File:EPIC-seq workflow.png

English: This flowchart delineates the workflow for EPIC-Seq, a comprehensive method for analyzing cell-free DNA (cfDNA). The initial step involves extracting cfDNA from patient plasma through liquid biopsy, providing a non-invasive means of sampling genetic material. Subsequently, the process advances to capturing reads within the Transcription Start Site (TSS) region of targeted genes utilizing specialized probes, ensuring precise genomic coverage. Once the cfDNA within the TSS region of targeted genes is captured, the next phase involves computing Fragmentomic Features such as promoter fragmentation entropy (PFE) and the Depth at nucleosome-depleted regions (NDR), providing insights into the structural characteristics of the DNA fragments. These features serve as crucial metrics for understanding genomic organization and regulatory dynamics. Finally, leveraging the NDR and PFE of all targets as features, a machine learning model is constructed to infer gene expression profiles in patients, facilitating the interpretation of molecular signatures and aiding in diagnostic and prognostic assessments.