{"entity":{"id":"idea-stack-ctdna-and-tumour-rna-residual-disease","kind":"idea","name":"Read tumour RNA and tumour DNA from the same blood draw to find and type residual cancer","aka":["Stacking ctDNA and ctRNA","Multi-analyte residual disease test","cfDNA plus cfRNA residual disease"],"tldr":"A proposal, unproven at residual disease levels: add the tumour's RNA to the tumour DNA a blood test already tracks, because a cell holds many more RNA copies of an active gene than DNA copies, and RNA could also show whether the cancer still makes the oestrogen receptor or TROP2.","summary":"Residual disease tests count tumour DNA fragments, and at a few parts per million a tube holds only a handful (see the bottleneck). A cell has two copies of each gene but between 50,000 and 300,000 messenger RNA molecules in total (Marinov 2014), and RNA carries what DNA cannot: whether ESR1 or TACSTD2 (TROP2) is switched on, splice forms such as AR-V7, and fusions. The proposal is to design both halves of the test from the tumour's own whole-genome and RNA sequencing: track the mutations in cell-free DNA as now, and in the same plasma read transcripts that the tumour expresses strongly and normal blood does not, plus the ESR1 and TACSTD2 transcripts.\n\nWhat is measured supports trying it. In lung cancer, reading EGFR mutations from vesicle RNA and cell-free DNA together raised sensitivity from 26 to 74 per cent in patients whose disease sheds little (Krug 2018); RNA alone caught ALK fusions in two patients whose DNA was negative (Heeke 2025); GRAIL found 68 per cent of genes silent in normal plasma and argued that tumour content amplifies cancer signal \"by orders of magnitude\" over tumour fraction (Larson 2021); and the change in tumour-only small RNAs across chemotherapy tracked outcome in 192 breast cancer patients (Wang 2026).\n\nWhat is measured also limits it. Free RNA is destroyed within seconds in plasma, so only packaged RNA counts and the fraction of a tumour cell's RNA that survives is unknown (Tsui 2002); about three-quarters of plasma RNA comes from blood cells (Larson 2021); detection depends on tumour fraction times expression, and in GRAIL's breast cohort the five patients with the highest tumour fraction had no detectable FABP7 (Larson 2021); for AR-V7, circulating tumour cells were more sensitive than cell-free or vesicle RNA (Nimir 2019). No study reports a cell-free RNA tumour fraction in parts per million, no study was found that reads ESR1 or TACSTD2 expression from plasma RNA in breast cancer, and no reference material for cell-free RNA assays was found, so no detection floor can yet be stated. Whether stacking helps below 10 parts per million is therefore open.","asOf":"2026-11-04","links":[{"label":"Krug et al., Ann Oncol 2018","url":"https://doi.org/10.1093/annonc/mdx765"},{"label":"Larson et al., Nat Commun 2021","url":"https://doi.org/10.1038/s41467-021-22444-1"},{"label":"Tsui et al., Clin Chem 2002","url":"https://doi.org/10.1093/clinchem/48.10.1647"}],"tags":["proposal"],"related":["idea-same-fragment-methylation-and-mutation","idea-bio1-cfrna-plasticity-tracking"],"cancers":["breast-cancer","breast-hr-positive","tnbc"],"sections":[],"technologies":["liquid-rna-biopsy","mrd-testing","liquid-biopsy","rna-seq","wes-wgs"],"targets":["trop2","estrogen-receptor"],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["ctdna","cfdna","mrd"],"trials":[],"people":[],"bottlenecks":["b-subclone-attribution-residual-disease","b-dormancy-mrd"],"keyPapers":["paper-krug-exosomal-rna-ctdna-egfr-ann-oncol-2018","paper-larson-cell-free-transcriptome-cancer-nat-commun-2021","paper-marinov-single-cell-transcriptome-stochasticity-genome-res-2014","paper-tsui-plasma-rna-stability-clin-chem-2002","paper-wang-orphan-rnas-breast-response-cell-rep-med-2026","paper-heeke-alk-ctrna-ctdna-jto-clin-res-rep-2025","paper-nimir-ar-v7-ctc-ctrna-exosomes-cells-2019","paper-rampazzo-plasma-tert-rna-rectal-cancer-br-j-cancer-2018","paper-yen-ev-protein-mrna-ovarian-ebiomedicine-2025","paper-antonarakis-ar-v7-resistance-nejm-2014","paper-northcott-next-personal-validation-oncotarget-2024","paper-abbosh-tracerx-ctdna-relapse-nature-2023"],"journals":[],"dependsOn":[],"notes":[],"hypothesis":"In