{"entity":{"id":"b-subclone-attribution-residual-disease","kind":"bottleneck","name":"Naming which clone or phenotype is left after treatment","aka":["Subclone attribution of residual disease","Which clone remains"],"tldr":"Blood tests can now find a few parts per million of tumour DNA after treatment, but at those levels there are too few molecules to say which branch of the tumour is left, or whether it still carries the oestrogen receptor or TROP2.","summary":"Ultrasensitive residual disease tests reach a few parts per million by adding up evidence across hundreds to about 1,800 tracked mutations: NeXT Personal reports a 95 per cent limit of detection of 3.45 parts per million (Northcott 2024). Saying which subclone the tumour DNA came from cannot pool that way, because it may use only the mutations private to that subclone. The published tool built for the job, ECLIPSE from TRACERx, states its operating point at 0.1 per cent clonal ctDNA (1,000 parts per million) with at least 10 ng of DNA, for a subclone present in 20 per cent of cancer cells and tracked by four mutations (Abbosh 2023). That is about a hundred to three hundred times above where detection now works.\n\nBreast cancer makes the gap wider. Patients in one early breast cancer study had a median of 57 trackable mutations (range 2 to 346) (Parsons 2020), against TRACERx's median of 200 in lung cancer, and commercial panels are deliberately built from clonal, trunk mutations. The phenotype question is harder still: TROP2 expression is set mainly by DNA methylation rather than by mutation (Notini 2026), TROP2 PET uptake changes with treatment (Liu 2026), and the methods that read oestrogen receptor activity from blood (Griffin, METER, cfChIP-seq) were validated at 3 to 5 per cent tumour fraction, four orders of magnitude above residual disease. The one published case tying a resistant subclone to a TROP2 change, TACSTD2 T256R on one branch and TOP1 E418K on another under sacituzumab govitecan, was read from tissue at progression (Coates 2021). No commercial residual disease report reviewed on 4 November 2026 names the clone that remains.","asOf":"2026-11-04","links":[{"label":"Abbosh et al., Nature 2023 (ECLIPSE)","url":"https://doi.org/10.1038/s41586-023-05776-4"},{"label":"Northcott et al., Oncotarget 2024","url":"https://doi.org/10.18632/oncotarget.28565"},{"label":"Parsons et al., Clin Cancer Res 2020","url":"https://doi.org/10.1158/1078-0432.CCR-19-3005"}],"tags":[],"related":["b-dormancy-mrd","b-tumor-heterogeneity","ctdna-mrd-positive"],"cancers":["breast-cancer","breast-hr-positive","tnbc"],"sections":[],"technologies":["mrd-testing","eclipse-subclone-ctdna","liquid-biopsy"],"targets":["trop2","estrogen-receptor"],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":[],"trials":["trak-er","c-trak-tn","serena-6","pada-1"],"people":[],"bottlenecks":[],"keyPapers":["paper-abbosh-tracerx-ctdna-relapse-nature-2023","paper-northcott-next-personal-validation-oncotarget-2024","paper-parsons-mrd-early-breast-cancer-clin-cancer-res-2020","paper-notini-trop2-pan-cancer-multiomic-npj-precis-oncol-2026","paper-coates-sacituzumab-resistance-tacstd2-cancer-discov-2021","paper-abbosh-phylogenetic-ctdna-lung-cancer-nature-2017","paper-fiala-ctdna-early-detection-bmc-med-2018"],"journals":[],"dependsOn":[],"notes":[],"stage":"prevention-detection","severity":"major","metrics":[{"label":"ECLIPSE operating point for calling a subclone (20% of cancer cells, 4 tracked mutations, 10 ng DNA; 94% sensitivity, estimated by simulation from the assay's dilution validation data)","value":"0.1% clonal ctDNA (1,000 parts per million)","source":"Abbosh et al., Nature 2023 (full text)","url":"https://doi.org/10.1038/s41586-023-05776-4"},{"label":"NeXT Personal 95% limit of detection for tumour DNA (all tracked variants pooled; detection threshold 1.67 ppm)","value":"3.45 parts per million","source":"Northcott et al., Oncotarget 2024","url":"https://doi.org/10.18632/oncotarget.28565"},{"label":"Trackable tumour mutations per patient in early breast cancer (whole-exome designed panels)","value":"Median 57 (range 2 to 346)","source":"Parsons et al., Clin Cancer Res 2020","url":"https://doi.org/10.1158/1078-0432.CCR-19-3005"},{"label":"Subclonal mutations on each TRACERx 2017 patient panel (of a median 18 tracked)","value":"Median 6 (range 0 to 16)","source":"Abbosh