NBDC Research ID: hum0232.v1
SUMMARY
Aims: To evaluate a clinical validity of circulating tumor DNA (ctDNA) of tumor-unique mutations identified in gastric cancer tissues, as a personalized tumor marker.
Methods: Pre- and post-operational plasma, primary tumor tissues, and peripheral blood mononuclear cells (PBMCs) were collected from 10 enrolled gastric cancer patients. The primary tumor specimens were taken from three regions immediately after the operation, and the cellularity of all specimens was microscopically confirmed to be >30%. DNAs are extracted from 30 primary tumor specimens and 10 PBMCs, and target capture sequencing for 151 genes that have been implicated in a wide range of cancers was performed.
Participants/Materials: Gastric cancer patients with preoperative diagnosis of Stage IB or higher. An individual written consent was obtained from each participant.
URL: https://nishizukalab.org/en/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000231 | NGS (Target Capture) | Controlled-access (Type I) | 2020/06/01 |
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MOLECULAR DATA
| Participants/Materials |
Gastric cancer (ICD10: C169): 10 cases primary tumor tissue: 30 samples PBMC: 10 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods |
Coding regions of the 151 disease-associated genes |
| Platform | Illumina [HiSeq 2000] |
| Library Source | DNAs extracted from primary tumor tissues and PBMC |
| Cell Lines | - |
| Library Construction (kit name) | ClearSeq SS Comprehensive Cancer kits |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000325 |
| Total Data Volume | 64 GB (fastq, bam [ref: GRCh37]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Satsoshi Nishizuka
Affiliation: Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences
Project / Group Name: -
URL： https://nishizukalab.org/en/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Establishment of selection process of molecular targeting drugs in response to biological heterogeneity in drug-resistant cancer cells | 16H01578 |
| KAKENHI Fund for the Promotion of Joint International Research (Fostering Joint International Research) | Identification of compounds that potentially lead to the cancer relapse suppression on the basis of drug-resistant cancer subpopulation model (original) | 15KK0317 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Circumvent practical issues for introducing ctDNA into daily practice | 19K09224 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Effect of immune response to Helicobacter pylori on adjuvant chemotherapy for gastric cancer | 19K09130 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Development of monitoring system for esophageal cancer by quantifying circulating tumor DNA | 17K10605 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Analysis of mutational and proteomic heterogeneity of gastric cancer suggests an effective pipeline to monitor post-treatment tumor burden using circulating tumor DNA | doi: 10.1371/journal.pone.0239966 | JGAD000325 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
