Cell-Free DNA Next-Generation Sequencing Prediction of Response and Resistance to Third-Generation EGFR Inhibitor

• Published in: Clinical lung cancer 2018-11, Vol.19 (6), p.518-530.e7
• Main Authors: Helman, Elena, Nguyen, Minh, Karlovich, Chris A., Despain, Darrin, Choquette, A. Karin, Spira, Alexander I., Yu, Helena A., Camidge, D. Ross, Harding, Thomas C., Lanman, Richard B., Simmons, Andrew D.
• Format: Article
• Language: English
• Subjects: Acrylamides - therapeutic use; Adult; Aged; Aged, 80 and over; Antinematodal Agents - therapeutic use; Carcinoma, Non-Small-Cell Lung - diagnosis; Carcinoma, Non-Small-Cell Lung - drug therapy; Carcinoma, Non-Small-Cell Lung - genetics; Cell-Free Nucleic Acids - analysis; Circulating tumor DNA; ctDNA gene panel; ctDNA sequencing; Drug resistance; Drug Resistance, Neoplasm - genetics; Drug response; EGFR C797S; EGFR T790M; ErbB Receptors - antagonists & inhibitors; ErbB Receptors - genetics; Female; High-Throughput Nucleotide Sequencing; Humans; Lung Neoplasms - diagnosis; Lung Neoplasms - drug therapy; Lung Neoplasms - genetics; Male; Middle Aged; Mutation - genetics; Neoplasm Metastasis; Neoplasm Staging; NSCLC; NTRK fusion; Plasma; Prognosis; Pyrimidines - therapeutic use; Third-generation TKI; Treatment Outcome; Tyrosine kinase inhibitor
• ISSN: 1525-7304; 1938-0690
• DOI: 10.1016/j.cllc.2018.07.008

The genomic alterations driving resistance to third-generation EGFR tyrosine kinase inhibitors (TKIs) are not well established, and collecting tissue biopsy samples poses potential complications from invasive procedures. Cell-free circulating DNA (cfDNA) testing provides a noninvasive approach to identify potentially targetable mechanisms of resistance. Here we utilized a 70-gene cfDNA next-generation sequencing test to interrogate pretreatment and progression samples from 77 EGFR-mutated non-small cell lung cancer (NSCLC) patients treated with a third-generation EGFR TKI. Rociletinib was evaluated in advanced or metastatic (second line or higher) disease with EGFR T790M-positive NSCLC in the TIGER-X (NCT01526928) and TIGER-2 (NCT02147990) studies. Plasma samples were collected at baseline and at the time of systemic progression while receiving rociletinib. The critical exons in 70 genes were sequenced in cfDNA isolated from plasma samples to elucidate a comprehensive genomic profile of alterations for each patient. Plasma-based cfDNA analysis identified 93% of the initial EGFR activating and 85% of the EGFR T790M resistance mutations in pretreatment samples with detectable tumor DNA. Profiling of progression samples revealed significant heterogeneity, with different variant types (eg, mutations, amplifications, and fusions) detected in multiple genes (EGFR, MET, RB1) that may be driving resistance in patients. Novel alterations not previously described in association with resistance to third-generation TKIs were also detected, such as an NTRK1 fusion. cfDNA next-generation sequencing identified initial EGFR activating and secondary T790M resistance mutations in NSCLC patients with high sensitivity, predicted treatment response equivalent to tissue analysis, and identified multiple novel and established resistance alterations. We profiled 77 non–small-cell lung cancer patients with paired baseline and progression blood samples treated with the third-generation EGFR tyrosine kinase inhibitor (TKI) rociletinib using a broad cell-free circulating DNA (cfDNA) next-generation sequencing (NGS) gene panel. We demonstrated a utility of cfDNA NGS to detect EGFR T790M and predict response comparable to tissue-based tests, even at low allele fractions, and we identified resistance mechanisms. Our findings highlight the genomic heterogeneity observed in disease after progression while receiving therapy with a third-generation EGFR TKI.