Evaluation of turnaround times and performance of in-house ChromaCode high-definition PCR compared to send-out next-generation sequencing in non-small cell lung cancer

Abstract

Objective Lung cancer is the leading cause of cancer deaths globally, with 1.8 million deaths annually. Advances in targeted therapy and molecular testing for key mutations in non-small cell lung cancer (NSCLC) have improved survival rates. The benchmark turnaround time for molecular testing is 10 days; however, send-out next-generation sequencing (NGS) can often take 14 to 28 days. Methods The ChromaCode NSCLC assay uses a novel "high-definition polymerase chain reaction (PCR)"technology on digital PCR instruments to detect mutations in 9 genes derived from the most current guidelines provided by the National Comprehensive Cancer Network, as well as separate testing guidelines as a collaborative effort by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. This includes testing for mutations in EGFR, BRAF, KRAS (G12C only), MET and RNA fusions in RET, ROS1, ALK, and NTRK1/2/3. This study retrospectively assessed the feasibility of implementing the assay in a medium-sized academic institution, with a detailed workflow analysis using 58 paraffin-embedded tissue specimens diagnosed as NSCLC. Results Of the 58 samples, 100% concordance was observed between NGS and ChromaCode assays, with all 5 (~8.6%) positive cases - including 1 ROS1, 1 EGFR L858R, 1 KRAS G12C, and 2 NTRK1/2/3 rearrangements - accurately detected. Implementation of the ChromaCode NSCLC assay allows for an average institution-specific turnaround time of 5.01 days, subject to logistical constraints, compared to 10.4 days for send-out next-generation sequencing (U statistic = 153; α = 0.05).