About

About Projects

Tohoku University Tohoku Medical Megabank Organization (ToMMo) was founded to establish an advanced medical system to foster the reconstruction from the Great East Japan Earthquake. The organization is developing a biobank that includes medical and genome information for supporting health and welfare in the Tohoku area.

(More details: http://www.megabank.tohoku.ac.jp/english/)

Objective

Integrative Japanese Genome Variation (iJGVD) provides data of genomic variations obtained by whole-genome sequencing of Japanese individuals, who participate in the genome cohort study by ToMMo. This database contains data of single nucleotide variations (SNVs) and their frequencies among the 1,070 Japanese individuals from the cohort.  The genome browser provides an intuitive view of SNV information along with the reference human genome sequence using hg19/GRCh37 coodinate system. SNVs and their information, such as allele frequency, can be retrieved with this browser.

 

Data release

  • The latest release (June. 15, 2016) contains data of nearly 28,000,000 autosomal SNVs detected by whole-genome sequencing of 2,049 Japanese individuals (2KJPN). This data set is available from DOWNLOAD page. The previous release of 1KJPN is also available.
  • The first release (Aug. 29, 2014) contains data of about 4,300,000 SNVs on autosomes. These SNVs exist at minor allele frequency of more than or equal to 5.0 % among the 1,070 individuals, and they are reported SNVs in dbSNP138.

 

Publications

  1. Nagasaki et al. (2015) “Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals” Nature Communications Volume:6, Article number: 8018 DOI:doi:10.1038/ncomms9018
  2. Yamaguchi-Kabata et al. (2015) “iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing” Human Genome Variation 2, Article number: 15050 (2015) doi:10.1038/hgv.2015.50

 

Download

  1. Frequency data of autosomal and common (>5%) SNVs (about 4,300,000): The whole table of SNV frequency data in iJGVD is available from NBDC website (hum0015).
  2. Frequency data of all autosomal SNVs (about 21,221,200) in 1KJPN: This data is available from DOWNLOAD page under agreement with “Rules of Use”. Users are required to enter name, organization, e-mail address, etc. The contact e-mail address is qsnATisDOTmegabankDOTtohokuDOTacDOTjp (Please replace “AT” with “@” and “DOT” with “.”).