et al., Nature 2017 (full text)","url":"https://doi.org/10.1038/nature22364"},{"label":"Arithmetic from sourced inputs: expected tumour fragments at one tracked position at 10 parts per million, from 30 ng of cell-free DNA (the top of NeXT Personal's validated 2 to 30 ng; its modal input is about 15 ng, which would halve these counts) at about 1,500 genome copies per 5 ng (Fiala 2018), assuming every molecule is recovered","value":"About 0.09 (9,000 copies x 0.00001)","source":"OnCo arithmetic on Northcott 2024 and Fiala and Diamandis 2018","url":"https://doi.org/10.1186/s12916-018-1157-9"},{"label":"Arithmetic from the same inputs: private mutations needed to expect three fragments (about a 95% chance of seeing at least one) from a subclone in 20% of cancer cells at 10 parts per million","value":"About 167 (3 / (0.09 x 0.2)); about 484 at 3.45 ppm","source":"OnCo arithmetic on Northcott 2024, Fiala and Diamandis 2018 and the ECLIPSE subclone size","url":"https://doi.org/10.1038/s41586-023-05776-4"},{"label":"TRAK-ER: patients with radiological recurrence already present when ctDNA was first detected on the first surveillance test","value":"65.9% (29 of 44)","source":"Cunningham et al., Ann Oncol 2026","url":"https://doi.org/10.1016/j.annonc.2026.10.1292"}],"causes":["Detection pools signal across the whole panel; attributing it to a subclone may use only that subclone's private mutations, which are few.","At 10 parts per million a 30 ng sample holds about 0.09 tumour fragments at any one tracked position (arithmetic above), so per-mutation counts are almost always zero and a ratio of allele fractions cannot be estimated.","Commercial panels choose clonal, high-fraction variants so that they stay positive whatever relapses, which leaves branch mutations off the panel.","Breast tumours carry relatively few mutations to track (median 57 in one study).","A panel built from one biopsy mislabels branch mutations as trunk ones; TRACERx's 'clonal illusion' analysis showed this with a single tumour region.","Oestrogen receptor and TROP2 status are mostly not encoded in mutations: TROP2 expression tracks DNA methylation, and both receptors can change with treatment.","Clonal haematopoiesis can put a single non-tumour molecule at a tracked position, which at these levels would be enough to call a false subclone without matched white-cell sequencing."],"currentEfforts":["ECLIPSE (TRACERx) calls subclones from plasma at 0.1% clonal ctDNA and above, in lung cancer.","Phased-variant sequencing (PhasED-Seq, Foresight CLARITY) puts several mutations on one fragment and reaches 0.7 parts per million in lymphoma.","Whole-genome approaches (MRDetect, MRD-EDGE, AccuScan) add up thousands of sites, though each site is read about once.","Geneplus labels tracked variants as clonal or subclonal in research data; clonal ones were the more prognostic.","Griffin, METER and plasma epigenomic profiling read oestrogen receptor activity from blood at percent-level tumour fractions in metastatic disease.","TROP2 PET (68Ga-MY6349, 68Ga-NOTA-T4) maps TROP2 on visible lesions.","SERENA-6 and PADA-1 act on a resistant subclone (ESR1-mutant) found in blood in advanced disease, where the mutation itself marks the clone and chooses the drug.","COGNITION-GUIDE assigns a genomics-guided drug, including a TROP2 antibody-drug conjugate, to patients with residual cancer after neoadjuvant therapy, by tumour profiling rather than a blood test."],"successLooksLike":"A blood test after treatment reports, with a stated limit, not only that tumour DNA is present but which clone it comes from and whether that clone carries the oestrogen receptor or TROP2, validated against tissue, so the choice between an endocrine drug and a TROP2 antibody-drug conjugate can follow what is actually left."