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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 (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 August 17, 2017)
    Brain Gray and White Matter Volume, White Matter Integrity, White Matter Lesion, Brain Perfusion, Brain Vessel Structure, Femoral Muscle Volume 5,499

     

    Integrative Japanese Genome Variation Database
    The locations and frequencies of single nucleotide variations (SNVs), identified through the analysis of the whole genome sequencing data of 3,554 Japanese, are available from the Integrative Japanese Genome Variation Database. Regarding the SNVs whose allele frequencies are over 5%, you can search them by the reference SNP ID number and the official gene symbol on the browser. You can also download the allele frequency data set of the SNVs including singletons if you confirm and agree on our DATA transfer agreement.

    For more details, please visit the following website.
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    integrative Japanese Genome Variation Database

    Japanese Reference Genome(JRG)
    We have been constructing the Japanese reference genome (JRG) by using a single-molecule long-read sequencing platform, PacBio RSII (Pacific Biosciences). JRG version 2 (JRGv2) is now available through our web site. JRGv2 is constructed from whole-genome sequencing data of three Japanese samples, whereas JRGv1 was based on one sample. We obtained 300-billion base data per sample (means each position/base gets sequenced 100 times on average), applied a method of information science called de novo assembly, assembling the sequences from scratch with high accuracy, and found 9,600 new insertion sequences (approximately six million bases in total) to the international human reference genome sequence GRCh38. These insertions, which are not included in GRCh38, have been released in two formats, JRGv2 (incorporated into GRCh38) and decoyJRGv2.

    For more details, please visit the following website.

    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.