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  • Facilities and Equipment

    The building for the Tohoku Medical Megabank was designed for Tohoku Medical Megabank Project and the construction of that completed in 2014. It is located on the southwest corner of the Seiryo campus. The building has seismically isolated structure and some characteristics specialized for the project. Around 300 people are working in this building for establishing the genome medicine.

    Floor 7 stories (partly 5 stories)
    Structure Precast concrete structure (base isolation system), joint complex with
    the "School of Medicine, Building No.6".
    Building area 3425.62m2
    Total floor area 18017.67m2
    Major facilities Biobank (biospecimen storage), MRI, NMR, sequence analyzing system,
    supercomputer system, Sendai Community Support Center.

    megabankoffince

     

    Sendai Community Support Center

    Sendai Community Support Center was established as an assessment center for Community Based Cohort Study and the Birth and Three-Generation Cohort Study performed by Tohoku Medical Megabank Organization. We attempt to make the basis for next-generation medicine by analyzing the genome information and make storage for these big data. Participants are explained individually by Genome Medical Research Coordinator (GMRC), and are made informed consent to join our project. In the center, there are more than ten equipment for medical examinations such as body composition analysis, bone density, respiratory function examinations and oral health check up. We also have MRI facilities and rooms for related cognitive tests and equipped the counseling rooms for mental healthcare and genetic counseling.

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    communitysupportcenter_02  communitysupportcenter_03

    Community Support Center
    • center_locationKesennuma Community Support Center
    • Osaki Community Support Center
    • Ishinomaki Community Support Center
    • Tagajo Community Support Center
    • Iwanuma Community Support Center
    • Shiroishi Community Support Center
    • *All support centers are located in Miyagi Prefecture

     

     

     

     

    Medical Examinations Equipment

    1, Booth for informed consent
    2, Central aortic blood pressure
    3, Blood test
    4, Body composition
    5, Grip strength and leg extension strength
    6, Bone mineral density
    7, Hearing test
    8, Oral health test
    9, Carotid ultrasound imaging
    10, Respiratory function tests
    11, Ophthalmic examination
    12, Questionnaire by touch screen
    13, MRI
    Two dedicated 3.0 Tesla high-resolution MRI scanners have been installed in the Tohoku Medical Megabank Building. These scanners will allow us to collect data from several thousand subjects every year. We will assess brain gray and white matter volumes, white matter integrities, white matter lesions, brain perfusions, and brain vessel structures through several scanning protocols. We also evaluate participants’ femoral muscle volumes. We are investigating how daily habits or genetic factors influence the brain, its cognitive functions, and psychological conditions in order to maintain a healthy brain and good cognitive functions for life.

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    Related Link

    Group of Community Support Center Operations

     

    Supercomputer System

    The supercomputer system is constructed to serve as the basis of the genome cohort and biobanking project for 150,000 people. In addition to being a databank that stores various kinds of data, it should also be a basis for conducting various analyses such as the large-scale genome analyses to support next-generation medical treatment. The system has 16,000-core CPU with a massively parallel hard disk of 19.4 petabytes that can carry out high-speed data analysis, and is equipped with the latest tape drive that is capable of storing data as a long-term storage. The system comprises the largest scale in Japan in the field of medical science. The system stores various kinds of data after deidentification, including genome and omics data, as well as the survey information collected from the cohort studies and physiological examination data, thereby ensuring a high level of security. At the same time, it is designed to efficiently conduct the necessary analyses for achieving personalized prevention and medical treatment.

    supercomputa_01-300x200 supercomputa_02

    Equipment Configuration
    Compute Node Shared Memory Type Computer High Performance Storage
    Total nodes: 800
    Total core: 16,000
    Total memory: 108 TB
    Total nodes: 8
    Total core: 480
    Total memory: 16 TB
    19.4 PB
    (Extensible to 50 PB)

    supercomputa_03 supercomput_04 supercomputer_05

    Related Link

    Group of Supercomputer System Administration

     

    Biobank (Biospecimen Storage)

