Project IOTA (input optimization for tissue-based assays): Improving turnaround time (TAT) of mutation profiling for non-small cell lung cancer (NSCLC).

Abstract

e23142 Background: Next-generation sequencing (NGS)–based biomarker testing is essential for guiding therapy in NSCLC, but limited tissue availability and reliance on formalin-fixed paraffin-embedded (FFPE) specimens can result in test failure and long turnaround times. To address these challenges, we developed Project IOTA, an agile, multidisciplinary workflow that streamlines specimen processing at the time of biopsy in parallel for both diagnostic and molecular pathology. This study aimed to evaluate the concordance and TAT of the NGS results obtained by IOTA workflow process versus standard of care (SOC) commercial NGS testing. Methods: This IRB-approved prospective study, funded by the National Comprehensive Cancer Network (NCCN), enrolled patients with known or suspected lung cancer at Roswell Park who were undergoing routine tissue biopsy for biomarker testing and/or histologic confirmation or disease staging. During the biopsy procedure, upon diagnosis of NSCLC from rapid on-site cytology evaluation for tissue adequacy, one of the fresh tissue needle passes that would have been otherwise incorporated into SOC FFPE processing was instead sent directly for mutation profiling using a custom Thermo Fisher NGS panel. The primary endpoint was an assessment of concordance of IOTA-based NGS testing results for genes with therapeutic relevance in NSCLC genes (ALK, BRAF, EGFR, HER2, KRAS, MET, NTRK, RET, ROS1) with SOC NGS. Secondary endpoints included a comparison of test failure rates and differences in TAT. Results: 80 biopsies were performed in 72 patients (7 patients underwent at least 1 repeat biopsy either due to disease progression or initial biopsies being negative for malignancy but with high index of suspicion for cancer). NSCLC was identified in 64 biopsies (remaining were small cell lung cancer n = 4, non-malignant pathology n = 12), all sent for SOC NGS. SOC NGS was successfully completed in 53 biopsies (83%), of which 34 (64%) yielded sufficient tissue for IOTA-based NGS testing. All 34 biopsies demonstrated 100% concordance between SOC and IOTA NGS results. Nineteen biopsies did not undergo parallel IOTA NGS testing, primarily due to inadequate tissue from the final needle pass. Of the 11 biopsies that failed SOC NGS due to insufficient tissue, 4 produced adequate material for IOTA NGS testing; results of which were concordant with either subsequent liquid biopsy or prior archival tissue NGS results. Turnaround time (TAT) for SOC NGS ranged from 2 to 33 days (median, 12 days), vs. 1 to 6 days (median, 1 day) for IOTA-based NGS testing. Conclusions: Custom NGS testing using the IOTA workflow has median TAT of 1 day and demonstrated 100% concordance with SOC NGS. Further studies are needed to improve specimen adequacy rate at the time of biopsy for IOTA workflow without compromising tissue adequacy for standard pathology and biomarker testing.