Validation of a NGS panel, with automated analysis, designed for detection of medically actionable tumor biomarkers for Latin America

Abstract

The genomic characterization of solid tumors and a rapidly growing repertoire of target drugs are revolutionizing cancer treatment. Next-generation sequencing (NGS) panels are progressively used in clinical practice for target therapy in high-income countries. In contrast, limited access to tumor sequencing, among other barriers, precludes precision cancer treatment in low- and middle-income countries. To build towards the implementation of precision oncology in Chile and Latin America, we designed a 25-gene panel that contains predictive biomarkers for currently or near-future available therapies in Latin America. Library preparation was optimized to account for DNA integrity variability in Formalin-Fixed Paraffin-Embedded (FFPE) tissue. The bioinformatic pipeline removes FFPE-induced artifacts and known germline variants; while identifying possible discrepancies in somatic mutations due to Latin Americans’ underrepresentation in the reference genome databases. Analytic sensitivity and accuracy were assessed using commercial standard controls for FFPE DNA and for germline BRCA1 and BRCA2 mutations, which are biomarkers for PARP inhibitors. Our panel detects small insertions and deletions and single nucleotide variants (SNVs) with 100% sensitivity and specificity down to allelic frequencies of 0.05, and with 100% between-run and within-run reproducibility for non-synonymous variants. The workflow was validated in 265 clinical samples, including breast, colorectal, gastric, ovarian, and gallbladder tumors and blood, leading to identifying 131 actionable variants. Therefore, this NGS panel constitutes an accurate and sensitive method for routine tumor biopsies that could replace multiple non-NGS assays and costly large NGS panels in the Latin American clinical context. The proposed streamlined assay and automated analysis are expected to facilitate the implementation of precision medicine in Latin America.