Methylation Profile Test (Methylscape) in Body Fluids for Multi-Cancer Detection and Monitoring in Colombia

Overview

DNA methylation changes occur early and broadly during carcinogenesis. Methylscape is a rapid assay that detects global DNA methylation patterns in body fluids (blood, urine, and saliva) and may detect a cancer signal and predict the cancer signal origin (CSO) from a single fluid sample, using the differential interaction between methylated and unmethylated DNA and gold nanoparticles. This prospective observational study evaluates the diagnostic performance (sensitivity and specificity) of the Methylscape test in Colombian patients with various biopsy-confirmed solid tumors compared with age- and sex-matched cancer-free (healthy) volunteers. The study is conducted in three parts: Phase 1 validates the assay in 250 patients with cancer; Sub-study 2a compares 1,500 patients with cancer against 1,500 matched cancer-free volunteers; and Sub-study 2b uses serial blood and urine sampling in 300 patients with early-stage disease to assess detection of disease relapse during follow-up, in parallel with standard imaging. The study also estimates positive and negative predictive values (PPV/NPV) and projects the budget impact and cost-effectiveness of Methylscape as a multi-cancer early detection (MCED) tool in an upper-middle-income Latin American setting.

Background. Most cancers lack reliable screening methods, often leading to advanced-stage diagnosis. Multi-cancer early detection (MCED) tests based on body fluids can screen for several cancer types from a single sample. DNA methylation, which occurs early in carcinogenesis and is tissue-specific, is the most commonly used marker in MCED assays. Methylscape leverages global differences in the genomic distribution of methylation between cancerous and normal tissues, detected electrochemically through differential adsorption of DNA on gold electrodes. Objective. To determine whether Methylscape can detect the methylation landscape across multiple cancer types with sufficiently high specificity to predict the cancer signal origin (CSO), and to assess its potential application as a population-scale MCED test among Colombians. Design. Single-center prospective observational study conducted at CTIC (Bogotá, Colombia), with sample processing at CTIC and Columbia University. Phase 1 (N=250 patients with cancer) provides initial validation across solid tumor types selected by local incidence. Sub-study 2a (1,500 patients with cancer and 1,500 matched cancer-free volunteers) provides large-scale clinical validation. Sub-study 2b (N=300 early-stage patients) evaluates serial blood/urine Methylscape testing for relapse detection during follow-up every 6 months. Phase 1 participants may enter Sub-studies 2a/2b only if they meet the corresponding criteria and provide new informed consent; cross-phase participation is flagged in the database to adjust statistical estimates. Biospecimens \& reference standards. Blood/plasma (K2EDTA), urine, saliva, and FFPE tumor tissue are collected and stored at -80 °C in the CTIC biobank. Cancers are coded with WHO ICD-O-3; stage per AJCC 8th edition. Reference standards: histopathology (MCED), RECIST 1.1 or biopsy (relapse), and absence of cancer by record review plus 12-month follow-up (cancer-free). Statistical analysis. Sensitivity and specificity are estimated overall and by stage/type (expected sensitivity 85-90%, specificity 98%; 95% confidence, 80% power). PPV/NPV are derived via Bayes' theorem with prevalence from GLOBOCAN 2022; 95% CIs by stratified bootstrap (1,000 resamples). Budget impact and cost-effectiveness (QALYs) are projected via microsimulation and Markov models.