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
SNVsINDELs
TotalNovelTotalNovel
Autosomes76,768,38735,660,42510,202,9084,152,671
X Chromosome2,898,5181,420,888410,435164,077

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 International License.

How to credit in your works

"GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel" by GEnome Medical alliance Japan Project (GEM-J) is licensed under CC BY 4.0. See also additional terms of use.

How to cite in your publications

"GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel". Japan: GEnome Medical alliance Japan Project (GEM-J). Available from: https://togovar.biosciencedbc.jp/doc/datasets/gem_j_wga.

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 IDAGD IDStudy titleFile formatSample size
In preparationGEM Japan Whole Genome Aggregation (GEM-J WGA) パネルの作成VCF7,609

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 "AGDS" to the NBDC Human database and the AMED group sharing database, respectively.

Dataset ID
(NBDC research ID)
Study titleParticipantsSample sizeData provider
Total7,609
JGAD00000000220
(hum0014)
The Tailor-made Medical Treatment Program (BioBank Japan: BBJ)The cohort participants registered in the BBJ from 2003 to 2007768BioBank Japan
AGDS_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2,089BioBank Japan
JGAD00000000117
(hum0103)
To investigate genomic alterations of Japanese biliary tract cancersBiliary tract cancer (non-tumor tissue)17RIKEN Center for Integrative Medical Sciences
JGAD00000000228
(hum0158)
To investigate genomic alterations of Japanese liver cancersLiver cancer (non-tumor tissue)220RIKEN Center for Integrative Medical Sciences
JGAD00000000233
(hum0160)
To investigate genomic alterations of Japanese esophageal squamous cell carcinomasEsophageal squamous cell carcinoma (non-tumor tissue)20RIKEN Center for Integrative Medical Sciences
JGAD00000000338
JGAD00000000339
(hum0184)
Construction of Japanese Whole-Genome databaseGeneral residents4,495Tohoku 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.