Other solid tumours (CRC, melanoma, ES) Flashcards
How are FFPE samples prepared for testing?
- Macrodissection of tumour region
- Deparaffinised
- Tissue digested
- Formalin bonds broken
- DNA cleaned up
- Results in pure but fragmented DNA
What cancers is BRAF commonly mutated in?
66% of melanoma
Also lung, CRC
What is the role of BRAF?
Ser/Thr kinase, part of MAPK pathway
Regulates cell growth & proliferation
What is the most common BRAF mutation & where is it located?
V600E
Kinase domain
What treatment is used for BRAF?
Dabrafenib & Trametinib combination
What genes commonly found on somatic cancer panels are also associated with germline cancer predisposition?
TP53 - Li-Fraumeni
PTEN - Cowden
RET - MEN2 & MEN3
RUNX1 - Familial platelet disorder with associated myeloid malignancy
Which RAS codons are commonly mutated in CRC?
12, 13, 61
What other genetic factor can impact response to EGFR-MAB in CRC?
BRAF mutations cause reduced response even if WT for RAS
What genes are routinely tested in sporadic CRC?
KRAS, NRAS, BRAF, PIK3CA
When is anti-EGFR therapy ineffective in CRC patients?
In CRC with RAS mutations
How does MSI testing inform treatment in CRC?
MSI-H tumours do not benefit from 5-FU chemotherapy - respond better to immunotherapy
What two tests suggest sporadic CRC rather than Lynch syndrome?
BRAF V600E and MLH1 promoter hypermethylation - sporadic
What abnormality is most commonly seen in CRC? How is it treated?
~90% have EGFR over-expression due to excessive EGF
Treated with EGFR monoclonal antibodies Cetuximab and Panitumumab
What genes are tested in GISTs?
KIT and PDGFRA
What genes are routinely tested for in adult melanoma?
BRAF, KIT, NRAS
What is the significance of NTRK mutations?
Form fusion proteins
Oncogenic drivers of a wide variety of adult and paediatric tumours (tumour agnostic) - common in rare cancers, rare in common cancers
What genes are involved in NTRK fusions?
Neurotrophin receptors
NTRK1-3
How are NTRK fusions treated?
TRK TKI inhibitors
Larotrectinib and entrectinib
What criteria must be met for an NTRK fusion to be reported?
- Must maintain reading frame
- Must include the full tyrosine kinase domain of an NTRK gene
- Must remove the extracellular ligand binding domain of an NTRK gene
How is Ewing sarcoma characterised?
Aggressive, highly metastatic cancer of bone and soft tissue
When is ES most commonly diagnosed?
Childhood/adolescence
What causes ES?
Translocations involving EWSR1 on chr 22
t(11;22) EWSR1-FLI1 is most common (85% of cases)
How does the ES oncoprotein cause disease
Acts as aberrant TF & deregulates hundreds of genes
Why is WGS used in cancer testing?
- Identify somatic driver mutations in a tumour - clinically actionable and may affect eligibility for targeted treatment or clinical trials
- Identify mutations predisposing to cancer - possible implications for management and surveillance of the patient and family
What are the considerations for how germline cancer susceptibility variants are followed up/reported?
ACMG list of 28 genes but variability in data on penetrance and efficacy of clinical intervention
ESMO list 40 genes where follow up should be considered, but dependent on a) tumour type, b) level of caution, c) age on patient
7 ‘most actionable’ genes (BRCA1, BRCA2, MLH1, MSH2, MSH6, PALB2, RET) with best data on penetrance and efficacy of interventions - follow up regardless of tumour type
33 genes in high & standard actionability groups - follow up only in associated tumour types
What considerations are there around reporting germline variants wrt tumour type?
Should patient’s current tumour type determine whether variant is reported?
No - in routine germline testing via clinical genetics, only variants in genes associated with a particular cancer type are reported
Yes - any result providing information about future cancer risk or familial risk would be of interest to a cancer patient, doesn’t matter if it didn’t contribute to their current cancer
What factors determine clinical actionability of germline variants in cancer predisposition genes?
- Penetrance
- Severity
- Availability of clinical management options that mitigate the increased cancer risk (screening, surgical prophylaxis, chemoprophylaxis and lifestyle modification)
What is GCR?
Germline conversion rate
Proportion of variants detected in tumour DNA that are germline in origin
High for BRCA1/2, low for TP53, STK11
What are the two main methods of NGS testing in solid tumours? Which is more common?
- Tumour only testing - more common due to cost & logistics
- Paired tumour-germline testing
