About Projects

Tohoku University Tohoku Medical Megabank Organization (ToMMo) and Iwate Tohoku Medical Megabank Organization (IMM) were founded to establish an advanced medical system to foster the reconstruction from the Great East Japan Earthquake. These organizations are developing a biobank that includes medical and genome information for supporting health and welfare in the Tohoku area. In the first stage, the part of our mission was to sequence the 4,000 individuals to construct Japanese whole-genome reference panel. In the second stage, the part of our mission is to increase the whole-genome sequencing as 8,000 individuals in order to nearly cover all SNVs with more than 0.01% allele frequency in Japanese population.

(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, IMM and other cohort projects in Japan. This initial database contained data of single nucleotide variations (SNVs) and their frequencies among the 1,070 Japanese individuals (1KJPN) from the ToMMo cohort. The genome browser provides an intuitive view of SNV information along with the reference human genome sequence using hg19/GRCh37 coordinate system.

In 15/Jun/2016, the total number was increased to 2,049 individuals (2KJPN) in ToMMo.

The latest release at 28/Oct/2017 is reached to 3,554 individuals (3.5KJPN) including IMM and other cohort participants to cover more diverse Japanese population. The details of participants are summarized in the following table.

Organization Location In total
Tohoku Medical Megabank Organization (ToMMo) Miyagi (Tohoku (North-East) area in Japan) 3,236
Iwate Medical Megabank Organization (IMM) Iwate (Tohoku (North-East) area in Japan) 108
The Nagahama Prospective Cohort for Comprehensive Human Bioscience (the Nagahama Study) Shiga (Kinki (Middle) area in Japan) 29
National Hospital Organization Nagasaki Medical Center Nagasaki (Kyuusyu (South-West) area in Japan) 181
Total 3,554

Genetic Background

Principle component analysis of EAST ASIA population and 1,070 ToMMo individuals.

Data release

  • The latest release (Sep. 28, 2017) contains allele frequency data of 37,067,715 reliable autosomal SNVs detected by whole-genome sequencing of 3,554 Japanese individuals (3.5KJPN). This data set is available from DOWNLOAD page. From the latest release 12,866,823 filtered out SNVs and 165,439 multi-allelic SNVs in 3.5KJPN while biallelic in 1KJPN or 2KJPN are also released as separate dataset, i.e. in total 49,934,538 SNVs.
  • SNV GUI search is avalable from this iJGVD website for 7,931,579 SNVs with more than or equal to 1% Japanese population allele frequency (including passed 5,914,593 SNVs, filtered out 1,978,287 SNVs and 38,699 multi-allelic SNVs).
  • The 2nd release (June. 15, 2016) contains allele frequency data of 27,997,593 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 allele frequency data of 4,301,546 SNVs on autosomes. These SNVs exist at minor allele frequency of more than or equal to 5.0 % among the 1,070 individuals, and most of them are reported SNVs in dbSNP138.

 

Search on Browser

You can explore the SNVs on 1KJPN / 2KJPN / 3.5KJPN from our iJGVD browser. The contents are summarized below. For more detail of the usage, please access to “how to use” page.

Panel Status Distributed allele frequency Data accessibility Total number of SNVs
1KJPN Passed 5% or more iJGVD browser 4,301,546
2KJPN Passed 5% or more 4,267,828
3.5KJPN Passed 1% or more 5,914,593
3.5KJPN Filtered 1% or more 1,978,287
3.5KJPN Multi-allelic 1% or more 38,699

 

Download

Full alelle frequency data of autosomal SNVs in 1KJPN, 2KJPN and 3.5KJPN can be downloaded as compressed text format after DTA.
These data are available from the below “Download” URL link 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 “.”). Tohoku Medical Megabank Organization, Tohoku University.

Panel release name Total individuals Distributed allele frequency Data accessibility Total number of SNVs
1KJPN 1,070 Passed SNVs of all frequency Download (need DTA) 21,221,195
2KJPN 2,049 Passed SNVs of all frequency Download (need DTA) 27,997,593
3.5KJPN 3,554 Passed, filtered and multi-allelic SNVs of all frequency Download (need DTA) 49,934,538
(37,067,715/
12,866,823)

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). Frequency data of autosomal and common (>=1%) SNVs of 3.5KJPN: The whole table of SNV frequency data in iJGVD will be available from NBDC website in future.

 

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

 

Acknowledgements

This work is mainly supported by grants from the Reconstruction Agency, from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), and from the Japan Agency for Medical Research and Development (AMED). All computational resources were provided by the ToMMo supercomputer system (https://sc.megabank.tohoku.ac.jp/en/). This research is (partially) supported by the Center of Innovation Program from Japan Science and Technology Agency, JST (http://www.jst.go.jp/EN/). We are indebted to all volunteers who participated in this Tohoku Medical Megabank project (TMM) and other corporated studies mentioned below. We thank members of TMM at the Tohoku University and the Iwate Medical University for seminal contribution to the establishment of the genome cohort and biobank and for help in the genome analyses. We also thank research collaborators in Japan for the construction of 3.5KJPN; the Nagahama Study and National Hospital Organization Nagasaki Medical Center.