Abstract 4126: BRAF mutation testing with a novel, rapid, fully-automated molecular diagnostics prototype platform.
Authors: Janku Filip , Angelo Laura S. , Devogelaere Benoit , Fachook Gerald S. , Fu Siqing , Huang Helen J. , Tsimberidou Apostolia M. , Hong David S. , Stepanek Vanda M. , Holley Veronica R. , Routbort Mark J. , Sablon Erwin , Maertens Geert , Kurzrock Razelle 
Published: August 2014

Abstract
Background: Mutations in the BRAF gene provide actionable targets for cancer therapy, and can be found in diverse cancers including melanoma, papillary thyroid and colorectal cancers. Novel, fast, and accurate diagnostic systems are needed for further implementation of personalized cancer therapy.
Methods: The molecular diagnostics (MDx) prototype platform (Biocartis, Mechelen, Belgium) is a fully integrated real-time PCR-based system with high sensitivity (1%) and quick turnaround time (&lt; 90 minutes), which requires no sample preparation and &lt;2 min hands-on time. Archival formalin-fixed paraffin-embedded tumor samples (1x to 5x of 10 μm shavings) from patients with advanced cancers previously tested for V600 BRAF mutations in the CLIA-certified Molecular Diagnostic Laboratory (PCR-based sequencing or Sequenom MassARRAY) were tested with a BRAF V600 mutation prototype assay using the MDx prototype platform for research only purposes. Concordance between methods and treatment outcomes with BRAF/MEK inhibitors were analyzed.
Results: Thirty-eight patients (melanoma, n=21; colorectal, n=7; other cancers, n=10) with available tissue and CLIA laboratory BRAF results were identified (BRAF V600 mutation, n=28; wild-type BRAF, n=10). Of the 36 patients for whom the same tissue block was used for MDx and CLIA, BRAF results were concordant in 35 (97%; kappa 0.93; 95% CI 0.80-1.06) of them. BRAF results by MDx were discordant with CLIA in a total of 3 of 38 patients (mutations found by CLIA, but not MDx), but in two of these individuals, different tissue blocks were used for MDx versus CLIA interrogation. Of 25 patients with BRAF mutations detected by MDx, 21 had previously been treated (on the basis of the CLIA lab results) with BRAF/MEK targeted therapies and 7 (33%) had a partial response (PR). Both of the patients with discrepant BRAF status (mutations found by CLIA, but not MDx) who were treated with a BRAF/MEK inhibitor did not respond. Detailed patient characteristics, mutation types and additional discrepancy analysis will be presented.
Conclusions: The BRAF V600 mutation MDx prototype platform is a fast (turn-around time about 1.5 hours) and simple (&lt;2 minutes hands-on time) test to determine BRAF mutation status. When identical tissue blocks are used, results from the MDx prototype platform and from CLIA laboratory PCR-based sequencing or Sequenom MassARRAY demonstrate 97% concordance.
Citation Format: Filip Janku, Laura S. Angelo, Benoit Devogelaere, Gerald S. Fachook, Siqing Fu, Helen J. Huang, Apostolia M. Tsimberidou, David S. Hong, Vanda M. Stepanek, Veronica R. Holley, Mark J. Routbort, Erwin Sablon, Geert Maertens, Razelle Kurzrock. BRAF mutation testing with a novel, rapid, fully-automated molecular diagnostics prototype platform. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4126. doi:10.1158/1538-7445.AM2013-4126