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Gastrointestinal stromal tumours are defined by activating alterations in KIT or PDGFRA. Which gene, and which exon within it, carries direct consequences. A minority lack both, and that group is biologically distinct and has its own separate workup, including a germline question.
Also called GIST.
Start here
GIST is the disease where genotype is not supplementary information but the core of the diagnosis, and where the specific mutation, down to the exon, shapes the entire treatment discussion.
Gastrointestinal stromal tumours are defined by activating alterations in KIT or PDGFRA. Which gene, and which exon within it, carries direct consequences. A minority lack both, and that group is biologically distinct and has its own separate workup, including a germline question.
01Before any molecular question
Usually established first: tumour site, size and mitotic rate, which together determine risk of recurrence, and whether the tumour is resectable. Immunohistochemistry supports the diagnosis, but genotyping is what completes it.
Usually already established
02
The divisions below are not labels. Each one changes what the treatment discussion is actually about.
KIT-mutant
The large majority. Exon 11 and exon 9 alterations behave differently from each other and the distinction is consequential.
PDGFRA-mutant
A distinct group. The D842V variant in particular behaves very differently from other PDGFRA alterations, which is one of the clearest examples in oncology of a single amino acid changing the entire discussion.
SDH-deficient
Wild-type for KIT and PDGFRA. More common in younger patients and in gastric tumours, and associated with inherited syndromes.
Other wild-type
Includes NF1-associated and BRAF-altered tumours. Each has its own implications.
03What is discussed
KIT exon 11 alterations are the most common, followed by exon 9. PDGFRA alterations account for a smaller share, and the D842V variant within it is specifically important because it responds differently from the rest. Tumours wild-type for both are grouped as KIT and PDGFRA wild-type, and are further characterised by SDH deficiency, NF1 alteration, BRAF alteration or fusions. Genotyping is considered part of characterising the disease rather than an optional addition, and the exon-level detail is what matters, not simply the gene name.
KIT
Exon-level detail matters. Exon 11 and exon 9 are not interchangeable findings.
PDGFRA
The D842V variant behaves differently from every other PDGFRA alteration.
SDHA, SDHB, SDHC, SDHD
Deficiency defines a distinct group, and raises an inherited-risk question.
NF1
Associated with a distinct wild-type subgroup.
BRAF
Found in a small number of wild-type tumours.
This is not an exhaustive list, and which markers are relevant depends on the individual case. Not every marker listed is assessed in every patient.
04What is tested, and from what
Genotyping is discussed for essentially all GIST where systemic treatment is being considered, and for high-risk tumours after surgery. It is not a late-line test. The report should state the exon, not simply the gene, because the exon carries the consequence. For wild-type tumours, additional testing for SDH deficiency and other alterations follows.
SDH-deficient GIST is associated with Carney-Stratakis syndrome and with hereditary paraganglioma and phaeochromocytoma syndromes. NF1-associated GIST occurs in neurofibromatosis type 1. Familial GIST syndromes with germline KIT alterations exist but are rare. A wild-type genotype, particularly in a younger patient, is a recognised prompt for germline evaluation.
Cancer genetics and hereditary riskPlasma testing is used in advanced GIST, particularly at progression, to detect acquired resistance alterations. Because resistance often emerges as several different secondary mutations in different lesions at once, plasma can capture a broader picture than a biopsy of one site.
More on ctDNA monitoring05The timing question
Testing that arrives after the decision it was meant to inform has already been made is a common and avoidable problem. This is the sequence in which molecular information tends to become relevant.
06Take these to your team
When a decision is being made
Questions worth raising with a treating team.
At progression, recurrence or resistance
The molecular picture at diagnosis is not always the molecular picture later.
07What shapes eligibility
Trial eligibility is written in precise genotype terms, frequently down to the exon and sometimes the specific variant. Prior treatment line is also central. GIST is a disease where an imprecise genomic report can prevent an otherwise eligible patient from being matched.
| Term | What it means |
|---|---|
| Exon | A specific segment of a gene. In GIST, which exon is altered changes what the alteration means. |
| Mitotic rate | How many cells are dividing, counted by a pathologist. Part of recurrence risk assessment. |
| Wild-type GIST | A tumour without KIT or PDGFRA alteration. Biologically distinct and requiring a different workup. |
| Secondary mutation | A new alteration in the same gene that arises under treatment and causes resistance. |
These are the services most often relevant to this cancer. Which of them applies is a clinical question, not an automatic one.
This entry is educational. It describes what is commonly discussed in this cancer, not what should happen for any individual. Which of it applies depends on the specific diagnosis, stage, prior treatment and the person themselves. Nothing here is a recommendation, and no list of biomarkers here is exhaustive. Decisions belong with a treating team who know the whole case.
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