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  • Facilities and Equipment

    The building for the Tohoku Medical Megabank Organization 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 18,017.67m2
    Major facilities Biobank (Biospecimen Storage), MRI, NMR, Genome Analyzing System,
    Supercomputer System, Sendai Community Support Center


    Sendai Community Support Center

    For cohort studies, we have established seven Community Support Centers in Miyagi Prefecture (Kesennuma, Osaki, lshinomaki, Tagajo, Sendai, lwanuma, and Shiraishi). The centers are equipped to handle various types of surveys after confirming consent from each individual by a Genome Medical Research Coordinator (GMRC). In Sendai, a dedicated facility for conduct­ing health surveys with particularly for children, called Sendai Child Health Square, was opened in June 2017. Also MRI equip­ment has also been installed in Sendai, and MRI imaging is provided to cohort participants who have been taking health surveys in the centers and wish to do so.


    Community Support Center

    *All support centers are located in Miyagi Prefecture
    *The satellite offices (assessment center same as our support center) in Iwate Prefecture are organized by Iwate Medical University Iwate Tohoku Medical Megabank Organization (IMM) 

    Health Survey Detail

    Informed consent, blood test, body composition, grip strength test, bone density measurement, hearing test, oral health check-up, carotid ultrasound imaging, respiratory function test, ophthalmic examination, questionnaire by touch screen, electro-cardiogram, MRI, cognitive assessment.



    Two dedicated 3.0 Tesla high-resolution MRI scanners have been installed in the building for the Tohoku Medical Megabank Organization. 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 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. Based on these studies, we are considering health damage such as PTSD after the disaster.


    Sendai Child Health Square

    The Sendai Child Health Square was established in June 2017 as a facility for conducting child health surveys to monitor the development of children. The facility is equipped to primarily survey the health of children aged 5, 10, and 16 years, who are already enrolled as participants in TMM BirThree Cohort Study, while also providing an enjoyable atmosphere for the participating children. The major equipment used for the surveys is similar to that in the Sendai Community Support Center. It is also furnished with special equipment related to child development, such as the Gazefinder (a social development evaluation system).



    Supercomputer System

    The supercomputer system is the data infrastructure for storing various data generated from a 150,000 people genome cohort, as well as the analysis infrastructure supporting large-scale genomic and omics analysis. As a data infrastructure, the system is equipped with a massively parallel hard disk drive that enables high-speed data analysis and storage consisting of tape libraries/object storage/optical disk libraries that can store data for a long period of time, making it the largest system in the life science field in Japan. As an analysis platform, the system is equipped with a large number of CPUs to perform large-scale genomic and omics analysis, which is essential for the construction of next-generation medicine, and enables high-speed data analysis. The system is designed to efficiently perform the analysis necessary to realize personalized healthcare while ensuring a high level of security for the diverse data from the complex biobank.

    supercomputa_01-300x200  supercomputa_02

    Equipment Configuration
      Compute Node(CPU) Shared Memory GPU Analysis Nodes Login Node Database Server
    Total nodes 130 3 3 8 6
    Total CPU cores 14,880 384 384 1,024 768
    Total memory size (TB) 60 12 1.5 8 3
    Total GPU - - 24 - -
    High Performance Storage Archive Storage
    55PB 10.5PB
    Common Terminal Room

    The common terminal room is equipped with several terminals that can be connected to the supercomputer system in a secure room with biometric authentication facilities. These are also dozens of remote security areas with similar function and access to the ToMMo supercomputer in Sendai from remote locations throughout Japan and the integrated database dbTMM can be used and analysis and calculations can be performed using the supercomputer.


    Biobank (Biospecimen Storage)

    The TMM biobank is one of the largest population-based biobanks in Japan that stores millions of biological specimens in state-of-the-art storage systems. Automated sample storage system can hold 4.5 million tubes which contain blood components, urine, breast milk and DNA at either -80℃ or 4℃. The system handles the specimens autonomously, minimizing the frequency of human errors and sample damage. The liquid nitrogen storage system can hold 1.3 million tubes in the vapor phase of liquid nitrogen below -180℃.
    The tubes contain peripheral and cord blood mononuclear cells, along with their derivatives. The specimen-associated information is managed by the Laboratory Information Management System (LIMS).

    biobank_01  biobank_02

    Equipment Configuration
    Automated sample storage
    Model Temperature/Purpose of Use Capacity Feature
    Brooks Biostore II -80°C /Storage of plasma, serum, buffy coat, urine, breast milk Around 5.9 million sample tubes in total Fully automated loading and unloading system.
    Small aperture to prevent the temperature change.
    Brooks SampleStore II 4°C / Storage of DNA


    Liquid nitrogen storage system
    Model Capacity Feature
    Taiyo Nippon Sanso
    DR-1000AT (G)-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
    Related Link

    Specimen and Data Collection

    Sample Processing in TMM Biobank (movie)


    Genome Sequence Analysis

    ToMMo sequencing facility has different types of next-generation sequencers. It has an annual output capacity of more than tens of thousands of high-grade whole human genome sequences. To perform such high throughput sequencing without any sample mix-ups, highly automated experimental pipelines for sample preparations. Using not only short-read sequencers but also long-read sequencers, various types of diversities with the human genome, such as single nucleotide variants and structural variants, are analyzed. In order to sequence a whole human genome with the best quality possible, 20 to 100 times the amount of data (up to 300 billion bases) must be collected for analysis. These massive amounts of data are protected by a highly secure information network and analyzed with our supercomputer system.

