NBDC Research ID: hum0338.v1
SUMMARY
Aims: Comprehensive genome data for advanced gastric cancer have already been accumulated, widely published, and available including the Cancer Genome Atlas (TCGA) published in 2014 and the Asian Cancer Research Group (ACRG) in 2015. Aging and inflammation associated with H. pylori (HP) is an important risk factor for gastric cancer. HP shows evidence of infection in most gastric cancer patients. However, there are also a small number of juvenile and HP-negative gastric cancers, and the details of their genomic profile are unknown. This study narrows down to a patient population without factors such as aging and HP infection to elucidate the molecular abnormalities essential to new carcinogenesis and cancer progression, search for new therapeutic targets and to analyze the function of them to verify their biological significance in vitro and in vivo.
Methods: Whole Exome Sequencing Analysis
Participants/Materials: H. Pylori uninfected gastric cancer: 27 patients, H. Pylori infected gastric cancer: 36 patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000575 | NGS (Exome) | Controlled-access (Type I) | 2022/11/22 |
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MOLECULAR DATA
| Participants/Materials |
H. Pylori uninfected gastric cancer (ICD10: C169): 27 cases tumor tissue: 27 samples, non-tumor tissue: 27 samples H. Pylori infected gastric cancer (ICD10: C169): 36 cases tumor tissue: 36 samples, non-tumor tissue: 36 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V4 + lincRNA, SureSelect Human All Exon V5 + lincRNA |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris E220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000701 |
| Total Data Volume | 3 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Seiichi Mori
Affiliation: Cancer Precision Medicine Center, Japanese Foundation for Cancer Research
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Takeda Japan Medical Office Funded Research Grant | ||
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genomic features of Helicobacter pylori-naïve diffuse-type gastric cancer | doi: 10.1002/path.6000 | JGAD000701 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