},"route":"/bottlenecks/b-subclone-attribution-residual-disease/","neighbours":{"bottleneck":[{"id":"b-dormancy-mrd","kind":"bottleneck","name":"Dormant cells and minimal residual disease","route":"/bottlenecks/b-dormancy-mrd/"},{"id":"b-tumor-heterogeneity","kind":"bottleneck","name":"Tumour heterogeneity and clonal evolution","route":"/bottlenecks/b-tumor-heterogeneity/"}],"biomarker":[{"id":"ctdna-mrd-positive","kind":"biomarker","name":"ctDNA MRD positivity (molecular residual disease after curative treatment)","route":"/biomarkers/ctdna-mrd-positive/"}],"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":"eclipse-subclone-ctdna","kind":"technology","name":"ECLIPSE (subclone tracking from ctDNA)","route":"/technologies/eclipse-subclone-ctdna/"},{"id":"epic-seq","kind":"technology","name":"EPIC-seq (expression inference from cell-free DNA)","route":"/technologies/epic-seq/"},{"id":"genome-wide-ctdna-mutation-integration","kind":"technology","name":"Genome-wide ctDNA mutation integration (MRDetect, MRD-EDGE)","route":"/technologies/genome-wide-ctdna-mutation-integration/"},{"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":"meter-methylome-subtyping","kind":"technology","name":"METER (methylome-based ctDNA detection and subtyping)","route":"/technologies/meter-methylome-subtyping/"},{"id":"mrd-testing","kind":"technology","name":"MRD / molecular residual disease testing","route":"/technologies/mrd-testing/"},{"id":"plasma-epigenomic-profiling","kind":"technology","name":"Plasma epigenomic profiling (cfChIP-seq)","route":"/technologies/plasma-epigenomic-profiling/"}],"target":[{"id":"estrogen-receptor","kind":"target","name":"Estrogen receptor (ERα)","route":"/targets/estrogen-receptor/"},{"id":"trop2","kind":"target","name":"TROP2","route":"/targets/trop2/"}],"trial":[{"id":"c-trak-tn","kind":"trial","name":"c-TRAK TN","route":"/trials/c-trak-tn/"},{"id":"pada-1","kind":"trial","name":"PADA-1","route":"/trials/pada-1/"},{"id":"serena-6","kind":"trial","name":"SERENA-6","route":"/trials/serena-6/"},{"id":"trak-er","kind":"trial","name":"TRAK-ER","route":"/trials/trak-er/"}],"paper":[{"id":"paper-liu-ga68-nota-t4-breast-eur-j-nucl-med-2026","kind":"paper","name":"[68Ga]Ga-NOTA-T4 PET/CT imaging of TROP2 expression in patients with HER2-negative breast cancer","route":"/key-papers/paper-liu-ga68-nota-t4-breast-eur-j-nucl-med-2026/"},{"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-clark-haystack-mrd-validation-j-mol-diagn-2026","kind":"paper","name":"Highly Accurate Detection of Circulating Tumor DNA for Monitoring Minimal Residual Disease in Solid Tumors: Analytical and Clinical Validation of the Haystack MRD Assay","route":"/key-papers/paper-clark-haystack-mrd-validation-j-mol-diagn-2026/"},{"id":"paper-notini-trop2-pan-cancer-multiomic-npj-precis-oncol-2026","kind":"paper","name":"Pan-cancer multi-omic integration of Trop2 reveals biological determinants and translational implications for ADC therapy","route":"/key-papers/paper-notini-trop2-pan-cancer-multiomic-npj-precis-oncol-2026/"},{"id":"paper-coates-sacituzumab-resistance-tacstd2-cancer-discov-2021","kind":"paper","name":"Parallel Genomic Alterations of Antigen and Payload Targets Mediate Polyclonal Acquired Clinical Resistance to Sacituzumab Govitecan in Triple-Negative Breast Cancer","route":"/key-papers/paper-coates-sacituzumab-resistance-tacstd2-cancer-discov-2021/"},{"id":"paper-liu-geneplus-personalised-mrd-medcomm-2025","kind":"paper","name":"Personalized and Tumor Informed Circulating Tumor DNA Assay for Molecular Residual Disease Monitoring of Solid Malignancies","route":"/key-papers/paper-liu-geneplus-personalised-mrd-medcomm-2025/"},{"id":"paper-abbosh-phylogenetic-ctdna-lung-cancer-nature-2017","kind":"paper","name":"Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution","route":"/key-papers/paper-abbosh-phylogenetic-ctdna-lung-cancer-nature-2017/"},{"id":"paper-cunningham-trak-er-surveillance-ann-oncol-2026","kind":"paper","name":"Prospective circulating tumour DNA surveillance in patients with early high-risk hormone receptor positive, HER2-negative breast cancer in the TRAK-ER study","route":"/key-papers/paper-cunningham-trak-er-surveillance-ann-oncol-2026/"},{"id":"paper-parsons-mrd-early-breast-cancer-clin-cancer-res-2020","kind":"paper","name":"Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer","route":"/key-papers/paper-parsons-mrd-early-breast-cancer-clin-cancer-res-2020/"},{"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-fiala-ctdna-early-detection-bmc-med-2018","kind":"paper","name":"Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection","route":"/key-papers/paper-fiala-ctdna-early-detection-bmc-med-2018/"}],"idea":[{"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/"}],"roadmap":[{"id":"ctdna-tests","kind":"roadmap","name":"ctDNA tests roadmap: from a curiosity in plasma to blood tests that decide treatment","route":"/roadmaps/ctdna-tests/"}]}}