Oncotarget (ONCOALVO): A custom NGS panel for therapeutic decision in solid tumors refractory to conventional therapy.

Abstract

140 Background: Next-generation sequencing (NGS) of tumor biopsies of solid tumors using commercially available platforms has broadly entered routine clinical practice to test for predictive biomarkers for patients with no available further standard therapies, as diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. However, the high cost of large multigenic panels and especially the sequencing of the entire tumor exome is a concern, especially in a developing country such as Brazil. Methods: We report the clinical application of a panel of 57 genes that we call ONCOTARGET (ONCOALVO) which is based on the Thermo Fisher Oncomine Focus Assay, for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance, but with the addition of 5 additional genes: the homologous recombination repair (HRR) genes BCRA1, BRCA2, ATM and CHEK2 that determine tumor sensitivity to inhibitors of the PARP enzyme and also KDR. 60 diagnostic samples of formalin-fixed, paraffin-embedded material submitted for molecular testing over a 2 year time period were analyzed so far. All patients had advanced solid tumors already refractory to conventional systemic therapy. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent S5 sequencer. Results: We found 40 potential therapy target pathogenic gene aberrations in 30 (50%) patients: KRAS - 10 (25%), BRCA1 - 8(20%), BRCA2 - 8(20%), PIK3CA - 4 (10%) mutations; and also 2 of each: ERBB2 (5%), BRAF-V600E (5%), KIT (5%), ALK (5%) mutations and one (2.5%) CCND1 amplification and one (2.5%) CDK4 mutacion. In 3 (7.5%) patients there were double mutations: BRCA1 and BRCA2 in 2 cases and BRCA2 and KRAS and one case. The Oncotarget workflow enabled a turnaround of 18½ days. Conclusions: ONCOTARGET was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics and therapeutic decisions with a potential to become an important asset for precision oncology in Brazil.