OnCo

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.

Light up a product:
Clonal evolution & minimal residual diseaseA 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 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.

Light up a product:
Ageing HSCs activates DNMT3A, TET2, ASXL1, PPM1D, TP53DNMT3A, TET2, ASXL1, PPM1D, TP53 activates CHIP clone (VAF ≥2%)CHIP clone (VAF ≥2%) activates Therapy-related MDS/AMLCHIP clone (VAF ≥2%) activates Inflammation → cardiovascular diseaseCHIP clone (VAF ≥2%) activates False-positive ctDNAChemo, PARPi, radioligands select activates CHIP clone (VAF ≥2%)Ageing HSCsAgeing HSCsDNMT3A, TET2, ASXL1, PPM1D, TP53: 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.DNMT3A, TET2, ASXL1, PPM1…CHIP clone (VAF ≥2%)CHIP clone (VAF ≥2%)Therapy-related MDS/AMLTherapy-related MDS/AMLInflammation → cardiovascular diseaseInflammation → cardiovasc…False-positive ctDNAFalse-positive ctDNAChemo, PARPi, radioligands selectChemo, PARPi, radioligand…activatesinhibitsdruggable target (click)hit by selected productescape route
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.

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.

Light up a product:+36 more via the Connected tab
Mitotic errors, WGD activates Chromosomal instabilityChromosomal instability activates Aneuploidy / karyotype heterogeneityAneuploidy / karyotype heterogeneity activates Clonal evolution, resistanceChromosomal instability activates Micronuclei → cytosolic DNAMicronuclei → cytosolic DNA activates cGAS-STINGChromosomal instability activates ecDNA oncogene amplificationecDNA oncogene amplification activates Clonal evolution, resistanceAneuploidy / karyotype heterogeneity activates Dependencies: KIF18A, SAC, BCL-XLTP53 loss permits activates Chromosomal instabilityMitotic errors, WGDMitotic errors, WGDChromosomal instabilityChromosomal instabilityAneuploidy / karyotype heterogeneityAneuploidy / karyotype he…Micronuclei → cytosolic DNAMicronuclei → cytosolic D…cGAS-STINGcGAS-STINGecDNA oncogene amplification: A growth receptor that is mutated in some lung cancers and overproduced in others; the first great success of targeted pills.ecDNA oncogene amplificat…Clonal evolution, resistanceClonal evolution, resista…Dependencies: KIF18A, SAC, BCL-XLDependencies: KIF18A, SAC…TP53 loss permits: 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.TP53 loss permitsactivatesinhibitsdruggable target (click)hit by selected productescape route
Chromosomal instability & aneuploidyMost 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.

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.

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.

How tumours escape

Records tied to this stage that describe resistance, evasion or tolerance. The resistance atlas lists the routes class by class.

Ideas that attack the escape
Papers on the escape

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?
Ideas 94 linked ideas

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.

18 more papers in the key-papers index →

How this page is built: the stage is one entry in a curated atlas (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.