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 November 1, 2018)

Biological Specimens	Tubes
DNA	234,600	> Storage Condition
Plasma	860,200	> Storage Condition
Serum	858,400	> Storage Condition
Buffy Coat Cells	319,200	for DNA Extraction
Peripheral Blood Mononuclear Cells	345,300	> 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	601,900	> Storage Condition
Breast Milk	70,300	-
Saliva	4,600	-

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
(Baseline Assessment and Repeat Assessment)

Questionnaire	the Number of Person Asked to Answer or Do Exam
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 person on August 17, 2017)

Brain Gray and White Matter Volume, White Matter Integrity, White Matter Lesion, Brain Perfusion, Brain Vessel Structure, and Femoral Muscle Volume

5,499

 

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 3,500 whole genome sequencing and construct genome reference panel for the Japanese population (3.5KJPNv2). 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).

 

・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).

 

・JG1

・JRG (v1,v2)

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 10,000 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.

 

*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.