Abstract C198: BRAF mutation testing of archival tumor samples with a novel, rapid, fully-automated molecular diagnostics prototype platform.
Authors: Huang Helen J. , Claes Bart , Falchook Gerald S. , Devogelaere Benoit , Naing Aung , Fu Siqing , Piha-Paul Sarina , Hong David S. , Holley Veronica R. , Tsimberidou Apostolia M. , Stepanek Vanda M. , Kim Kevin B. , Angelo Laura S. , Subbiah Vivek , Wheler Jennifer J. , Zinner Ralph G. , Karp Daniel D. , Luthra Rajyalakshmi , Sablon Erwin , Maertens Geert , Meric-Bernstam Funda , Kurzrock Razelle , Scherer Stefan , Janku Filip 
Published: August 2014

Abstract
Background: Novel, fast, and accurate diagnostic systems are needed for further implementation of personalized therapy. Mutations in the BRAF gene can provide actionable targets for cancer therapy in melanoma and other tumor types.
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 (pts) with advanced cancers previously tested for V600 BRAF mutations in a CLIA-certified Molecular Diagnostic Laboratory (PCR-based sequencing, Sequenom MassARRAY) were tested for BRAF V600 mutations using the MDx prototype platform. MDx prototype platform and the BRAF V600 mutation prototype assay were used for research purposes only. Concordance between different methods and treatment outcomes with BRAF/MEK inhibitors were analyzed.
Results: Seventy-nine pts (melanoma, n=34; colorectal, n=20; papillary thyroid, n=6; ovarian, n=4; other cancers, n=15) with available tissue and CLIA laboratory BRAF results were identified (BRAF V600 mutation, n=49; wild-type BRAF, n=30). Of the 70 pts for whom the same tissue block was used for MDx and CLIA, BRAF results (V600 mutation yes/no) were concordant in 67 of them (96%; kappa 0.91; 95% CI 0.81-1.01; discrepancies: V600E mutation from CLIA only in prostate cancer, V600E mutation from CLIA only in melanoma, V600E mutation from MDx only in colon cancer). In addition, BRAF results by MDx were discrepant with CLIA in one case (melanoma) in the mutation subtype (V600K vs. V600E). In all 79 pts (including 9 patients with different blocks tested) MDx and CLIA BRAF results (V600 mutation yes/no) were concordant in 75 (95%; kappa 0.89; 95% CI 0.79-1.00) of them (additional discrepancy: V600K mutation from CLIA only in colon cancer). Of 49 pts with BRAF mutations detected by MDx, 30 were treated on protocols (on the basis of the CLIA lab results) with BRAF/MEK inhibitors and 8 (27%) had a partial response. Of interest, 2 of 3 pts with BRAF mutations from CLIA, but not MDx, received a BRAF/MEK inhibitor and did not respond. Detailed patient characteristics, mutation types and 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 for determining BRAF mutation status, having 96% concordance with CLIA laboratory results in identical tissue blocks.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C198.
Citation Format: Helen J. Huang, Bart Claes, Gerald S. Falchook, Benoit Devogelaere, Aung Naing, Siqing Fu, Sarina Piha-Paul, David S. Hong, Veronica R. Holley, Apostolia M. Tsimberidou, Vanda M. Stepanek, Kevin B. Kim, Laura S. Angelo, Vivek Subbiah, Jennifer J. Wheler, Ralph G. Zinner, Daniel D. Karp, Rajyalakshmi Luthra, Erwin Sablon, Geert Maertens, Funda Meric-Bernstam, Razelle Kurzrock, Stefan Scherer, Filip Janku. BRAF mutation testing of archival tumor samples with a novel, rapid, fully-automated molecular diagnostics prototype platform. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C198.