Whole-genome sequencing (WGS) data was generated from tumor DNA (DatasetID A) and paired normal DNA from peripheral blood mononuclear cells (DatasetID B) from 144 patients with stage III colorectal cancer (CRC). This included two patients with synchronous tumors (n = 2), resulting in a total of 146 tumor biopsies. Tumor samples were either acquired as fresh-frozen (n = 111) or formalin-fixed paraffin-embedded (n = 35) tissue biopsies. Furthermore, WGS data was generated for plasma-derived cell-free DNA (DatasetID D) from 1283 serially collected plasma samples from the 144 stage III CRC patients.
Processed sequencing files generated by Mutect2, Strelka2, and FACETS were generated for all tumor samples (n = 146) (DatasetID D) and post-operative plasma samples with an estimated tumor fraction above 10% (n = 17) (DatasetID E). For all plasma samples, ctDNA status (positive/negative), and the estimated tumor fractions were computed (DatasetID F). Clinical information, such as sample collection timepoint (relative to primary surgery), treatment information, recurrence status, and information on recurrence intervention were collected for all patients (DatasetID G).
| Dataset ID | Samples | Sample Type | Technology | Sequencing Platform |
|---|---|---|---|---|
| A | CRC-001_T01, CRC-002_T01, CRC-003_T01, … etc. | Tumor DNA | Illumina NGS | Illumina NovaSeq 6000 |
| B | CRC-001_N01, CRC-002_N01, CRC-003_N01, … etc. | Normal DNA | Illumina NGS | Illumina NovaSeq 6000 |
| C | CRC-001_P01, CRC-001_P02, CRC-001_P03, CRC-001_P04, CRC-002_P01, CRC-002_P02, … etc. | cfDNA | Illumina NGS | Illumina NovaSeq 6000 |
| Dataset ID | Samples | Sample Type | Method | File type |
|---|---|---|---|---|
| D | CRC-001_T01, CRC-002_T01, CRC-003_T01, … etc. | Tumor DNA | Mutect2, Strelka2, FACETS | VCF |
| E | CRC-039_P02, CRC-039_P06, CRC-041_P05, CRC-041_P06, CRC-059_P07, … etc. | cfDNA | Mutect2, Strelka2, FACETS | VCF |
| F | CRC-001_P01, CRC-001_P02, CRC-001_P03, CRC-001_P04, CRC-002_P01, CRC-002_P02, … etc. | cfDNA | Tumor-informed ctDNA results using custom proprietary algorithm | CSV |
| G | CRC-001, CRC-002, CRC-003, … etc. | Patient level information | N/A | CSV |
Amanda Frydendahl, Jesper Nors, Mads H. Rasmussen, et al,
Detection of circulating tumor DNA by tumor-informed whole-genome sequencing enables prediction of recurrence in stage III colorectal cancer patients,
European Journal of Cancer, Volume 211, 2024, 114314, https://doi.org/10.1016/j.ejca.2024.114314.
https://www.sciencedirect.com/science/article/pii/S0959804924009705
External researchers (academic or commercial) interested in analysing the colorectal cancer dataset will need to contact the Data Access Committee via email to cla@clin.au.dk. Access to clinical data and processed sequencing data output files (Mutect2 v4.2.4.1, Strelka2 v2.9.10, and FACETS v0.6.2) used in the article requires that the data requestor (legal entity) enter into Collaboration and Data Processing Agreements, with the Central Denmark Region (the legal entity controlling and responsible for the data). Request for access to raw sequencing data furthermore requires that the purpose of the data re-analysis is approved by The Danish National Committee on Health Research Ethics. Upon reasonable request, the authors, on behalf of the Central Denmark Region, will enter into a collaboration with the data requestor to apply for approval.