Clonal evolution
A tumour is a population, not a clone. Subclones compete, therapy selects the fittest, and relapse is usually a minority that was there all along. Chromosome shuffling speeds evolution; blood tests can follow it in real time.
Diagram
Pick a product above a diagram to see the nodes it hits and the escape routes below the block. Hover or tap any node or arrow for what it is; every node opens its target, glossary entry or the pathway page. Violet boxes are druggable targets.
Clonal evolution is like weeding a field with one herbicide year after year: the field fills with the one weed that shrugs it off. Rotating herbicides and leaving some susceptible weeds to crowd out the resistant ones is the evolutionary alternative.
Weeds in the blood's seed bank. Harmless individually, they spread with age and after chemical sprays, some turn into leukaemia, and their DNA litters the blood, so a test for tumour DNA can mistake weeds for cancer.
Chromosomal instability is a library that reshuffles and duplicates random shelves every night. Most rearrangements are useless, some ruin the building, but occasionally one yields a book the librarian needs to survive a new rule, and the mess itself keeps the fire alarms twitching.
What happens
In plain words, then the glossary entries the stage rests on. Chapter 2, How a cell becomes cancer: Cancer is evolution inside a body.
A tumour is a population, not a clone. Subclones compete, therapy selects the fittest, and relapse is usually a minority that was there all along. Chromosome shuffling speeds evolution; blood tests can follow it in real time.
Clonal evolution & minimal residual disease. A tumour is a population that evolves by natural selection. Treatment kills the sensitive cells and selects the rest, which is why resistance is the rule; measuring the surviving population (MRD) and adapting therapy is the counter-strategy.
Clonal haematopoiesis (CHIP). As we age, blood stem cells with cancer-like mutations quietly expand in most people. These clones raise leukaemia and heart disease risk, are accelerated by chemotherapy, and confuse blood tests for cancer DNA.
Chromosomal instability & aneuploidy. Most cancers have the wrong number of chromosomes and keep shuffling them at every division. This chaos fuels evolution and drug resistance, but it also stresses the cell and can trigger immune alarms, a double edge that researchers are trying to exploit.
The molecular players
The proteins and genes at this stage, with their role and how many products act on each. Listed players come from the atlas; drawn players sit as nodes in the diagrams above.
TP53 is the 'guardian of the genome', broken in half of all cancers. Fixing it directly has so far defeated every attempt, so drugs exploit what its loss makes cancers depend on.
A growth receptor that is mutated in some lung cancers and overproduced in others; the first great success of targeted pills.
Where medicines act
Products grouped by the node they hit, most advanced first, with the cancers an approved product is linked to. Pick one above the diagram to see it light up.
- SelinexorApprovedEndometrial cancerMultiple myelomaDiffuse large B-cell lymphoma
- OSE2101Phase 3
- KRT-232Phase 2
- EprenetapoptNegative
- AfatinibApprovedNon-small-cell lung cancerEGFR-mutated non-small-cell lung cancerHER2-mutant non-small-cell lung cancer
- AmivantamabApprovedNon-small-cell lung cancerEGFR-mutated non-small-cell lung cancerMET exon 14 and MET-amplified non-small-cell lung cancer
- AumolertinibApprovedNon-small-cell lung cancer
- CetuximabApprovedColorectal cancerHead and neck squamous cell carcinomaRecurrent or metastatic head and neck squamous cell carcinoma
- Cetuximab sarotalocanApprovedHead and neck squamous cell carcinoma
- cobas EGFR Mutation Test v2ApprovedNon-small-cell lung cancer
- DacomitinibApprovedNon-small-cell lung cancer
- EncorafenibApprovedColorectal cancerMelanomaNon-small-cell lung cancer
- +42 more at EGFR →
- SignateraEstablished
How tumours escape
Records tied to this stage that describe resistance, evasion or tolerance. The resistance atlas lists the routes class by class.
- early clinicalresearchA multi-cancer platform trial of adaptive (dose-holiday) therapy
Instead of hitting a tumour with the maximum dose until it stops working, adjust the dose to keep the tumour small and let drug-sensitive cells suppress resistant ones. Test this properly across several cancers.
