GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel

Summary

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).

  • Version/last update: 2020/07/27
  • Sample size: 7,609
  • Number of variant loci: 90,280,248
SNVs INDELs
Total Novel Total Novel
Autosomes 76,768,387 35,660,425 10,202,908 4,152,671
X Chromosome 2,898,518 1,420,888 410,435 164,077

Note: Novel variants were not registered in dbSNP152.

Terms of use

Creative Commons License
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 Inteternational 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 number
In preparation GEM Japan Whole Genome Aggregation (GEM-J WGA) パネルの作成 [Controlled access] VCF 7,609

WGS datasets used for joint variant calling [Controlled access]

If you would like to use the datasets, apply for data use of them whose ID begins with "JGAD" and "AGDD" to the NBDC Human database and the AMED group sharing database, respectively.

Dataset ID
(NBDC research ID)
Study title Participants Sample size Data provider
Total 7,609
JGAD00000000220
(hum0014)
The Tailor-made Medical Treatment Program (BioBank Japan: BBJ) The cohort participants registered in the BBJ from 2003 to 2007 768 BioBank Japan
AGDD_00000000005
(agd0008)
バイオバンク・ジャパンの運営・管理と個別化医療の実現に向けた疾患バイオマーカー探索
(English page is under construction)
心筋梗塞、胃がん(非腫瘍組織)、認知症 2,089 BaioBank Japan
JGAD00000000117
(hum0103)
To investigate genomic alterations of Japanese biliary tract cancers Bilary tract cancer (non-tumor tissue) 17 RIKEN Center for Integrative Medical Sciences
JGAD00000000228
(hum0158)
To investigate genomic alterations of Japanese liver cancers Liver cancer (non-tumor tissue) 220 RIKEN Center for Integrative Medical Sciences
JGAD00000000233
(hum0160)
To investigate genomic alterations of Japanese esophageal squamous cell carcinomas Esophageal squamous cell carcinoma (non-tumor tissue) 20 RIKEN Center for Integrative Medical Sciences
JGAD00000000338
JGAD00000000339
(hum0184)
日本人全ゲノムデータベースの構築
(The web page is in preparation)
一般住民 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.