Comprehensive plasma genotyping of patients with EGFR positive NSCLC as a monitoring tool for therapy response and disease progression.
Authors: Shafi Gowhar , Behel Vichitra , Bharade Atul , Bhonde Mandar , Patil Vijay Maruti , Noronha Vanita , Chougule Anuradha , Chandrani Pratik , Kaushal Rajiv Kumar , Prajapati Sangeeta , Ratnaparkhi Mrunal , Hariramani Kanchan , Mobeen Fauzul , Basavalingegowda Madhura , Uttarwar Mohan , Bose Chirantan , Prabhash Kumar , Khandare Jayant 
Published: June 2023

e20598

Background: Targeted therapy against molecular drivers has revolutionized the NSCLC standard of care. EGFR activating mutations (mEGFR) are most prominent in Asian NSCLC patients and can benefit from tyrosine kinase inhibitor (TKi) therapy. NCCN guidelines recommend screening lung tumors for detecting mEGFR as a standard of care for TKi inhibitor therapy. However, a significant number of patients with mEGFR do not respond well to TKi due to naturally occurring or therapy-induced TKi blunting mutations. Small gene panels may fail to detect concomitant rare mutations, e.g genomic instability. We longitudinally monitored mEGFR dynamics and the presence of cooccurring clinically important mutations using a comprehensive gene panel in NSCLC patients. Methods: We retrospectively analyzed outcomes from the plasma genotyping of 150 samples from 25 mEGFR-positive NSCLC pts on TKi therapy. For NGS, ctDNA was isolated from longitudinally collected plasma samples (at diagnosis, and during Tx including PD). Libraries prepared using a custom-designed comprehensive gene panel OncoIndx to target 600 cancer-relevant exons, including MSI and HRR pathway genes, were target captured and sequenced in pair-end mode on Illumina platform Nextseq2000. Variant calling was performed using an in-house developed bioinformatics pipeline based on GATK environment. Results: ex 19 deletion variant was the most frequent (35 %) mEGFR followed by L858R (20 %) and T790M (10 %). Rest 10 % had other mutations, including TP53, KRAS, TGFBR1 and PTEN and 25 % of the longitudinal samples did not show any mutations. In 40 % of patients increase in mEGFR vaf correlated with the clinical progression. Surprisingly, these patients had either TP53, RB1 or TGFBR1 variants cooccurring with mEGFR. For the remaining patients, we did not observe a clear temporal correlation with mEGFR vaf. This was corroborated well by the absence of any TKi blunting mutations among these patients. T790M variants were detected only at the progression onset and were absent at earlier time points. MGA, TP53, and RB1 variants were detected along high mEGFR vaf in 10 % of patients around the time of clinical progression. At the genomic scale, TMB scores were low and did not vary longitudinally among the pts. HRD and LOH sores were high and correlated well in patients with mEGFR cooccurrence along variants such as KRAS, TP53, PTEN, and BAP1. Conclusions: Comprehensive plasma genotyping identified cooccurring key drivers that correlated with the clinical progression. Their presence may suggest the blunting effect of TKi and early progression. The patient with high genome instability scores may benefit from HRR inhibitor +TKi combination therapy in EGFR-positive pts. A small patient cohort limits the interpretation of this data and warrants further investigation through clinical trials.