- early clinicalphilanthropyA national rapid research autopsy network for end-stage cancer
When patients who agreed in advance die of cancer, sampling every tumour within hours reveals how the disease evolved and escaped every drug. Few hospitals can do this today.
- early clinicaldataA national residual-disease weather service: serial blood tests for every curatively treated patient, pooled
After surgery or curative treatment, everyone gets regular blood tests for leftover cancer DNA, and the pooled results power forecasts of who will relapse and trials of acting early.
- early clinicalresearchA test to tell true oligometastatic disease from hidden widespread spread
Some people have only a few sites of spread and can be treated at each one; others have further deposits not yet visible, and counting lesions cannot tell them apart. A signature built from tumour DNA levels, microRNA classifiers and clonal diversity across lesions would define the biology and spare futile ablation.
- early clinicalresearchAutonomous closed-loop adaptive therapy driven by blood tests and evolutionary models
Rather than giving the same dose until the cancer grows, measure tumour DNA in blood every few weeks and let a validated algorithm raise, lower, pause or switch drugs to keep the cancer suppressed for longer.
- early clinicalclinicBiopsy the one lesion that is growing while the others shrink
When a scan shows most tumours shrinking but one growing, that odd lesion holds the escape mechanism. Sampling it, and treating it locally, should be routine.
- early clinicalctDNA-guided adjuvant therapy in stage II-III melanoma
Most stage II patients never relapse, yet all are offered a year of immunotherapy. Use a blood test to treat only those with detectable residual disease.
- early clinicalctDNA-guided switching among FGFR inhibitors
Track FGFR2 resistance mutations in blood and switch to the next-generation inhibitor that still covers them, before the scan shows progression.
- early clinicalregulatorFormally qualify tumour-DNA blood tests as a surrogate endpoint for adjuvant trials
If a blood test reliably shows whether cancer will come back after surgery, trials could use it instead of waiting years for relapse. Regulators have a process to bless such a test; oncology should use it.
- early clinicalpayerFund a biopsy at progression, every time, as standard care
When a treatment stops working, the tumour is rarely re-sampled, so nobody learns why. Paying for a biopsy at that moment would build the missing map of resistance.
- 2026translationalc-TRAK TN analysis: tissue-free versus tumour-informed ctDNA assays for residual disease in early triple-negative breast cancerJAMA Oncology
- 2025rctChildren's Oncology Group AALL1731: blinatumomab added to chemotherapy for children with standard-risk B-cell ALLNew England Journal of Medicinechanged practice
- 2023observationalGALAXY: tumour DNA in blood four weeks after bowel cancer surgery predicts relapse tenfoldNature Medicine
- 2023translationalTRACERx 421: the full-cohort picture of how lung cancer evolves and which subclones drive relapseNature
- 2020observationalCancer therapy shapes the fitness landscape of clonal hematopoiesisNature Genetics
- 2018rctMURANO: two years of venetoclax plus rituximab versus chemo-immunotherapy in relapsed CLLNew England Journal of Medicinechanged practice
Measured by
Biomarkers, tests and assays in the corpus that read this stage in a patient.
Open questions
What is not known at this stage: the atlas's own questions, the bottlenecks it bears on, and the ideas in the corpus that try to answer them.
- Can evolution be steered (adaptive therapy) rather than only outrun?
- How early in life do the first driver clones arise, and could they be intercepted?
- being tested at scalepolicyA national platform trial that every ctDNA-positive patient can join
Blood tests can now find leftover cancer months before scans, but most patients who test positive have nothing to enrol in. One standing trial per country would fix that.
- being tested at scalectDNA-guided adjuvant therapy as the default in stage II-III colon cancer
Use a blood test after surgery to decide who gets chemotherapy: spare the negatives, and find something that actually works for the positives.
- being tested at scaleMolecular-class-directed adjuvant therapy in endometrial cancer
Give adjuvant treatment by the tumour's molecular class rather than by stage and grade: nothing for POLE-mutated, immunotherapy for MMRd, chemotherapy plus targeted agents for p53-abnormal, hormones for NSMP.
