NBDC Research ID: hum0227.v1

 

SUMMARY

Aims: Identification of lifestyle and germline mutations (genetic factors) that predispose to gastric cancer in an Asian population

Methods: Whole exome sequencing (NGS) and whole transcriptome seuquencing (NGS) analyses

Participants/Materials: Stomach adenocarcinoma patients

 

Dataset IDType of DataCriteriaRelease Date
JGAS000228 NGS (Exome, RNA-seq) Controlled-access (Type I) 2021/06/04

*Release Note

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

 

MOLECULAR DATA

Exome

Participants/Materials

Stomach adenocarcinoma (ICD10: C16): 102 cases

      tumor tissues: 102 samples

      non-tumor tissues: 102 samples

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source DNAs extracted from clinical specimens (tumor tissues and matched non-tumor tissues) of stomach adenocarcinoma
Cell Lines -
Library Construction (kit name) Agilent SureSelect Human All Exon Kit v4 and v5+ LincRNA
Fragmentation Methods Ultrasonic fragmentation (Covaris SS)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000320
Total Data Volume 3 TB (fastq)
Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

Stomach adenocarcinoma (ICD10: C16): 81 cases

      tumor tissues: 81 samples

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNAs extracted from clinical specimens (tumor tissues) of stomach adenocarcinoma
Cell Lines -
Library Construction (kit name) TruSeq Stranded mRNA Sample Prep Kit
Fragmentation Methods included in the above library construction kit
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000321
Total Data Volume 3 TB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Hiroyuki Aburatani

Affiliation: RCAST, the University of Tokyo

Project / Group Name: Genome Science laboratory

URL: https://www.genome.rcast.u-tokyo.ac.jp/en/research

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (S) Elucidation of the evolution of cancer cell populations by integrative genomic analysis 24221011
KAKENHI Grant-in-Aid for Scientific Research (A) Comprehensive understanding of interdependent signaling between cancer and the stroma 16H02481
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) Identification of the mechanism of development and progression of human epithelial tumors and the novel therapeutic targets JP19cm0106502
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) Elucidation of the diversity of gastric cancer genomics with a focus on humoral immunity and the exploration of intervention methods. JP19cm0106551
Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) Integrated analysis of large-scale Japanese cancer genomic, omics, and clinical data for international collaborative research and construction of a knowledge base for the promotion of genomic medicine JP20ck0106547

 

PUBLICATIONS

TitleDOIDataset ID
1 Defined lifestyle and germline factors predispose Asian populations to gastric cancer doi: 10.1126/sciadv.aav9778

JGAD000320

JGAD000321

JGAD000322

JGAD000323

2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Takashi Kohno Division of Genome Biology, National Cancer Center Research Institute Identification of genetic risk factors in AYA (Adolescence and Young Adult) cancer JGAD000320, JGAD000321 2021/11/29-2025/03/31
Michiaki Hamada Faculty of Science and Engineering, Waseda University Japan Construction of RNA-targeted Drug Discovery Database JGAD000321 2022/12/26-2025/03/31
Tetsuo Ushiku Department of Pathology, Graduate School of Medicine, The University of Tokyo Japan Genetic analysis of upper gastrointestinal tumors and their clinicopathological significance JGAD000320, JGAD000321 2023/03/18-2028/03/31