted by the Agency for Medical Research and Development (AMED).
Note that the GRCh37-based data was lifted over to GRCh38 by using CrossMap.
- GRCh37 version/last update: 2020/07/27
- Sample size: 7,609
- Number of alternative alleles after the liftover from GRCh37 to GRCh38：94,961,154
GEM-J Whole Genome Aggregation (WGA) panel by GEnome Medical alliance Japan (GEM-J) is licensed under a Creative Commons Attribution 4.0 International License. As additional terms, it is prohibited from identifying and contacting research participants. No warranty or liability is assumed for the data. This is complied with Article 5 (No Warranty and Limitation of Liability) of the Creative Commons Attribution 4.0 International License.
How to credit in your works
How to cite in your publications
Variant frequency [Unrestricted access]
Click here to download VCF files.
Result of joint variant calling [Controlled access]
If you would like to use the dataset, apply for data use to the AMED group sharing database.
|Dataset ID||AGD ID||Study title||File format||Sample size|
|In preparation||GEM Japan Whole Genome Aggregation (GEM-J WGA) パネルの作成||VCF||7,609|
WGS datasets used for joint variant calling [Controlled access]
(NBDC research ID)
|Study title||Participants||Sample size||Data provider|
|The Tailor-made Medical Treatment Program (BioBank Japan: BBJ)||The cohort participants registered in the BBJ from 2003 to 2007||768||BioBank Japan|
(English page is under construction)
|To investigate genomic alterations of Japanese biliary tract cancers||Biliary tract cancer (non-tumor tissue)||17||RIKEN Center for Integrative Medical Sciences|
|To investigate genomic alterations of Japanese liver cancers||Liver cancer (non-tumor tissue)||220||RIKEN Center for Integrative Medical Sciences|
|To investigate genomic alterations of Japanese esophageal squamous cell carcinomas||Esophageal squamous cell carcinoma (non-tumor tissue)||20||RIKEN Center for Integrative Medical Sciences|
|Construction of Japanese Whole-Genome database||General residents||4,495||Tohoku Medical Megabank Organization|
Note: Those datasets above provide fastq/bam file formatted data. The result data will be shown in our database soon. The sample size of each dataset indicates the sample number after quality control in this current study.