patients after curative treatment for breast cancer, adding tumour-informed cell-free RNA targets (transcripts highly expressed in the patient's tumour and absent from normal plasma) to a tumour-informed cell-free DNA panel, read from the same plasma, increases the expected number of tumour-derived molecules per sample and the detection rate at tumour fractions below 10 parts per million, and classifies ESR1 and TACSTD2 expression of the residual disease better than chance.","rationale":"Measured: 50,000 to 300,000 transcripts per cell against two DNA copies (Marinov 2014); a near threefold rise in mutation detection in low-shedding lung cancer when vesicle RNA was added to cell-free DNA (Krug 2018); tumour genes silent in normal plasma (Larson 2021). The subclone bottleneck shows that the number of tumour molecules in the tube, not sequencing accuracy, is what limits detection and attribution below 10 parts per million, so a second source of molecules is the lever, and RNA is the only blood analyte that carries expression directly.","test":"First, measure the multiplier: in plasma from patients with known tumour DNA fractions, count tumour-specific RNA molecules (by unique molecular identifiers, against added RNA standards of known quantity) and tumour DNA fragments for the same genes in the same draw, and report tumour RNA molecules per tumour DNA fragment; if the ratio is not well above one for the best transcripts, stop. Second, dilute patient plasma into healthy plasma to 100, 10 and 1 parts per million of tumour DNA and compare detection by DNA alone, RNA alone and both, with blood-cell background measured in matched buffy coat RNA. Third, in metastatic breast cancer with paired biopsies, test whether plasma ESR1 and TACSTD2 transcript levels track tissue status. Only then, in the plasma banks of residual disease trials, test after curative treatment.","maturity":"preclinical-evidence","actor":"research"},"route":"/ideas/idea-stack-ctdna-and-tumour-rna-residual-disease/","neighbours":{"idea":[{"id":"idea-bio1-cfrna-plasticity-tracking","kind":"idea","name":"Detect tumours changing cell type from RNA in the blood","route":"/ideas/idea-bio1-cfrna-plasticity-tracking/"},{"id":"idea-same-fragment-methylation-and-mutation","kind":"idea","name":"Read methylation and mutation on the same cell-free DNA fragment to tell what kind of cancer is left","route":"/ideas/idea-same-fragment-methylation-and-mutation/"}],"cancer":[{"id":"breast-cancer","kind":"cancer","name":"Breast cancer (all types)","route":"/cancers/breast-cancer/"},{"id":"breast-hr-positive","kind":"cancer","name":"HR-positive / HER2-negative breast cancer","route":"/cancers/breast-hr-positive/"},{"id":"tnbc","kind":"cancer","name":"Triple-negative breast cancer (TNBC)","route":"/cancers/tnbc/"}],"technology":[{"id":"liquid-biopsy","kind":"technology","name":"Liquid biopsy (ctDNA)","route":"/technologies/liquid-biopsy/"},{"id":"liquid-rna-biopsy","kind":"technology","name":"Liquid RNA biopsy (cell-free, vesicle and platelet RNA)","route":"/technologies/liquid-rna-biopsy/"},{"id":"mrd-testing","kind":"technology","name":"MRD / molecular residual disease testing","route":"/technologies/mrd-testing/"},{"id":"rna-seq","kind":"technology","name":"RNA sequencing & expression