NBDC Research ID: hum0145.v1
SUMMARY
Aims: To identify the biomarkers of predicting metastasis and reccurence in colorectal cancer (CRC).
Methods: Genomic DNAs were extracted from several samples (as shown below) and performed a target capture deep sequencing analysis by using of the HaloPlex Cancer Research Panel.
1) Tumor tissues obtained from 3-5 locations in the primary tumor by endoscopic biopsy prior to neoadjuvant chemotherapy (NAC)
2) Tumor tissues and adjacent normal intestinal mucosa (non-tumor tissues) obtained from fresh-frozen surgically resected specimens after NAC and resecting metastais lesions, if patients were experienced recurrence
3) Blood samples obtained from patients at the time of surgery
Participants/Materials: Ten colorectal cancer patients with locally advanced primary tumors who underwent primary tumor resection following NAC
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000222 | NGS (Target Capture) | Controlled-access (Type I) | 2020/04/03 |
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MOLECULAR DATA
| Participants/Materials |
Colorectal cancer (ICD10: C189): 10 cases (36 samples) - Primary tumor tissues obtained by endoscopic biopsy prior to NAC: 10 cases (10 samples) - Tumor tissues from resected specimens after NAC: 10 cases (10 samples) - Non-tumor tissues from resected specimens after NAC: 10 cases (10 samples) - Blood plasma: 3 cases (4 samples) - Metastatic tumor tissues from resected specimens: 2 cases (2 samples) |
| Targets | Target Capture |
| Target Loci for Capture Methods | ClearSeq Halo HS Cancer Research Panel |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor and matched non-tumor tissues from CRCs |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect/HaloPlex Target Enrichment System |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000313 |
| Total Data Volume | 193 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Koshi Mimori
Affiliation: Department of Surgery, Kyushu University Beppu Hospital
Project / Group Name: -
URL: https://www.beppu.kyushu-u.ac.jp/gekareview/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| The Shinnihon Foundation of Advanced Medical Treatment Research (2017) | Construction of precision medicine about neoadjuvant chemotherapy for hepatic metastasis of colorectal cancer by using comprehensive gene aberration analysis and mathematical simulation. | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Serial mutational tracking in surgically resected locally advanced colorectal cancer with neoadjuvant chemotherapy. | doi: 10.1038/s41416-018-0208-5 | JGAD000313 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
