Other solid tumours (CRC, melanoma, ES)

Question 1

How are FFPE samples prepared for testing?

Answer 1

• Macrodissection of tumour region
• Deparaffinised
• Tissue digested
• Formalin bonds broken
• DNA cleaned up
• Results in pure but fragmented DNA

Question 2

What cancers is BRAF commonly mutated in?

Answer 2

66% of melanoma

Also lung, CRC

Question 3

What is the role of BRAF?

Answer 3

Ser/Thr kinase, part of MAPK pathway

Regulates cell growth & proliferation

Question 4

What is the most common BRAF mutation & where is it located?

Answer 4

V600E

Kinase domain

Question 5

What treatment is used for BRAF?

Answer 5

Dabrafenib & Trametinib combination

Question 6

What genes commonly found on somatic cancer panels are also associated with germline cancer predisposition?

Answer 6

TP53 - Li-Fraumeni
PTEN - Cowden
RET - MEN2 & MEN3
RUNX1 - Familial platelet disorder with associated myeloid malignancy

Question 7

Which RAS codons are commonly mutated in CRC?

Answer 7

12, 13, 61

Question 8

What other genetic factor can impact response to EGFR-MAB in CRC?

Answer 8

BRAF mutations cause reduced response even if WT for RAS

Question 9

What genes are routinely tested in sporadic CRC?

Answer 9

KRAS, NRAS, BRAF, PIK3CA

Question 10

When is anti-EGFR therapy ineffective in CRC patients?

Answer 10

In CRC with RAS mutations

Question 11

How does MSI testing inform treatment in CRC?

Answer 11

MSI-H tumours do not benefit from 5-FU chemotherapy - respond better to immunotherapy

Question 12

What two tests suggest sporadic CRC rather than Lynch syndrome?

Answer 12

BRAF V600E and MLH1 promoter hypermethylation - sporadic

Question 13

What abnormality is most commonly seen in CRC? How is it treated?

Answer 13

~90% have EGFR over-expression due to excessive EGF

Treated with EGFR monoclonal antibodies Cetuximab and Panitumumab

Question 14

What genes are tested in GISTs?

Answer 14

KIT and PDGFRA

Question 15

What genes are routinely tested for in adult melanoma?

Answer 15

BRAF, KIT, NRAS

Question 16

What is the significance of NTRK mutations?

Answer 16

Form fusion proteins

Oncogenic drivers of a wide variety of adult and paediatric tumours (tumour agnostic) - common in rare cancers, rare in common cancers

Question 17

What genes are involved in NTRK fusions?

Answer 17

Neurotrophin receptors

NTRK1-3

Question 18

How are NTRK fusions treated?

Answer 18

TRK TKI inhibitors

Larotrectinib and entrectinib

Question 19

What criteria must be met for an NTRK fusion to be reported?

Answer 19

1. Must maintain reading frame
2. Must include the full tyrosine kinase domain of an NTRK gene
3. Must remove the extracellular ligand binding domain of an NTRK gene

Question 20

How is Ewing sarcoma characterised?

Answer 20

Aggressive, highly metastatic cancer of bone and soft tissue

Question 21

When is ES most commonly diagnosed?

Answer 21

Childhood/adolescence

Question 22

What causes ES?

Answer 22

Translocations involving EWSR1 on chr 22

t(11;22) EWSR1-FLI1 is most common (85% of cases)

Question 23

How does the ES oncoprotein cause disease

Answer 23

Acts as aberrant TF & deregulates hundreds of genes

Question 24

Why is WGS used in cancer testing?

Answer 24

1. Identify somatic driver mutations in a tumour - clinically actionable and may affect eligibility for targeted treatment or clinical trials
2. Identify mutations predisposing to cancer - possible implications for management and surveillance of the patient and family

Question 25

What are the considerations for how germline cancer susceptibility variants are followed up/reported?

Answer 25

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

Question 26

What considerations are there around reporting germline variants wrt tumour type?

Answer 26

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

Question 27

What factors determine clinical actionability of germline variants in cancer predisposition genes?

Answer 27

1. Penetrance
2. Severity
3. Availability of clinical management options that mitigate the increased cancer risk (screening, surgical prophylaxis, chemoprophylaxis and lifestyle modification)

Question 28

What is GCR?

Answer 28

Germline conversion rate

Proportion of variants detected in tumour DNA that are germline in origin

High for BRCA1/2, low for TP53, STK11

Question 29

What are the two main methods of NGS testing in solid tumours? Which is more common?

Answer 29

1. Tumour only testing - more common due to cost & logistics
2. Paired tumour-germline testing