From Background to Signal: Simultaneously derived Copy Numbers from Methylation-Dependent Sequencing cell-free DNA

Cell-free DNA (cfDNA) analysis offers a powerful, non-invasive approach to cancer diagnostics and monitoring by revealing tumor-specific genomic and epigenetic alterations. Here, we demonstrate the versatility of MeD-seq, a methylation-dependent sequencing assay, for comprehensive cfDNA analysis, including methylation profiling, chromosomal copy number (CN) alterations, and tumor fraction (TF) estimation. MeD-seq-derived CN profiles and TF estimates from 38 colorectal cancer with liver metastases (CRLM) and 5 ovarian cancer patients were highly comparable to shallow whole-genome sequencing (sWGS) validating our approach. These findings establish MeD-seq as a robust and cost-effective platform for detecting cancer-specific signals directly from plasma without prior tissue-based information. Future work should expand its application to other cancer types, solidifying MeD-seq as a versatile tool for minimally-invasive cfDNA profiling.