{"entity":{"id":"epic-seq","kind":"technology","name":"EPIC-seq (expression inference from cell-free DNA)","aka":["EPIC-seq","Epigenetic expression inference from cell-free DNA-sequencing"],"tldr":"A blood test method that infers which genes a tumour is using from how DNA fragments are cut at the start of each gene.","summary":"EPIC-seq (Esfahani et al., Nature Biotechnology 2022) uses targeted sequencing of gene promoters and a feature called promoter fragmentation entropy to predict RNA expression at individual genes from cell-free DNA. In 329 blood samples from 201 patients with cancer and 87 healthy adults it classified subtypes of lung carcinoma and diffuse large B-cell lymphoma, and inferred expression profiles correlated with response to PD-1 or PD-L1 inhibitors. In the full text, lung cancer histology accuracy was 87 per cent at mean allele fractions above 5 per cent, 81 per cent between 1 and 5 per cent and 73 per cent below 1 per cent.","status":"emerging","asOf":"2026-11-04","links":[{"label":"Esfahani et al., Nat Biotechnol 2022 (EPIC-seq)","url":"https://doi.org/10.1038/s41587-022-01222-4"}],"tags":[],"related":["griffin-nucleosome-profiling","plasma-epigenomic-profiling"],"cancers":["nsclc","dlbcl"],"sections":["diagnostics"],"technologies":["fragmentomics","liquid-biopsy"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["cfdna","ctdna"],"trials":[],"people":[],"bottlenecks":["b-subclone-attribution-residual-disease"],"keyPapers":["paper-esfahani-epic-seq-nat-biotechnol-2022"],"journals":[],"dependsOn":[],"notes":[],"principle":"Active promoters lose a well-positioned nucleosome, so the sizes of fragments starting there are more varied; that variety (entropy) tracks how much the gene is expressed in the cells that shed the DNA.","strengths":["Gene-level expression from blood","Targeted, so it is cheaper than whole-genome approaches"],"limitations":["Accuracy falls with tumour fraction","Shown for lung cancer histology and lymphoma cell of origin, not for oestrogen receptor or TROP2"],"since":2022},"route":"/technologies/epic-seq/","neighbours":{"technology":[{"id":"fragmentomics","kind":"technology","name":"cfDNA fragmentomics","route":"/technologies/fragmentomics/"},{"id":"griffin-nucleosome-profiling","kind":"technology","name":"Griffin (nucleosome profiling of cell-free DNA)","route":"/technologies/griffin-nucleosome-profiling/"},{"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/"}],"cancer":[{"id":"dlbcl","kind":"cancer","name":"Diffuse large B-cell lymphoma","route":"/cancers/dlbcl/"},{"id":"nsclc","kind":"cancer","name":"Non-small-cell lung cancer","route":"/cancers/nsclc/"}],"section":[{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"}],"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/"}],"bottleneck":[{"id":"b-subclone-attribution-residual-disease","kind":"bottleneck","name":"Naming which clone or phenotype is left after treatment","route":"/bottlenecks/b-subclone-attribution-residual-disease/"}],"paper":[{"id":"paper-esfahani-epic-seq-nat-biotechnol-2022","kind":"paper","name":"Inferring gene expression from cell-free DNA fragmentation profiles","route":"/key-papers/paper-esfahani-epic-seq-nat-biotechnol-2022/"}]}}