    Our biobank has one of the largest storage facilities in Japan, which can host millions of biological samples. Live cells are preserved in -180°C vapor phase liquid nitrogen in 22 gigantic containers, some of which utilize automatic rotators. Automated sample storage systems harbor DNA samples at 4°C, urine and blood component samples at -80°C and work with the laboratory information management system. Temperature fluctuation during input/output operations is less than 1°C due to minimal opening areas and high-speed picking systems. In this way, our biobank facility maintains stable sample management and quality control for an extended period of time.

    biobank_01  biobank_02

    Equipment Configuration
    Automated sample storage
    Model Temperature/Quantity/Purpose of Use Capacity Feature
    Brooks Biostore II -80°C / 2 /
    Storage of plasma, urine
    Around 4.6million sample tubes in total Fully automated loading and unloading system.
    Small aperture to prevent the temperature change.
    Brooks SampleStore II 4°C / 1 / Storage of DNA

     

    Cryopreservation container
    Model Quantity Capacity Feature
    Taiyo Nippon Sanso
    DR-1000AT (G)-16
     16 Around 1.3 million sample
    tubes in total
    Automatic filling device of liquid nitrogen.
    Sample storage under homogenized gas phase below -180°C.
    Chart MVE
    1894R-190AF-GB
     6
    Related Link

    Group of Biobank

     

    Genome Seuquence Analysis

    ToMMo sequencing facility has six different types of next-generation sequencers (22 machines in total). Its annual output can be more than 3,000-4,800 high-grade whole human genome sequences (90 gigabases/person). To perform such high throughput sequencing without any sample mix-ups, we set up highly-automated experimental pipelines for sample preparations. We also have a variety of analytical platforms for numerous types of human genomic diversities, such as single-nucleotide variants and copy number variations. In order to sequence a whole human genome with the best quality possible, 30 times the amount of data (90 billion letters) must be collected for analysis. These massive amounts of data are protected by a highly-secure information network and analyzed with our supercomputer system.

    seuquence_01  seuquence_02

    Equipment Configuration
     
    Model Quantity Purpose of Use
    Hiseq2500
    (Illumina)
     12 Constructing the genome reference panel.
    Miseq
    (Illumina)
    2 Quality control of the genome reference panel and gene analysis
    (including metagenomics).
    NextSeq500
    (Illumina)
    1 Gene analysis.
    Ion Proton
    (Thermo Fisher)
    5 Exome analysis of cancer cells.
    Ion PGM
    (Thermo Fisher)
    1 Targeted analysis of multiple sites.
    PacBio RS II
    (Pacific Biosciences)
    1 Constructing the reference genome.
    Related Link

    Group of Genome Sequence Analysis

     

    Omics Analysis

    The cutting-edge omics analysis facility is able to analyze and quantify, to a high degree of precision, the various metabolites and proteins that are contained in the blood and urine samples stored in the biobank facility. Three high-field and high-sensitive nuclear magnetic resonance (NMR) spectroscopy system (800MHz and 600MHz) and 14 units of various types of mass spectrometry system (LC-MS, GC-MS, etc.) have been installed for supporting wide variety of analysis. Each system has an auto-sampler, making it possible to analyze several thousands of samples per year. The obtained data are stored in the supercomputer system. Our study provides the standard omics information (types and quantity of metabolites and proteins) of the Japanese people, which is useful for a wide range of medical treatment and research.

    omics_01  omics_02

    Equipment Configuration
    Nuclear magnetic resonance (NMR) spectroscopy system
    Model Resonant frequency Purpose of Use Equipment
    Bruker 800 NMR 800MHz Targeted metabolome analysis. High Sensitivity Cryogenic Probe
    Bruker 600 NMR 600MHz Comprehensive metabolome analysis. Auto-Sample Changer
    Mass spectrometry system
    Model Quantity Purpose of Use Equipment
    Synapt G2-Si
    QExactive
    Orbitrap Fusion
    Orbitrap Elite
    5 Comprehensive metabolome analysis. Ultra-High Pressure
    Liquid Chromatograph,
    HPLC, Nanos-LC
    Xevo TQ-S
    TSQ Quantum Ultra
    TSQ Quantiva
    TQ8040
    7 Targeted metabolome analysis. Ultrahigh-speed Liquid Chromatograph, HPLC,
    Gas Chromatograph
    TT5600 2 Targeted and comprehensive proteome analysis. Nano-LC
    Related Link

    Group of Omics Analysis