NBDC Research ID: hum0232.v1
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.
|Data Set ID||Type of Data||Criteria||Release Date|
|JGAS000231||NGS (Target Capture)||Controlled Access (Type I)||2020/06/01|
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data.
Gastric cancer (ICD10: C169): 10 cases
primary tumor tissue: 30 samples
PBMC: 10 samples
|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|
|Library Construction (kit name)||ClearSeq SS Comprehensive Cancer kits|
|Fragmentation Methods||Ultrasonic fragmentation (Covaris)|
|Read Length (without Barcodes, Adaptors, Primers, and Linkers)||100 bp|
|Japanese Genotype-phenotype Archive Data set ID||JGAD000325|
|Total Data Volume||64 GB (fastq, bam [ref: GRCh37])|
|Comments (Policies)||NBDC policy|
Principal Investigator: Satsoshi Nishizuka
Affiliation: Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences
Project / Group Name: -
Funds / Grants (Research 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|
|Title||DOI||Data Set 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|
USRES (Controlled-Access Data)
|Principal Investigator:||Affiliation:||Data in Use (Data Set ID)||Period of Data Use|