Somatic Mutation
in Solid Tumours

Somatic Mutation and Targeted Therapy in Cancer

The advent of molecular profiling overcame the limitations of morphological solid tumour classification methods. The presence or absence of activated therapeutic driver mutations or gene targets (e.g., BRAF in melanoma, KRAS in colorectal cancer, and EGFR mutation, or ALK/RET/ROS1 rearrangements in non-small cell lung cancers [NSCLC]) is currently employed to guide treatment decisions.

An increasing number of therapies are approved to treat cancers harbouring specific genomic biomarkers. However, not all alterations (variants, copy-number changes, or fusions) in actionable genes confer sensitivity to available drugs.

Genetic profiling in tumours can identify resistant mutations in response to therapy (i.e., BRAF K601E mutation is resistant to the known RAF inhibitors vemurafenib or dabrafenib). Some genetic variants, such as KRAS and TP53 gene mutations, may predict a poor prognosis in cancer.

Next Generation Sequencing at Clinical Labs

Clinical Labs uses a high-quality genomic analysis, such as Next Generation Sequencing (NGS) testing panels designed to investigate multiple relevant actionable mutations in formalin-fixed paraffin-embedded (FFPE) tumour samples.

The efficiency of NGS of DNA and RNA has led to an increasing number of large, targeted multi-gene somatic mutation panels that provide a more efficient, cost- and tissue-saving tumour analysis. They confer greater depth of coverage in selected areas of interest (e.g., hotspot regions with known actionable mutations, rarer mutations and tumour sub-clones), faster turnaround, and more clinically relevant data. However, despite the high sensitivity of NGS, there are limitations and caveats to consider for each test type that vary by biomarker and tumour type.

What Do We Test?

An FFPE sample of 5-10 μm thickness from the tumour tissue. NGS can detect variants using inputs of ~20ng of FFPE-extracted DNA/RNA and from specimens with a tumour cell content less than 50%, for which, when possible, we recommend micro-dissection.

Options of Somatic Mutation Testing Panels:

Comprehensive Oncomine Precision Assay (OPA) Gene Panel (ThermoFisher Scientific)

Local and International Guidelines (NCCN & ASCO) strongly recommend comprehensive multi-gene panel–based genomic sequencing for cancer patients with the goal of identifying rare driver mutations for which effective drugs may already be available. Comprehensive tumour profiling aids clinicians in selecting the most appropriate treatment for their cancer patients, avoiding unnecessary toxic therapy, resistance, or overtreatment, or in suggesting potential synergistic drug combinations (e.g., combination of BRAF and MEK inhibitors in BRAF mutant melanoma)²⁵. This approach is also of valuable use if the tumour is poorly differentiated or of unknown origin.

Lung Cancer (New Medicare Items)

Mutation in EGFR occurs in ~35% of NSCLC patients of East Asian origin and ~16% in Western populations^8,9,10. Studies have confirmed EGFR mutations as a predictive biomarker of treatment response to tyrosine kinase inhibitors (TKIs), Gefitinib, and Erlotinib^11,12. A third-generation EGFR TKI is approved in Australia and is effective in patients with tumours harbouring the resistance p.T790M EGFR mutation (~50-60% of lung cancer patients^13,14,15) following progression on EGFR TKIs^16,17. Detection of KRAS or BRAF mutations (observed in 2-4% of NSCLC patients) is considered a negative predictor of response to anti-EGFR treatment and is associated with poorer survival^20;22,24.

From November 2022, testing for MET exon 14 skipping mutation (3-4%) should be performed for patients with all types of NSCLC to determine the eligibility for MET inhibitors capmatinib and tepotinib²⁵.

RNA Fusion Test Panel in Solid Tumours

RNA-based fusion testing is recommended for patients with no other oncogenic driver detected by DNA. Approximately 5% of NSCLC patients display a rearrangement in ALK (2-5%), while ROS proto-oncogene 1 (ROS1) and RET proto-oncogene (RET) rearrangements are observed in 1-2% of patients. With variable prevalence, the presence of neurotrophic tyrosine receptor kinase (NTRK) fusions provides a rationale for genomic testing for all solid tumours for patients who may be candidates for TRK-inhibitor therapy. NTRK1-3 fusion is described in 90-100% of secretory salivary gland carcinomas (also known as MASC). They may also be present in 2-15% of papillary thyroid carcinomas and in less than 1% of other head and neck tumours²⁵.

Colorectal Cancer (CRC)

Mutations in proto-oncogene KRAS are detected in up to 40% of CRC⁵, which can confer resistance to treatment with EGFR antibodies, and only patients with wild-type KRAS tumours obtain benefit from these agents^6,7. It is, therefore, vital that the KRAS mutation status of a patient’s colorectal tumour can be detected to allow patients access to treatment.

Melanoma

Targeted therapy with Anti-BRAF (vemurafenib or dabrafenib) remains the first-line treatment for melanoma tumours which harbour a BRAF mutation, particularly in Australia¹⁸. In cutaneous melanoma, the BRAF gene is mutated in ~60% of cases and p.V600E (c.1799TA) accounts for more than 90% of BRAF mutations¹⁹. Detection of cKIT mutations may guide the selection of KIT TKIs (imatinib and sunitinib) for melanoma treatment^21,23 and may lead to better outcomes compared to BRAF melanoma patients treated with BRAF inhibitors²³.

Breast Cancer

In breast cancer, oncogenic mutations in PIK3CA or ERBB2 amplification (along with TP53 mutations) occur in ~25% of cases^1,2. As such, mutated PI3K has become an attractive therapeutic target in breast cancer therapy, and a number of agents targeting the PI3K pathway are currently in clinical development²⁵.

Thyroid Cancer

In anaplastic thyroid cancer (ATC), BRAF p.V600E mutation occurs in ~40% of patients with papillary thyroid carcinoma (PTC) and is associated with a more aggressive disease^3,4. Medullary thyroid cancer (MTC) is associated with oncogenic mutations in RET (40-60%) that can be targeted by therapeutic treatments²⁵.

Conclusion

Precision medicine has already transformed cancer care: both common and rare malignancies can be targeted by specific therapies to improve clinical outcomes in patients.

For further information about Somatic Mutation testing available at Clinical Labs, including gene panels, pricing, and request forms, click here.

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