The study included 63 patients diagnosed with UICC stage III colorectal cancer (CRC), 20 patients with colorectal adenomas, 10 patients with pT1 CRC, and 10 patients with known “high-burden” circulating tumor DNA (ctDNA), totaling 103 CRC patients. Additionally, the study included 45 healthy individuals.
For CRC patients, DNA from tumor tissue and normal DNA from white blood cells (WBC) were obtained. Furthermore, cfDNA from plasma samples were available from the patients as indicated in Table 1. For healthy individuals, cfDNA was collected.
WGS was performed on all collected samples using the NovaSeq platform from Illumina. The MRD-EDGE tool was used to assess ctDNA status and level. For a subset of patients (n = 48), digital droplet PCR (ddPCR) was conducted on a second aliquot of the plasma sample.
| Cohort | Patients | Sample types | Comment |
|---|---|---|---|
| Stage III CRC | 48 | Tumor, normal, 2x pre-OP plasma | Used for MRD-EDGE >< ddPCR comparison |
| Stage III CRC | 15 | Tumor, normal, pre-OP plasma, post-OP plasma | |
| High Burden CRC | 10 | Tumor, normal, high-burden ctDNA plasma | 5 used for training, 5 used in relation to adenoms/pT1 analysis |
| Adenoma | 20 | Tumor, normal, pre-resection plasma | |
| pT1 | 10 | Tumor, normal, pre-resection plasma | |
| Healthy Controls | 45 | Plasma | 5 used for training, 40 used as non-cancer controls |
| Restricted table number | Table name | Content |
|---|---|---|
| 1 | MRD-EDGESNV disease-specific model train, validation, test sets and model performance | Info on 5 high-burden and 5 healthy cfDNA samples used for model training. |
| 4 | In silico and experimental mixing studies | Info on 2 high-burden and 2 healthy cfDNA samples used for in silico mixing studies. |
| 5 | Plasma sample sequencing metrics | Various metrics on all plasma samples, including (but not limited to) blood collection tube, library preparation details, sequencing platform, and post-sequencing metrics. |
| 6 | Clinical data for individual patients | Clinical info on CRC patients and patient with colorectal adenomas, including age, gender, stage, MSI status, histology type, and recurrence information. |
| 7 | Tumor-informed MRD-EDGE Z scores | MRD-EDGE Z scores (CNV and SNV) and related details on all plasma samples. |
| 8 | Adenoma histology features | Info on 20 colorectal adenomas, including location, histological subtype, tumor size, and grade of differentiation. |
| 11 | Tumor tissue sequencing metrics | Various metrics on all tumor samples, including (but not limited to) library preparation details, sequencing platform, and post-sequencing metrics. |
| 12 | Normal tissue sequencing metrics | Various metrics on all normal samples, including (but not limited to) library preparation details, sequencing platform, and post-sequencing metrics. |
| 15 | CRC plasma samples used in comparison with ddPCR | Info on 48 CRC patients and plasma samples used for MRD-EDGE <> ddPCR comparison. Includes information on gender, age, tumor location and size, MSI status as well as MRD-EDGE and ddPCR ctDNA results. |
Widman et. al. Ultrasensitive plasma-based monitoring of tumor burden using machine learning-guided signal enrichment
External researchers (academic or commercial) interested in analyzing the Danish colorectal cancer dataset will need to contact the Data Access Committee via email to cla@clin.au.dk. Access to clinical data and supplementary information (Table 2) related to 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 a reasonable request, the authors, on behalf of the Central Denmark Region, will enter into a collaboration with the data requestor to apply for approval.