biostudies-literatureUnknownJang MKPatient monitoring is a cornerstone in clinical practice to define disease phenotypes and guide clinical management. Unfortunately, this is often reliant on invasive and/or less sensitive methods that do not provide deep phenotype assessments of disease state to guide treatment. This paper examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) to define molecular gene sets in physiological and heart transplant patients taking immunosuppression medications. We show cfChIP-seq reliably detect gene signals that correlate with gene expression. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of the relevant immune and non-immune molecular pathways that were predomibioRxiv : the preprint server for biology2023.01.24.525414https://www.ebi.ac.uk/biostudies/studies/S-EPMC9928031biostudies-literatureCell-free Chromatin Immunoprecipitation to detect molecular pathways in Physiological and Disease States.PMC9928031Markowitz TEAgbor-Enoh SApalara ZAndargie TEJang MKKuhn SfalseCell-free Chromatin Immunoprecipitation to detect molecular pathways in Physiological and Disease States.Patient monitoring is a cornerstone in clinical practice to define disease phenotypes and guide clinical management. Unfortunately, this is often reliant on invasive and/or less sensitive methods that do not provide deep phenotype assessments of disease state to guide treatment. This paper examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) to define molecular gene sets in physiological and heart transplant patients taking immunosuppression medications. We show cfChIP-seq reliably detect gene signals that correlate with gene expression. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of the relevant immune and non-immune molecular pathways that were predomi2023-01-01T00:00:00Z2023 Jan2026-04-08T13:31:33.401Z2025-04-05T11:23:54.502ZS-EPMC99280313678942110.1101/2023.01.24.525414