127P - EGFR copy number aberrations detected in cfDNA from advanced NSCLC patients

Abstract

Background: Copy number aberrations (CNA) in the epidermal growth factor receptor (EGFR) represent a mechanism of tyrosine kinase activation and oncogenic signaling in advanced non-small cell lung cancers (NSCLC). High copy number gains (CNG) may predict TKI sensitivity but when acquired are postulated to reflect resistance. Treatment with monoclonal antibodies may have a role and therefore CNA integration in molecular diagnostics is potentially important. Methods: Cell free (cf) DNA was from extracted from NSCLC patients undergoing treatment with EFGR-TKIs. A validated Liquid Biopsy Sequencing (LB-Seq) method for hybrid capture followed by ultra deep sequencing (> 20,000X) evaluated coding exons of KRAS, NRAS, BRAF, PIK3CA, and EGFR (18 kb). Subsequent filtering of mutation calls using a novel algorithm enabled detection of tumor-derived fragments at concentrations down to 0.2%. EGFR CNAs were assessed using a modified version of the VisCap algorithm. Mutation calls were compared to tissue biospy results for EGFR mutations. Results: Targeted sequencing has been performed on 12 samples to date: 10 patients with classical EGFR mutations in L858R and del19, 1 with an exon 20 insertion and 1 with an exon 18 G718X mutation. All patients had progressed on at least one EGFR-TKI. % mutant reads ranged from 0.25% to 33%. EGFR CNGs were detected in 3 patients: 1 patient with T790M+ve disease confirmed in both tissue and cfDNA was found to have a co-occurring BRAF mutation (p.33_34insGA). The remaining 2 patients’ tissue samples tested negative for T790M; T790M was detected in cfDNA in 1 patient, who is currently receiving osimertinib, and in the other patient rapid progression on gefitinib occurred with an EGFR-G719X mutation. Copy number losses were detected in 2 patients. 2 of 6 patients with EGFR-T790M positive tissue were confirmed in cfDNA, the remaining 4 negative results were verified by ddPCR. An intronic variant of unknown significance (c.747 + 9C>T), not covered in tissue testing, was also captured in cfDNA. Conclusions: Copy number aberrations in EGFR can be detected from targeted sequencing of cfDNA in patients with EGFR mutated NSCLC. Longitudinal evaluation in patients receiving EGFR-TKIs may provide insights into mechanisms of resistance. Legal entity responsible for the study: Natasha Leighl Funding: None Disclosure: N.B. Leighl: Research funding (institution): Novartis. Travel/honoraria: AstraZeneca, Merck Sharp Dohme, Pfizer, Bristol-Myers Squibb. All other authors have declared no conflicts of interest.