Genetic biomarkers of chemotherapy response and resistance in lung cancer patients

In advanced lung cancer, careful selection of systemic anticancer therapy (SACT) is of vital importance. Companion biomarkers can optimise treatment selection, such as with the use of EGFR tyrosine kinase inhibitors (EGFR TKi) in patients with EGFRmut+ve adenocarcinoma of the lung. There is increasing interest in mutation detection and monitoring, in circulating cell free tumour DNA (ctDNA). This thesis reports that Next Generation Sequencing (NGS) with software VarScan with Annovar, can detect mutations at a 10-fold lower alternate allele frequency compared to alternative software available through Ion Torrent, but with a greater number of low level ‘false positive’ genetic variants. Droplet digital PCR (ddPCR) is more sensitive than NGS, successfully detecting mutations as low as 0.1% alternate allele frequency. Lung cancer mutations were successfully detected in small, formalin-fixed, paraffin embedded (FFPE) tumour tissue samples, and ctDNA, from lung cancer patients, using the same NGS technique, with a commercially available, targeted 50 gene cancer hotspot panel. Results are compared to a custom 22-gene panel. The kinetics of mutation levels in serial ctDNA samples is reported in a case series. In EGFRmut+ve lung adenocarcinoma patients treated with EGFR TKi, decreases in levels of mutant EGFR in ctDNA were observed. Levels remained undetectable during periods of disease control/stability, and increases in mutant EGFR in ctDNA were seen several weeks before the diagnosis of clinical or radiological disease progression. NGS of ctDNA during disease progression revealed novel genetic mutations that were not detected in the original tumour biopsy, and may inform subsequent treatment options. Similar ctDNA kinetics was seen in advanced SCLC patients treated with SACT. The levelof mutated ctDNA, at diagnosis may be an independent prognostic biomarker, using a cut-off of 44.3% alternate allele frequency. SCLC patients who experienced a greater absolute decrease in mutant ctDNA had a poorer prognosis