{"entity":{"id":"paper-baca-plasma-epigenomic-profiling-nat-med-2023","kind":"paper","name":"Liquid biopsy epigenomic profiling for cancer subtyping","aka":[],"tldr":"Reading chemical marks on DNA and its packaging from 1 mL of blood let researchers infer which genes advanced cancers had switched on, including the targets of some drugs.","summary":"An immunoprecipitation-based method targeting histone modifications and DNA methylation measured 1,268 epigenomic profiles in plasma from 433 people with one of 15 cancers. It served as a proxy for transcriptional activity, inferring expression of diagnostic markers and drug targets, the activity of targetable transcription factors, and epigenetic mechanisms of resistance.","asOf":"2026-11-04","links":[{"label":"Baca et al., Nat Med 2023","url":"https://doi.org/10.1038/s41591-023-02605-z"},{"label":"PubMed","url":"https://pubmed.ncbi.nlm.nih.gov/37865722/"}],"tags":[],"related":[],"cancers":[],"sections":["diagnostics"],"technologies":["plasma-epigenomic-profiling","liquid-biopsy"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["cfdna","ctdna"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":["nature-medicine"],"dependsOn":[],"notes":[],"journal":"Nature Medicine","year":2023,"doi":"10.1038/s41591-023-02605-z","pmid":"37865722","authors":"Baca SC, Seo JH, Davidsohn MP, et al.","paperType":"translational","findings":["1,268 plasma epigenomic profiles from 433 individuals with 15 cancers, from 1 mL of plasma.","Inferred expression of drug targets and activity of targetable transcription factors."],"whatItMeans":"Blood can show what a tumour is doing, not only what mutations it has. It is a proof of concept in advanced cancer.","caveats":["Advanced cancers; analyses were restricted to samples above 3 per cent ctDNA in the full text.","TROP2 is not among the targets reported."],"participants":433},"route":"/key-papers/paper-baca-plasma-epigenomic-profiling-nat-med-2023/","neighbours":{"section":[{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"}],"technology":[{"id":"liquid-biopsy","kind":"technology","name":"Liquid biopsy (ctDNA)","route":"/technologies/liquid-biopsy/"},{"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/"},{"id":"ctdna","kind":"term","name":"Circulating tumour DNA (ctDNA)","route":"/terms/ctdna/"}],"journal":[{"id":"nature-medicine","kind":"journal","name":"Nature Medicine","route":"/journals/nature-medicine/"}]}}