Methods Mol Biol. 2026 ;3005
435-447
Cell-free DNA (cfDNA) provides a non-invasive means to monitor physiological states and diagnose diseases, with widespread applications in oncology. Our lab utilizes cfDNA as a tool to investigate the state of the tumor and the tumor microenvironment in patients with cancer. This chapter outlines methods for cfDNA extraction from plasma, library preparation for sequencing, and subsequent computational analysis that will enable analysis of cfDNA footprints genome-wide. By examining cfDNA fragment lengths and their genomic origins, we can infer cellular dynamics and identify potential biomarkers for various health conditions, offering valuable insights into the body's internal processes with significant implications for advancing diagnostic and therapeutic approaches.
Keywords: Chromatin; Epigenomics; Subnucleosome; cfDNA