profiling","route":"/technologies/rna-seq/"},{"id":"wes-wgs","kind":"technology","name":"Whole-exome & whole-genome sequencing","route":"/technologies/wes-wgs/"}],"target":[{"id":"estrogen-receptor","kind":"target","name":"Estrogen receptor (ERα)","route":"/targets/estrogen-receptor/"},{"id":"trop2","kind":"target","name":"TROP2","route":"/targets/trop2/"}],"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/"},{"id":"mrd","kind":"term","name":"Minimal / molecular residual disease (MRD)","route":"/terms/mrd/"}],"bottleneck":[{"id":"b-dormancy-mrd","kind":"bottleneck","name":"Dormant cells and minimal residual disease","route":"/bottlenecks/b-dormancy-mrd/"},{"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-larson-cell-free-transcriptome-cancer-nat-commun-2021","kind":"paper","name":"A comprehensive characterization of the cell-free transcriptome reveals tissue- and subtype-specific biomarkers for cancer detection","route":"/key-papers/paper-larson-cell-free-transcriptome-cancer-nat-commun-2021/"},{"id":"paper-northcott-next-personal-validation-oncotarget-2024","kind":"paper","name":"Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay","route":"/key-papers/paper-northcott-next-personal-validation-oncotarget-2024/"},{"id":"paper-antonarakis-ar-v7-resistance-nejm-2014","kind":"paper","name":"AR-V7 and resistance to enzalutamide and abiraterone in prostate cancer","route":"/key-papers/paper-antonarakis-ar-v7-resistance-nejm-2014/"},{"id":"paper-nimir-ar-v7-ctc-ctrna-exosomes-cells-2019","kind":"paper","name":"Detection of AR-V7 in Liquid Biopsies of Castrate Resistant Prostate Cancer Patients: A Comparison of AR-V7 Analysis in Circulating Tumor Cells, Circulating Tumor RNA and Exosomes","route":"/key-papers/paper-nimir-ar-v7-ctc-ctrna-exosomes-cells-2019/"},{"id":"paper-marinov-single-cell-transcriptome-stochasticity-genome-res-2014","kind":"paper","name":"From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing","route":"/key-papers/paper-marinov-single-cell-transcriptome-stochasticity-genome-res-2014/"},{"id":"paper-krug-exosomal-rna-ctdna-egfr-ann-oncol-2018","kind":"paper","name":"Improved EGFR mutation detection using combined exosomal RNA and circulating tumor DNA in NSCLC patient plasma","route":"/key-papers/paper-krug-exosomal-rna-ctdna-egfr-ann-oncol-2018/"},{"id":"paper-heeke-alk-ctrna-ctdna-jto-clin-res-rep-2025","kind":"paper","name":"Longitudinal Tracking of ALK-Rearranged NSCLC From Plasma Using Circulating Tumor RNA and Circulating Tumor DNA","route":"/key-papers/paper-heeke-alk-ctrna-ctdna-jto-clin-res-rep-2025/"},{"id":"paper-tsui-plasma-rna-stability-clin-chem-2002","kind":"paper","name":"Stability of endogenous and added RNA in blood specimens, serum, and plasma","route":"/key-papers/paper-tsui-plasma-rna-stability-clin-chem-2002/"},{"id":"paper-wang-orphan-rnas-breast-response-cell-rep-med-2026","kind":"paper","name":"Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers","route":"/key-papers/paper-wang-orphan-rnas-breast-response-cell-rep-med-2026/"},{"id":"paper-rampazzo-plasma-tert-rna-rectal-cancer-br-j-cancer-2018","kind":"paper","name":"The predictive and prognostic potential of plasma telomerase reverse transcriptase (TERT) RNA in rectal cancer patients","route":"/key-papers/paper-rampazzo-plasma-tert-rna-rectal-cancer-br-j-cancer-2018/"},{"id":"paper-abbosh-tracerx-ctdna-relapse-nature-2023","kind":"paper","name":"Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA","route":"/key-papers/paper-abbosh-tracerx-ctdna-relapse-nature-2023/"},{"id":"paper-yen-ev-protein-mrna-ovarian-ebiomedicine-2025","kind":"paper","name":"Tumour extracellular vesicle surface Protein-mRNA integration assay for early detection of epithelial ovarian cancer","route":"/key-papers/paper-yen-ev-protein-mrna-ovarian-ebiomedicine-2025/"}]}}