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A blood test method that infers which genes a tumour is using from how DNA fragments are cut at the start of each gene.
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.
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.
Query for this technology: (TITLE:"EPIC-seq" OR ABSTRACT:"EPIC-seq" OR TITLE:"expression inference from cell-free DNA" OR ABSTRACT:"expression inference from cell-free DNA" OR TITLE:"Epigenetic expression inference from cell-free DNA-sequencing" OR ABSTRACT:"Epigenetic expression inference from cell-free DNA-sequencing") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about EPIC-seq (expression inference from cell-free DNA), not a curated reading list.
Shares Plasma epigenomic profiling (cfChIP-seq), Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA), Liquid biopsy (ctDNA).
Shares Naming which clone or phenotype is left after treatment, Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA), Liquid biopsy (ctDNA).
Shares Griffin (nucleosome profiling of cell-free DNA), cfDNA fragmentomics, Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA).
Shares Griffin (nucleosome profiling of cell-free DNA), Naming which clone or phenotype is left after treatment, Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA).
Shares Plasma epigenomic profiling (cfChIP-seq), Cell-free DNA (cfDNA).
Shares cfDNA fragmentomics, Cell-free DNA (cfDNA), Liquid biopsy (ctDNA).
Shares Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA), Liquid biopsy (ctDNA).
Shares Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA), Liquid biopsy (ctDNA), Non-small-cell lung cancer.
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