EPIMETRIC: A cfDNA Methylation-Based Algorithm for COPD Diagnosis and Stratification

To develop a blood-based algorithm using cell-free DNA (cfDNA) methylation profiles to diagnose and stratify patients with COPD according to the Global Initiative for Chronic Obstructive Lung Disease (GOLD) classification.

Between 2021 and 2023, 166 participants were enrolled, including patients with COPD (N=80) and healthy controls (N=86) from three hospitals in Andalusia. Genome-wide cfDNA methylation analysis was performed in 128 individuals to identify CpG sites discriminating COPD from healthy individuals and to stratify COPD patients by GOLD categories. A hierarchical support vector machine (SVM) classifier was implemented, and functional enrichment analyses were conducted to assess biological relevance.

Differential methylation analysis identified 354 genes associated with COPD, 496 with GOLD classification, and 125 overlapping genes. The SVM classifier trained on cfDNA methylation features achieved complete separation between COPD and control groups, enabling a hard-margin model. This cfDNA-based classifier (EPIMETRIC) also distinguished GOLD A, B, and D subgroups. Enrichment analysis revealed pathways including glutamatergic synapse, nicotine addiction, tight junction, and Hippo signaling.

EPIMETRIC represents the first blood-based cfDNA methylation signature for COPD diagnosis and GOLD stratification. It provides a minimally invasive and highly accurate tool for early detection, personalized treatment, and identification of high-risk patients.