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  • Specimen and Data Collection
  • Specimen and Data Collection

    Tohoku Medical Megabank Project collects biological specimens such as blood and urine, from 150,000 healthy Japanese participants with informed consent in Miyagi and Iwate prefectures. We also collect data from physiological examinations, physical measurements, medical and lifestyle information from the questionnaires, and MRI data of a part of the participants who offered their information at our sub-branches, which are located in several community areas. These information is stored in the data storage system, and at the same time, biological specimens are preserved at appropriate temperatures and under suitable conditions. The results of analysis of the biological specimens are combined with information above to construct our integrated database. A part of the data is available to public through the websites as follows.

    The Biobank in Tohoku Medical Megabank Projects obtained certification of ISO 9001 Quality Management System (Group of Biobank) and ISO 27001 Information Security Management System (Group of Biobank, but also Group of Integrated Database, and Group of Materials and Information Management).

    Biological Specimens

    (Number of tubes on June 1, 2019)

    Biological Specimens Tubes  
    DNA 286,800 > Storage Condition
    Plasma 897,100 > Storage Condition
    Serum 901,300 > Storage Condition
    Buffy Coat Cells 327,900    for DNA Extraction
    Peripheral Blood Mononuclear Cells 375,500 > Storage Condition
    Cord Blood Mononuclear Cells 74,100 > Storage Condition
    EBV-Transformed B Cells 9,700 > Storage Condition
    Stimulated T Cells 12,500 > Storage Condition
    Urine 638,600 > Storage Condition
    Breast Milk 70,200  -
    Saliva 5,100  -
    Storage Condition
    DNA Isolation Autopure LS (QIAGEN), QIAsymphony (QIAGEN)
    Quantification Quant-iT PicoGreen dsDNA Assay Kit
    Quality check O.D. 260/280 ratio
    Solvent QIAGEN DNA Hydration Solution
    Storage tubes 1 mL Matrix 2D Barcoded Storage Tubes (Thermo Scientific)
    Storage temperature 4 °C
    Aliquots for distribution (size, concentration) 10-50 µL (50 ng/µL)
    Distribution format 96 well format deepwell storage plate
    Plasma / Serum Storage tubes 1 mL Matrix 2D Barcoded Storage Tubes (Thermo Scientific)
    Aliquots (size and number) 700 µL, 4 tubes
    Storage temperature -80 °C
    Peripheral Blood Mononuclear Cells Storage tubes 1 mL Matrix 2D Barcoded Storage Tubes (Thermo Scientific)
    Aliquots (size and number) 500 µL (from 2.5 mL of blood), 2-3 tubes
    Storage temperature Below -180 °C (liquid nitrogen, vapor phase)
    Cord Blood Mononuclear Cells Storage tubes 1 mL Matrix 2D Barcoded Storage Tubes (Thermo Scientific)
    Aliquots (size and number) 500µL (from 2.25mL of blood), 4 tubes
    Storage temperature Below -180 °C (liquid nitrogen, vapor phase)
    EBV-Transformed B Cells Storage tubes 1 mL Matrix 2D Barcoded Storage Tubes (Thermo Scientific)
    Aliquots (size and number) 700 µL, 3 tubes
    Storage temperature Below -180 °C (liquid nitrogen, vapor phase)
    Stimulated T Cells Storage tubes 1 mL Matrix 2D Barcoded Storage Tubes (Thermo Scientific)
    Aliquots (size and number) 700 µL, 3 tubes
    Storage temperature Below -180 °C (liquid nitrogen, vapor phase)
    Urine Storage tubes 1 mL Matrix 2D Barcoded Storage Tubes (Thermo Scientific)
    Aliquots (size and number) 700 µL, 3 tubes
    Storage temperature -80 °C

    *Customized LIMS (Laboratory Information Management System) based on LabVantage (LABVANTAGE Solutions) is used for specimen handling and inventory management. Specimens are aliquoted into Matrix 2D Barcoded Storage Tubes. Freedom EVO robotic dispensers (TECAN) are used to aliquot liquid specimens automatically.

