NBDC Research ID: hum0543.v1
SUMMARY
Aims: Although colorectal cancer is one of the tumors with the best-understood carcinogenesis mechanisms, proposed as a multistage process where multiple cancer genes and tumor suppressor gene abnormalities accumulate in normal colonic mucosal epithelium, leading to progression through adenoma, mucosal carcinoma, and invasive carcinoma, the mechanisms by which large-scale genomic structural abnormalities, such as whole-genome duplication, contribute to carcinogenesis remain poorly understood. This study aims to estimate the occurrence of chromosomal structural abnormalities during the multistage carcinogenesis process. It seeks to elucidate the relationship between cancer heterogeneity and the evolution of cancer clones, as well as the association with tumor progression and metastasis.
Methods: whole genome sequencing
Participants/Materials: 62 patients with colorectal cancer
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000872 | NGS (WGS) | Controlled-access (Type I) | 2026/06/10 |
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MOLECULAR DATA
| Participants/Materials |
colorectal cancer (ICD10: C189): 62 cases tumor tissue: 62 samples non-tumor tissue (normal tissues): 62 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissue |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-Free HT Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001015 |
| Total Data Volume | 14.2 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shinichi Yachida
Affiliation: Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Integrated Analysis of Large-Scale Japanese Cancer Genomic, Multi-Omics, and Clinical Data to Advance Precision Prevention and Genomic Medicine through International Collaboration | JP25ck0106800 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Deciphering Gut Microenvironmental Dynamics Associated with Colorectal Carcinogenesis in High-Risk Individuals and Developing Personalized Strategies for Colorectal Cancer Prevention | JP22ck0106546 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Development of Personalized Colorectal Cancer Prevention Strategies Based on Integrated Characterization of the Gut Ecosystem Using Stool and Biopsy Specimens from Ultra-High-Risk Individuals | JP25ck0106799 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Establishment of a Nationwide Whole-Genome Medicine Platform and Development of Innovative Therapeutics for Refractory Gastrointestinal Cancers through Comprehensive Integration of Whole-Genome Sequencing and Clinical Data | JP25ck0106874 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Large-Scale International Collaborative Research Leveraging Integrated Cancer Genomic and Multi-Omics Analyses in Japanese Populations to Advance Innovative Prevention, Diagnosis, and Treatment | JP26ck0106162 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Development of Gut Microbiome-Based Predictive Biomarkers for Adverse Events Associated with Anticancer Therapies | JP21cm0106477 |
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Elucidating the Etiology of Early-Onset Colorectal Cancer through Integrated Analyses of Diet, Gut Microbiota, and Inflammation, and Developing Risk Assessment and Early Detection Strategies | JP25ama221430 |
| Research Program on the challenges of Global Health issues, Japan Agency for Medical Research and Development (AMED) | Disease-Oriented Research on Infection-Associated Cancers under the Framework of the U.S.–Japan Cooperative Medical Sciences Program | JP23jk0210009 |
| Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST) | Elucidating the Impact of Individual and Sex-Specific Variations in the Local Intestinal Microbiome on the Colorectal Pre-Disease State and Developing Microbiome-Based Preventive Strategies | JP26gm2010009 |
| Advanced International Collaborative Research Program - Adopting Sustainable Partnerships for an Innovative Research Ecosystem (ASPIRE), Japan Agency for Medical Research and Development (AMED) | The ELDER Study: Defining the Timing of Cancer Initiation through High-Resolution Quantification of Organ-Specific Aging | JP26jf0126022 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Metagenomic Characterization of Familial Adenomatous Polyposis and Its Application to Elucidating Mechanisms of Colorectal Tumor Initiation and Progression | 20H03662 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Characterization of Gut Microenvironmental Alterations Along the Serrated Pathway of Colorectal Tumorigenesis | 23H02892 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer | JGAD001015 | |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
