NBDC Research ID: hum0066.v1
SUMMARY
Aims: Investigating a genomic-level intratumor heterogeneity in colorectal carcinoma
Methods: DNA were extracted from multiregional tumor samples and performed a whole exome sequencing analysis
Participants/Materials: Samples which obtained during surgery from patients who underwent radical resection of primary and/or liver metastatic tumors
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000060 |
NGS (Exome) | Controlled-access (Type I) | 2016/08/01 |
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MOLECULAR DATA
| Participants/Materials | colorectal carcinoma: 9 cases (84 samples [tumor tissues: 71 samples, non-cancerous tissues: 9 samples, liver metastatic tumor tissues: 4 samples]） |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source | DNAs extracted from tumor, non-cancerous tissues or liver metastatic tumor tissues from colorectal carcinoma patients |
| Cell Lines | - |
| Library Construction (kit name) |
SureSelect Human All Exon Kit v4.0 (Agilent Technologies) 1 cases 9 samples (tumor tissues: 8 samples, non-cancerous tissues: 1 sample) SureSelect Human All Exon Kit v5.0 (Agilent Technologies) 8 cases 75 samples (tumor tissues: 63 samples, non-cancerous tissues: 8 samples, liver metastatic tumor tissues: 4 samples) |
| 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 | JGAD000060 |
| Total Data Volume | 1545 GB (1650 fastq files) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Koshi Mimori
Affiliation: Department of Surgery, Kyushu University Beppu Hospital
Project / Group Name:
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Funding Program for Next Generation World-Leading Researchers (NEXT Program) | Investigating mechanism of tumor recurrence and metastasis by non-coding RNA | LS094 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Systems Cancer Research | 4201 |
| Strategic Programs for Innovative Research (SPIRE) Field 1 | Supercomputational Life Science | SCLS Theme4 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution. | doi: 10.1371/journal.pgen.1005778 | JGAD000060 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Christina Curtis | Stanford Univ. | JGAD000060 | 2016/08/04-2018/08/01 | ||
| Kouya Shiraishi | Division of Genome Biology, National Cancer Research Institute | Elucidation of immune-system networks between host and tumor based on genomic analysis | JGAD000060 | 2019/08/05-2023/03/31 | |
| Ruping Sun | Department of laboratory medicine and pathology, University of Minnesota | Accounting for Copy Number States in Quantifying Tumor Heterogeneity | JGAD000060 | 2020/03/19-2022/08/01 |
