{"entity":{"id":"paper-sadeh-cfchip-seq-nat-biotechnol-2021","kind":"paper","name":"ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin","aka":[],"tldr":"Pulling down DNA in blood that was still wrapped in the marks of active genes showed which genes the cells it came from were using.","summary":"Chromatin immunoprecipitation of cell-free nucleosomes carrying active chromatin modifications, followed by sequencing (cfChIP-seq), was applied to 268 human samples. In healthy donors it identified bone marrow megakaryocytes, but not erythroblasts, as major contributors to cell-free DNA; in liver disease it identified pathology-related changes in hepatocyte transcription; and in metastatic colorectal carcinoma it detected patient-specific information including transcriptionally active HER2 amplifications, at low sequencing depth.","asOf":"2026-11-04","links":[{"label":"Sadeh et al., Nat Biotechnol 2021","url":"https://doi.org/10.1038/s41587-020-00775-6"},{"label":"PubMed","url":"https://pubmed.ncbi.nlm.nih.gov/33432199/"}],"tags":[],"related":[],"cancers":["colorectal"],"sections":["diagnostics"],"technologies":["plasma-epigenomic-profiling"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["cfdna"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":["nature-biotechnology"],"dependsOn":[],"notes":[],"journal":"Nature Biotechnology","year":2021,"doi":"10.1038/s41587-020-00775-6","pmid":"33432199","authors":"Sadeh R, Sharkia I, Fialkoff G, et al.","paperType":"methods","findings":["268 samples profiled by cfChIP-seq.","Transcriptionally active HER2 amplifications detected in metastatic colorectal cancer."],"whatItMeans":"The first demonstration that gene activity in the tissue of origin can be read from nucleosomes in blood.","caveats":["Metastatic disease for the cancer findings."]},"route":"/key-papers/paper-sadeh-cfchip-seq-nat-biotechnol-2021/","neighbours":{"cancer":[{"id":"colorectal","kind":"cancer","name":"Colorectal cancer","route":"/cancers/colorectal/"}],"section":[{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"}],"technology":[{"id":"plasma-epigenomic-profiling","kind":"technology","name":"Plasma epigenomic profiling (cfChIP-seq)","route":"/technologies/plasma-epigenomic-profiling/"}],"term":[{"id":"cfdna","kind":"term","name":"Cell-free DNA (cfDNA)","route":"/terms/cfdna/"}],"journal":[{"id":"nature-biotechnology","kind":"journal","name":"Nature Biotechnology","route":"/journals/nature-biotechnology/"}]}}