• Top
  • Research
  • Integrative Genomics
  • Integrative Genomics

    Research Activities

    With the aim of advancing personalized medicine and personalized prevention, we conduct genome analyses of biological specimens provided by cohort studies using next-generation sequencer. We also conduct omics analyses of protein and low-molecular metabolites using NMR, mass spectrometer, among other instruments. This data is processed using a super computer and other technologies.
    In parallel with these analyses, we are developing technologies for analyzing biological specimens, as well as software and information analysis methodologies for processing large quantities of data, including genome data.
    One of our goals is to create a benchmark genome reference panel of Japanese people through whole-genome analyses of more than 2,000 people.
    We have furthermore developed a tool for analyzing the genomes of Japanese people, which have allowed the analysis of quasi-whole-genome sequences of Japanese people (Japonica Array).

    Key Word: Massive parallel sequencing, Population genetics, Proteomics, Metabolomics, Bioinformatics, High performance computing


    Department of Integrative Genomics
    Group of Disease Risk Prediction
    Group of Supercomputer System Administration
    Group of Integrated Database Systems
    Group of Genome Sequence Analysis
    Group of in silico analysis
    Group of Omics Analysis
    Group of Early Prediction by Bioinformatics for Pregnancy Related Disorders


    • The structural origin of metabolic quantitative diversity
    • iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing
    • Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals

    More Publications related to Integrative Genomics in ToMMo. (mendeley)

    Data Sharing

    integrative Japanese Genome Variation Database(iJGVD)
    Tohoku University Tohoku Medical Megabank Organization (ToMMo) publicly made available the data from its whole genome sequencing for 2,049 people, namely, data on single nucleotide polymorphism (SNP) frequencies. Our platform offers capabilities to perform SNP searches from the reference SNP ID number and Gene Symbol and to identify location information on the international human genome reference sequence.

    integrative Japanese Genome Variation Database

    Batch data download is available on NBDC Human Database by National Bioscience Database Center (NBDC). (Data ID:hum0015.v1).

    Japanese Reference Genome(JRG)
    ToMMo has constructed the Japanese reference genome v1 (JRGv1) with a long-read-type next generation sequencer, PacBio RSII (Pacific Biosciences), and the data is now available online.
    We repeatedly sequenced Japanese genomic DNA to obtain sequence information of 300-billion bases (as much as 100 times repeated sequencing of a genome). Then, we have applied a method of information science called de novo assembly, assembling the sequences from scratch with high accuracy. And finally we succeeded construction include 903 new insertion sequences (approximately a million bases in total) to the international human reference genome sequence GRCh38, and release of the present Japanese Reference Genome.
    Some sequences determined by long-read-type sequencer were not easily fit to the specific sites on GRCh38. We have collected such those sequences and released as decoyJRGv1. Now those were also be opened on the net.
    Japanese Reference Genome

    Japanese Multi Omics Reference Panel (jMorp)
    A database of metabolome and proteome data in plasma in ToMMo, is available online. Metabolome data were measured by proton NMR and LC-MS, and proteome data were obtained by nanoLC-MS. Metabolome data obtained from more than 1,000 adult people, and proteome data obtained from more than 500 adult people. We measured several thousand metabolites including the uncharacterized ones, and several hundred proteins until now. The data will be released after carefully checking each metabolite and protein in order. We also released correlation among metabolites and observed peptides of 256 abundant proteins.

    Japanese Multi Omics Reference Panel (jMorp)


    We use the next-generation genome sequencer to analyze the whole genome sequences of the part of cohort participants.


    -3/11, Disaster Medicine, & ToMMo: Perspectives from the Executive Director (Interview with Dr. Yamamoto, November 10th, 2015)

    Press Releases

    -Genetic Diversity of Enzymes Alters Metabolic Individuality (Sep. 2, 2016)
    -Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals (Aug. 21, 2015)
    -Japonica Array: Improved genotype imputation by designing a population-specific SNP array with 1,070 Japanese individuals (June 24, 2015)
    -Partial release of data from Tohoku Medical Megabank Project's Whole Genome Reference Panel (Sep. 5, 2014)
    -Tohoku Medical Megabank Organization high-accuracy whole genome sequencing of 1,000 healthy Japanese people: A base to search for the causes of diseases-Collection of over 15 million new gene polymorphisms- (Nov. 29, 2013)


    -We enlarged Japanese Multi Omics Reference Panel "jMorp", 1,008 people Metabolome data are now online (Sep. 12, 2016)
    -Announcing release of JRG v1 (Aug. 25, 2016)
    -Release of locations and allele frequencies of all SNVs in whole genome sequences of 2,049 Japanese individuals
     (June 6, 2016)
    -Access for the locations and allele frequencies of all SNVs in the Whole Genome Reference Panel (Dec. 10, 2015)