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  • Specimen & Data Collection
  • Specimen & Data Collection

    Tohoku Medical Megabank Project collects biological specimens such as blood and urine, from a hundred and fifty thousand 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. The information is stored in the data storage system, and at the same time, the biological specimens are preserved at appropriate temperatures and under suitable conditions. The results of analysis of the biological specimens are combined with the 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 ISO 27001 (Group of Biobank, but also Group of Integrated Database, and Group of Materials and Information Management).

    Biological Specimens
    (number of tubes on June 1, 2017)
    DNA 129,000 > Storage Condition
    Plasma 735,000 > Storage Condition
    Serum 723,000 > Storage Condition
    Buffy Coat Cells 369,000    for DNA extraction
    Peripheral Blood Mononuclear Cells 256,000 > Storage Condition
    Cord Blood Mononuclear Cells 74,000 > Storage Condition
    EBV-transformed B cells 5,000 > Storage Condition
    Stimulated T cells 8,000 > Storage Condition
    Urine 485,000 > Storage Condition
    Breast Milk 70,000  -
    Saliva 2,500  -
    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 & Life-Style Information, Health Data
    (number of person on February 25, 2016)
    Questionnaire  (Japanese-Cohort Standard)
    Age, Sex, Area, Job, Sleep, Exercise, Food, Alcohol, Smoking, History, Prescription, Gynecologic Problems, Mental Health Psychosocial Factors (Disaster-Related Problems)
    51,431
    Disaster-Related Questions (Damage, Life-Style Change)  13,323
    Physiological Exam
    Blood Pressure, Vascular, Respiratory, Ophthalmologic tests, Audibility test
    13,323

     

    MRI Exam (number of person on July 4, 2016)
    Brain Gray and White Matter Volume, White Matter Integrity, White Matter Lesion, Brain Perfusion, Brain Vessel Structure, Femoral Muscle Volume  3,039

     

    Integrative Japanese Genome Variation Database
    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.

    Please visit the website.
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    integrative Japanese Genome Variation Database

    Japanese Reference Genome(JRG)
    ToMMo has constructed the Japanese reference genome v2 (JRGv2) 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 9,600 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 decoyJRGv2. Now those were also be opened on the net.
    topix_JRG_LOGO
    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.

    Please visit the website.

    jMorp8

    *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.