NBDC Research ID: hum0447.v1
SUMMARY
Aims: Intractable cancers (pancreatic, lung, colorectal, ovarian, uterine, esophageal, breast, bladder, kidney, and head and neck cancers; bone and soft tissue sarcoma; and malignant melanoma), as well as cancers that are more common in Japan (gastric, liver, and biliary tract cancers), were targeted. To clarify the onco-genomic landscape in relation to pathological conditions, we are conducting comprehensive, exploratory genomic analyses with the following aims: 1. To clarify genomic abnormalities. 2. To identify correlations between genomic abnormalities and malignant phenotypes of tumors (e.g., metastasis and invasion) that affect responses to various therapies and prognosis. 3. To establish new effective treatments and diagnostic methods.
Methods: Whole Genome sequencing
Participants/Materials: Colorectal tumor tissues and peripheral blood cells from 138 Japanese colorectal cancer patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000696 | NGS（WGS） | Controlled-access (Type I) | 2026/06/09 |
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MOLECULAR DATA
| Participants/Materials |
colorectal cancer (ICD10: C189): 138 cases tumor tissues: 138 samples non-tumor tissues (blood): 128 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues or non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-free kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | BWA-MEM (version 0.7.8) |
| Mapping Quality | Mean mapping rate 99.5% |
| Reference Genome Sequence | GRCh37/hg19 (reference_accession: GCF_000001405.13) |
| Coverage (Depth) | tumor tissues: 51.4x, non-tumor tissues: 38.1x |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000829 |
| Total Data Volume | 28.5 TB (bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Tatsuhiro Shibata
Affiliation: Division of Cancer Genomics, National Cancer Center Research Institute
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) | Establishment of a Large-Scale Integrated Japanese Cancer Genome, Multi-Omics, and Clinical Data Resource for International Collaborative Research, Genome-Based Prevention, and Precision Medicine. | JP25ck0106800 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer | JGAD000829 | |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
