NBDC Research ID: hum0184.v1

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SUMMARY

Aims: Tohoku University Tohoku Medical Megabank Organization (ToMMo) and Iwate Tohoku Medical Megabank Organization (IMM) were founded to establish an advanced medical system to foster the reconstruction from the Great East Japan Earthquake. These organizations are developing a biobank that includes medical and genome information for supporting health and welfare in the Tohoku area. In the first stage, the part of our mission was to sequence the 4,000 individuals to construct Japanese whole-genome reference panel.

Methods: Whole genome sequencing

Participants/Materials: 4,566 Japanese general residents

URL: https://jmorp.megabank.tohoku.ac.jp/

 

Data Set IDType of DataCriteriaRelease Date
JGAS000239 NGS (WGS) Controlled Access (Type II) 2020/09/01

*Release Note

* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data.

 

MOLECULAR DATA

JGAS000239

Participants/Materials: 4,566 Japanese general residents
Targets WGS
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500, NovaSeq 6000]
Library Source DNA extracted from peripheral blood cells
Cell Lines -
Library Construction (kit name) TruSeq DNA PCR-Free Library Prep Kit
Fragmentation Methods Ultrasonic fragmentation (Covaris LE220)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)

HiSeq 2500: 162 bp / 259 bp

NovaSeq 6000: 150 bp

Japanese Genotype-phenotype Archive Data set ID

JGAD000338

JGAD000339

Total Data Volume

JGAD000338: 260 TB (fastq)

JGAD000339: 230 TB (bam, gvcf, vcf [ref: GRCh37/hg19 (hs37d5)])

Comments (Policies)

NBDC policy & hum0184 policy

Contact Information of ToMMo Supercomputer:

 

DATA PROVIDER

Principal Investigator: Masayuki Yamamoto

Affiliation: Tohoku Medical Megabank Organization

Project / Group Name: Tohoku Medical Megabank Project

URL: https://www.megabank.tohoku.ac.jp/english/

Funds / Grants (Research Project Number):

NameTitleProject Number
Japan Agency for Medical Research and Development (AMED) Tohoku Medical Megabank Project (Tohoku University) Special Account of the Great East Japan Earthquake Disaster Recovery JP20km0105001
Japan Agency for Medical Research and Development (AMED) Tohoku Medical Megabank Project (Tohoku University) General Accounting JP20km0105002
Japan Agency for Medical Research and Development (AMED) Tohoku Medical Megabank Project (Iwate Medical University) Special Account of the Great East Japan Earthquake Disaster Recovery JP20km0105003
Japan Agency for Medical Research and Development (AMED) Tohoku Medical Megabank Project (Iwate Medical University) General Accounting JP20km0105004

 

PUBLICATIONS

TitleDOIData Set ID
1 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome doi: 10.1038/s41439-019-0059-5 hum0015.v3.3.5kjpnv2.v1
2

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use