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A way of reading which genes are switched on in a tumour from the pattern of where DNA in the blood is protected, used to tell whether a breast cancer still carries the oestrogen receptor.
Griffin (Doebley et al., Nature Communications 2022) profiles nucleosome protection and accessibility at transcription factor binding sites from cell-free DNA, with a GC correction tailored to fragment size, using whole-genome sequencing at coverage as low as 0.1x. It predicted oestrogen receptor subtype in 139 patients with metastatic breast cancer who had at least 5 per cent detectable ctDNA, with an area under the curve of 0.89, and 0.96 in independent cohorts. Performance depends on tumour fraction, so it reads the phenotype of advanced disease, not of residual disease at parts-per-million levels.
Where a transcription factor such as the oestrogen receptor is bound and active, the DNA is accessible and is cut differently when cells die; summing fragment coverage around thousands of its binding sites in plasma gives a readout of that factor's activity in the cells shedding DNA.
Query for this technology: (TITLE:"Griffin" OR ABSTRACT:"Griffin" OR TITLE:"nucleosome profiling of cell-free DNA" OR ABSTRACT:"nucleosome profiling of cell-free DNA") 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 Griffin (nucleosome profiling of cell-free DNA), not a curated reading list.
Shares METER (methylome-based ctDNA detection and subtyping), Read methylation and mutation on the same cell-free DNA fragment to tell what kind of cancer is left, Cell-free DNA (cfDNA), Estrogen receptor (ERα).
Shares Plasma epigenomic profiling (cfChIP-seq), Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA), Liquid biopsy (ctDNA).
Shares EPIC-seq (expression inference from cell-free DNA), cfDNA fragmentomics, Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA).
Shares Naming which clone or phenotype is left after treatment, Cell-free DNA (cfDNA), Circulating tumour DNA (ctDNA), Liquid biopsy (ctDNA).
Shares Plasma epigenomic profiling (cfChIP-seq), Cell-free DNA (cfDNA).
Shares Naming which clone or phenotype is left after treatment, Estrogen receptor (ERα), Circulating tumour DNA (ctDNA), Liquid biopsy (ctDNA).
Shares Read methylation and mutation on the same cell-free DNA fragment to tell what kind of cancer is left, Naming which clone or phenotype is left after treatment, Circulating tumour DNA (ctDNA).
Shares cfDNA fragmentomics, Cell-free DNA (cfDNA), Liquid biopsy (ctDNA).
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