Early detection of competing resistance mutations using plasma next-generation sequencing (NGS) in patients (pts) with EGFR-mutant NSCLC treated with osimertinib.

Abstract

11529 Background: In pts with EGFR+ NSCLC, genotyping of plasma cell-free DNA (cfDNA) has become a routine option for non-invasive detection of EGFRT790M. We hypothesized that serial NGS of cfDNA would allow early detection of co-existent resistance mutations during osimertinib treatment. Methods: Serial plasma samples were collected from pts with advanced EGFR+ NSCLC and T790M+ acquired resistance treated with osimertinib. Up to 4 specimens were analyzed, blinded to tumor genotype: baseline, initial 2 follow-ups, and progression. Plasma NGS was performed using enhanced tagged amplicon sequencing of hotspots and coding regions from 36 genes. Diagnostic accuracy was compared to tumor genotype (including NGS when available) and droplet digital PCR (ddPCR) of cfDNA. Results: 94 specimens from 26 pts underwent plasma NGS. Studying 26 baseline specimens, plasma NGS was more sensitive than ddPCR for known EGFR driver mutations (100% vs 88.5%). In 8 pts with pretreatment tumor NGS, 5 of 6 TP53 mutations were detected; one plasma positive/tissue negative result was seen across 36 genes, a PIK3CA mutation (0.6% AF) which was confirmed using ddPCR (99.6% specificity). Quantitative concordance of AF compared to ddPCR was high (R = 0.94). 21 pts had detectable EGFR driver mutations at resistance. Among 6 pts with maintained T790M, 4 acquired C797S and 2 of these additionally acquired low level KRAS mutations (G13D, Q61K). Among 15 pts with loss of T790M, 7 had competing non- EGFR alterations identified: MET amp, PIK3CA E545K, BRAF V600E (n = 2), HER2 amp, KRAS G12S, and FGFR1 amp. Resistance mutations detected at AF > 0.3% were confirmed with ddPCR. In 3 pts, a competing resistance mutation (1 KRAS, 2 BRAF) could be detected in plasma NGS pretreatment and reemerged as putative drivers at time of resistance. Conclusions: In this retrospective blinded validation, tagged amplicon-based plasma NGS was more sensitive than ddPCR with high specificity and quantitative concordance. In a subset of cases, serial plasma NGS can detect emergence of competing resistance mutations, creating an opportunity for the study of osimertinib-based targeted therapy combinations.