Aspyre Lung enables robust variant calling in samples that fail next generation sequencing quality control

Molecular testing in non-small cell lung cancer (NSCLC) identifies patients likely to respond to targeted therapeutics. Panel-based testing often employs next-generation sequencing, but challenges include high sample failure rates, quality control issues, high tissue requirements and long turnaround times. Significant proportions of patients do not receive appropriate targeted therapy, with inferior clinical outcomes. Aspyre Lung is a targeted genomic profiling assay for 114 actionable or prognostic genomic variants across 11 genes with a two-day turnaround time of specimen to result. We profiled 198 NSCLC patient tissue samples using Aspyre Lung and a next-generation sequencing- (NGS)-based assay. Cohort A comprised 107 samples that failed to inform due to NGS quality checks, and Cohort B 91 samples that underwent successful NGS testing. Results were compared, and discrepancies resolved by orthogonal methods. For Cohort A (NGS fails), 103 (96 %) passed Aspyre Lung quality control, successfully yielding genomic results, including 48 (47 %) samples with ≥ one variant. In Cohort B (NGS pass), all samples passed Aspyre quality control with 97 % concordance to NGS-based testing. Notably, 80 % EGFR variant-positive samples were stages I and II. Aspyre Lung profiled 96 % of samples where NGS-based methods failed, and uncovered variants in samples successfully tested by NGS and deemed negative. Aspyre Lung detected ALK and EGFR variants from patients with early-stage disease, demonstrating utility as a rapid screening assay prior to neoadjuvant immuno-chemotherapy consideration.