    Medical and Life-Style Information, Health Data
    (Baseline Assessment and Repeat Assessment)
      Number of People
    Health and Life-style Questionnaire  (Japanese-Cohort Standard)
    Basic Information (Age, Sex, Area, Job), Lifestyle (Sleep, Exercise, Food, Alcohol, Smoking), Physical Health, Social Environments, Mental Health, and Psychosocial Factors (Disaster-Related Problems)
    Disaster-Related Questionnaire
    Damage by the Great East Japan Earthquake, and Lifestyle Change
    Diet Questionnaire
    Food
    c.a. 155,000
    Questionnaire by Touch Screen Device in Community Support Centers
    Damage by the Great East Japan Earthquake, Lifestyle (Exercise), Social Environments, Mental Health, Psychosocial Factor, and Oral Health Questions
    c.a. 33,000
    Physiological Exam in Community Support Centers
    Audibility Test, Blood Test, Body Composition, Blood Pressure, Bone Mineral Density, Cartoid Ultrasound Imaging, Electro-Cardiogram, Grid Strength, Ophthalmologic Tests, Oral Health Test, Vascular, and Respiratory
    c.a. 33,000

    * Baseline Assessment was doing during 2013 to 2017. Repeat Assessment is stated since June 2017.

    MRI Exam

    (Number of people on July 2019)

    MRI Images (3D T1-Weighted Imaging, MR Angiography etc)  ca. 11,000
    3D Imaging of Thighs - Muscle Volume ca. 4,000

     

    Japanese Multi Omics Reference Panel (jMorp)

    “jMorp” is a database consisted of genome, metabolome and proteome data in plasma. Multiple omics analysis data obtained by ToMMo is integrated to “jMorp”, and opened to the researchers online.

    Genome Variation

    We performed around 4,700 whole genome sequencing and construct genome reference panel for the Japanese population (4.7KJPN). Information on frequencies and locations of all found single-nucleotide variants (SNV) on the panel is available through the “jMorp”.
    You can search your interested SNVs on our platform by the reference SNP ID number (rsID), Gene Symbol and locate information on the international human genome reference sequence. All found SNVs frequencies in our reference panel are displayed and you can compare with gnomAD. All the frequencies and locate information are downloadable by a single file for each chromosome. In addition to enhancements of jMorp, it includes such as X chromosome data, mitochondria data, and implementation of the variant-structure mapping visualization tool.

    You can access the former versions of our genome reference panels, such as 1KJPN around 1,000 whole genome sequencing released as the first version of our panel in 2013, 2KJPN released in 2015, and 3.5KJPN released in 2017 on Integrative Japanese Genome Variation Database (iJGVD).

    2019 major update of Japanese Multi Omics Reference Panel "jMorp":15,000 people metabolome data and 4.7K Japanese individual genome variation [Press Release] (2019.09.13)

    ・After 3.5KJPNv2

    ・1KJPN, 2KJPN, and 3.5KJPN

    Achievement of Research product by Whole Genome Reference Panel: Japonica Array
    The “Japonica Array”, DNA microarray designed for genome analysis of Japanese population, is developed in 2014 by ToMMo, and it has been used for our genome analyses of tens of thousands of cohort participants. The array contains common SNPs in the Japanese population as well as disease-related SNPs. A whole genome sequence can be imputed very precisely with our genome reference panel.

     

    Genome Sequence

    ToMMo has released the Japanese reference genome, JG1, constructed by integrating three de novo assembled genomes of Japanese male individuals. The Japanese reference genome is available online.
    You can access the former versions of the Japanese reference genome v1 (JRGv1) released on 2016, or v2 (JRGv2) released on 2017 with a long-read-type next-generation sequencer, PacBio RSII (Pacific Biosciences).

    The Japanese reference genome, JG1, constructed by integrating three de novo assembled genomes of Japanese male individuals [Press Release] (2019/02/25)

    ・JG1

    ・JRG (v1,v2)
    topix_JRG_LOGO

    Metabolome and Proteome

    On “jMorp”, the results of global metabolome analysis for metabolites in serum and proteome analysis are available online. You can find the distribution and frequencies information for major metabolites for several thousand populations and proteins for several hundred populations.
    Metabolome data were measured by proton NMR and LC-MS, and proteome data were obtained by nanoLC-MS. Metabolome and proteome data obtained from more than 15,000 adults. We measured several thousand metabolites including the uncharacterized ones and several hundred proteins by now. The data will be released after carefully checking each metabolite and protein in order. We also released a correlation among metabolites and observed peptides of 256 abundant proteins.

    iMorp

     

    *Information collected in our biobank such as blood/urine test data, questionnaire information, biochemical test data, MRI data, genome sequences, omics data and medical/nursing data is stored in Integrated Database in the data bank section of the supercomputer after de-identification.