NBDC Research ID: hum0226.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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000229 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2021/06/04 |
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MOLECULAR DATA
| Participants/Materials |
Stomach adenocarcinoma (ICD10: C16): 141 cases tumor tissues: 141 samples non-tumor tissues: 141 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 | JGAD000322 |
| Total Data Volume | 5 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Stomach adenocarcinoma (ICD10: C16): 103 cases tumor tissues: 103 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 | JGAD000323 |
| Total Data Volume | 5 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):
| Name | Title | Project 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
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Defined lifestyle and germline factors predispose Asian populations to gastric cancer | doi: 10.1126/sciadv.aav9778 | |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000323 | 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 | JGAD000322, JGAD000323 | 2023/03/18-2028/03/31 |
