NBDC Research ID: hum0479.v1
SUMMARY
Aims: To explore new biomarkers for predicting the effectiveness of an anti-epidermal growth factor receptor (anti-EGFR) antibody in patients with advanced colorectal cancer. The investigation involves analyzing the entire exome, conducting a genome-wide association study (GWAS), and analyzing copy number variations (CNVs) using single nucleotide polymorphism (SNP) arrays. Genetic material from both tumor and non-tumor tissues, as well as blood samples from patients who received the anti-EGFR antibody treatment, were used. The goal is to identify genetic mutations and SNPs associated with treatment efficacy and adverse events, and to assess the correlation between their presence and treatment effectiveness using statistical methods.
Methods: Whole exome sequencing for exploratory cohort, Target capture sequencing for inference cohort
Participants/Materials: Unresectable and advanced recurrent colorectal cancer
- exploratory cohort: 92 patients treated with cetuximab
- inference cohort: 150 patients treated with cetuximab or panitumumab
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000779 | Controlled-access (Type I) | 2025/04/14 |
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MOLECULAR DATA
| Participants/Materials |
Unresectable and advanced recurrent colorectal cancer (ICD10: C18.9): 92 cases tumor and non-tumor tissue pairs: 92 cases (184 samples) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Hiseq 2000/1500] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V4+UTRs Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Mapping Methods | BWA |
| Mapping Quality | - |
| Reference Genome Sequence | hg19 |
| Coverage (Depth) | x161 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000921 |
| Total Data Volume | 8.4 TB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Unresectable and advanced recurrent colorectal cancer (ICD10: C18.9): 150 cases tumor tissues : 63 cases (63 samples) tumor and non-tumor tissue pairs : 87 cases (174 samples) |
| Targets | Target Capture |
| Target Loci for Capture Methods | 31 genomic loci found in the first cohort. (Gene list) |
| Platform | Illumina [Hiseq 2000/1500] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V4+UTRs Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Mapping Methods | BWA |
| Mapping Quality | - |
| Reference Genome Sequence | hg19 |
| Coverage (Depth) | x694 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000921 |
| Total Data Volume | 8.4 TB (bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Katsuya Tsuchihara
Affiliation: Exploratory Oncology Research and Clinical Trial Center, National Cancer Center
Project / Group Name: BREAC Study
URL: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Adaptable and Seamless Technology transfer Program through targetdriven R&D, Japan Science and Technology Agency (JST) | Development of a Predictive Diagnostic Kit for Evaluating the Efficacy of Anti-EGFR Antibody Therapy Based on Comprehensive Genomic Analysis | JPMJTT11S8 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Clinical significance of BRAF non-V600E mutations on the therapeutic effects of anti-EGFR monoclonal antibody treatment in patients with pretreated metastatic colorectal cancer: the Biomarker Research for anti-EGFR monoclonal Antibodies by Comprehensive Cancer genomics (BREAC) study | doi:10.1038/bjc.2017.308 | JGAD000921 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