    Equipment Configuration
    Model Feature / Use
    NovaSeq 6000
    Max output:3,000 Gb / flow cell
    Max paired end reads:10 billion reads/run
    Max read length:150 bp×2 (with S4 flowcell)
    The whole genome sequence of 60 individuals can be analyzed at a time.
    HiSeq 2500
    Max output:90 Gb / flow cell (Rapid Run Mode)
    Max paired end reads:300 million reads/run (Rapid Run Mode)
    Max read length:150 bp×2 (Rapid Run Mode)
    Installed when our project started in 2012, and is currently only used for small-scale analysis.
    Max output:15 Gb / flow cell
    Max paired end reads:2.5 million reads/run
    Max read length:300 bp×2
    Used for metagenome analysis of microbiome and the quality control of sequencing libraries.
    PromethION 24
    (Oxford Nanopore Technology)
    Output:~75 Gb /flow cell* (depending on the protocol)
    Read length:~25,000 bp* (depending on the quality of samples)
    Categorized into long-read sequencers, and thus used for the structural variation detection.
    * Under the protocol used for the construction of JSV1:Japanese Structural Variation.


    Omics Analysis

    The cutting-edge facility for omics analysis allows the analysis and quantification, to a high degree of precision, of the various metabolites and proteins that are contained within 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 various types of mass spectrometry system (LC-MS, GC-MS, etc.) have been installed to enable a wide variety of analysis to take place. Each system has an auto-sampler, allowing analyze several thousands of samples to be analyzed per year. The obtained data are then stored in the supercomputer system. Our study provides the standard omics information (types and quantity of metabolites and proteins) of 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 (Waters), QExactive (Thermo Fisher Scientific)  3 Comprehensive metabolome analysis. Ultrahigh-speed Liquid Chromatograph
    Xevo TQ-S (Waters), Xevo TQ-XS (Waters), 
    TQ8040 (Shimadzu)
    5 Targeted metabolome analysis. Ultrahigh-speed Liquid Chromatograph, Gas Chromatograph
    Orbitrap Fusion (Thermo Fisher Scientific) 1 Comprehensive metabolome analysis.
    Targeted and comprehensive proteome analysis.
    Ultrahigh-speed Liquid Chromatograph, Nano-LC


    Array Analysis

    SNP genotyping using microarray techniques are performed in the facility designated for array analyses. Several types of microarray systems are used according to the purpose of each project Each system is equipped with a Laboratory Information Management System (LIMS) to record samples and reagents information, conditions of dispensing robots, and information regarding to process control. The microarray data are then sent to our supercomputer system where quality checks and genotype imputation are performed.


    Equipment Configuration
    Model Quantity  Feature
    GeneTitanTM: Fully-automated hybridization and scanner system (Thermo Fisher Scientific) 2 Equipment for analyzing fully-customized arrays loaded with approximately 700,000 SNPs (Japonica Array®). With the standard specifications, 1 machine can obtain data from 384 specimens per week.
    iSCAN scanner system (Illumina) 2 Equipment for analyzing BeadChip microarrays. Used to obtain data from Omni2.5 arrays, which are loaded with approximately 2.5 million SNPs.


    Clinical Biobank

    As one of the facilities of INGEM, the clinical biobank operates along with the Tohoku University Hospital Personalized Medicine Center to collect precious biological specimens through medical care from the Tohoku University Hospital. Not only does it store liquid samples such as blood components, but also various types of other samples, including tissue specimens from surgery. All the biological specimens are anonymized and preserved at appropriate temperatures for future research.


    Equipment Configuration
    Equipment Quantity Operating Temperature Capacity
    Ultra-low temperature freezer 10 -80 °C Liquid samples: over 300,000 sample tubes (1 cc)
    Tissue samples: over 40,000 sample cases


    Cryo-electron Microscopy

    Cryo-electron microscopy (CRYO ARMTM 300 II, JEOL Ltd.) installed in the Tohoku Medical Megabank building is a device that enables structural analysis of various biological macromolecules with the world's highest resolution. In addition, a super­computer enables processing of large-scale measurement data. We will actively accept the use of this instrument not only within the university, but also from external companies and research institutions. It is expected to elucidate the mechanism of disease onset and realize drug discovery based on structural information.


    About INGEM

    In 2017, Tohoku University was selected as the first three Designated National Universities in Japan. The conferment of the Designated National University title is a recognition of the university's abilities to lead and shape global education and research. As a world-class research center and a leader of creativity and innovation. we have established a hub for next-generation medicine and founded INGEM as the organization that will play a central role within this hub.
    In cooperation with ten departments within Tohoku University. We have created a structure that brings together our collective capabilities

    Related Link

    the Advanced Research Center for Innovations in Next-GEneration Medicine (INGEM)