NBDC Research ID: hum0242.v1
SUMMARY
Aims: To evaluate clinical validity of circulating tumor DNA (ctDNA) of tumor-unique mutations identified from colorectal cancer tissues, as a personalized tumor marker.
Methods: Pre- and post-operational plasma, primary tumor, and peripheral blood mononuclear cells (PBMCs) were collected from 12 enrolled patients. Among these patients, two patients had two separate colorectal tumors. 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%. DNA was extracted from 42 primary tumor specimens and 12 PBMCs, and target sequencing using a HiSeq 2000 System (Illumina) conducted for 151 genes that have been implicated in a wide range of cancers was performed.
Participants/Materials: Colorectal cancer patients with preoperative diagnosis of Stage III or higher. Individual written consent was obtained from each participant.
URL: https://nishizukalab.org/en/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000243 | NGS (Target Capture) | Controlled-access (Type I) | 2021/01/05 |
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MOLECULAR DATA
| Participants/Materials |
Colorectal cancer (ICD10: C189): 12 cases primary tumor tissue: 42 samples PBMC: 12 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 | JGAD000343 |
| Total Data Volume | 119 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 |
| KAKENHI Grant-in-Aid for Young Scientists (B) | Development of longitudinal monitoring system for gastrointestinal cancer using circulating tumor DNA | 18K15326 |
| KAKENHI Grant-in-Aid for Young Scientists (B) | The new estimation method of recurrence and metastasis on circulating tumor DNA detection in colorectal cancer patients | 16K19951 |
| JSPS Fujita Memorial Fund for Medical Research | Impact of intratumor heterogeneity for ctDNA of colon cancer | - |
| Keiryoukai Research Grant | Development of precision medicine for esophageal cancer patients using circulating tumor mutational DNA | 136 |
| Iwate Prefectural Regional Innovation Grant | Development of high-sensitive individualized tumor markers for quantitative evaluation of advanced cancer | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