- early clinicalresearchA biomarker-directed trial of vitamin D after surgery for digestive tract cancers
A Japanese trial found vitamin D supplements did not help everyone after digestive cancer surgery, but appeared to help a subgroup identified by a tumour marker. That subgroup deserves its own trial.
- early clinicaldataA clone report from blood at every treatment cycle
Blood tests can already detect tumour DNA. Reporting which sub-populations of the tumour are growing or shrinking, cycle by cycle, would turn the test into an evolution monitor.
- early clinicalresearchA short pre-surgery drug window as the default early test of new agents
Between diagnosis and surgery there are usually a few weeks. Giving a new drug in that window and comparing the tumour before and after surgery shows whether it hits its target in real people, quickly and cheaply.
- early clinicalregulatorAn annual blinded shoot-out for liquid biopsy tests
Once a year, send the same blinded blood samples to every company selling a tumour-DNA test and publish how each performed.
- early clinicalresearchAn independent programme that validates surrogate endpoints, setting by setting
Trials often measure a stand-in for survival, such as time until the cancer grows on scans. An independent body would test, for each cancer and treatment type, whether the stand-in actually predicts survival, and publish the answer.
- early clinicalindustryAn open-science consortium on the undruggable drivers, open until a candidate
Companies and public funders would pool money and scientists to crack the hardest cancer proteins, such as MYC and mutant p53, sharing everything openly until there is a real drug candidate, then competing on the final product.
- early clinicalresearchBlock the recycling that keeps dormant cells alive
Sleeping cancer cells survive by recycling their own contents. An old malaria drug blocks that recycling and is being tested in people with no visible cancer but detectable residual cells.
84 more ideas are linked to this stage's pathways, targets and terms; see the rankings →
Key evidence
Papers in the corpus tied to this stage's pathways, targets and terms, newest first.
- 2026translationalc-TRAK TN analysis: tissue-free versus tumour-informed ctDNA assays for residual disease in early triple-negative breast cancerJAMA Oncology
- 2025rctAMPLIFY: fixed-duration acalabrutinib plus venetoclax, with or without obinutuzumab, versus chemo-immunotherapy in fit CLL patientsNew England Journal of Medicinechanged practice
- 2025rctChildren's Oncology Group AALL1731: blinatumomab added to chemotherapy for children with standard-risk B-cell ALLNew England Journal of Medicinechanged practice
- 2025rctIMvigor011: using a blood test for leftover cancer to decide who gets immunotherapy after bladder surgeryNew England Journal of Medicinechanged practice
- 2024rctECOG-ACRIN E1910: adding blinatumomab to chemotherapy for adults with B-cell ALL already in MRD-negative remissionNew England Journal of Medicinechanged practice
- 2024rctMARIPOSA: amivantamab plus lazertinib versus osimertinib as first treatment for EGFR-mutated lung cancerNew England Journal of Medicinechanged practice
- 2023observationalGALAXY: tumour DNA in blood four weeks after bowel cancer surgery predicts relapse tenfoldNature Medicine
- 2023translationalTRACERx 421: the full-cohort picture of how lung cancer evolves and which subclones drive relapseNature
- 2022rctDYNAMIC: a blood test safely halved chemotherapy use after surgery for stage II colon cancerNew England Journal of Medicinechanged practice
- 2020rctADAURA: three years of osimertinib after surgery for EGFR-mutated lung cancerNew England Journal of Medicinechanged practice
- 2020observationalCancer therapy shapes the fitness landscape of clonal hematopoiesisNature Genetics
- 2020observationalDETECT-A: a blood test plus PET-CT found treatable cancers in 10,000 women with no symptomsScience
src/data/mechanics-atlas.ts). Players, medicines, escape routes, tests, ideas and papers are resolved from the knowledge graph at build time through the stage's pathways, targets and terms, so every item here has its own page and sources. Where a section is missing, the corpus has no record tied to the stage yet. Nothing here is medical advice; see about and methodology. Stage 2.3 of 56.