Abstract 4213: BRAF V600 mutation testing on FFPE samples using a novel fully integrated molecular diagnostics platform: A concordance study with reference methods.
Authors: Devogelaere Benoit , Van Acker Koen , De Baere Inky , Holemans Pascale , Ivens Tania , Claes Bart , Rondelez Evelien , Vandercruyssen Geneviève , Van der Auwera Marijke , Kockx Mark , Vanden Bempt Isabelle , Vandenbroucke Ina , Maertens Geert , Sablon Erwin 
Published: August 2014

Abstract
Introduction
Activating mutations in the BRAF gene are common in skin and colorectal tumors. In more than 90% of the cases, these mutations are located in the BRAF V600 codon (V600E and V600K). Targeted therapies like vemurafenib and dabrafenib have shown objective response rates in up to half of metastatic melanomas harboring these BRAF V600 mutations. Tumor mutation status is usually assessed starting from formalin-fixed, paraffin-embedded (FFPE) tumor tissue shavings. Typically, the test involves shipment of the paraffin block from the local pathology lab to a specialized molecular lab, where several steps need to be performed.
Methods
The Biocartis molecular diagnostics (MDx) prototype platform is a novel, random access, sample-in result-out automated qPCR system. It uses a disposable cartridge which can simultaneously detect and quantify up to 30 molecular markers from a wide range of solid and liquid sample types, including blood, feces, and sputum. For FFPE-based assays, a single curl or shaving is directly placed into the cartridge. The complete process time for sample preparation, PCR and reporting is less than 90 min, with &lt;2 minutes hands-on time. We hereby present a concordance study of the Biocartis BRAF V600 Mutation prototype assay (which detects BRAF V600E, V600K, V600R, V600E2, V600D and V600M) with the Roche cobas® 4800 BRAF V600 Mutation Test (Cobas). Sixty-four FFPE samples from melanoma and other tumors, with varying amounts of melanin, % tumor, and % BRAF V600 mutated tumor cells were randomly selected and tested. Both the Biocartis MDx prototype platform and the Biocartis BRAF V600 Mutation prototype assay were used for research use only purposes. Deep sequencing was performed using MiSeq (Illumina) with over 5,000-fold coverage and sensitivity of 1% of minority species for each sample.
Results
One sample was not eligible for Cobas testing because of low tumor content. Three other samples failed on both platforms. For the remaining 60 samples, results on the Biocartis MDx platform and Cobas were concordant in 58 (96.7%) samples (44 BRAF V600 WT and 14 BRAF V600 mutant samples, of which 36 samples were randomly selected and confirmed by deep sequencing). In 2 (3.3%) samples, no BRAF V600 mutation was detected by Cobas, while a BRAF V600 mutation was detected by both the Biocartis MDx platform and by deep sequencing. Both were melanoma samples (one of which was highly pigmented), excised in 1993 and 2005, and contained 4.6% V600E and 5.6% V600K (as determined by deep sequencing), respectively.
Conclusions
The new MDx platform is a fast and reliable method for BRAF V600 mutation testing directly on FFPE tumor shavings with superior analytical sensitivity, ease of use, and turnaround time compared to existing diagnostic tests. The BRAF V600 Mutation prototype assay provided excellent concordance with both Cobas (96.7%) and deep sequencing (100%).
Citation Format: Benoit Devogelaere, Koen Van Acker, Inky De Baere, Pascale Holemans, Tania Ivens, Bart Claes, Evelien Rondelez, Geneviève Vandercruyssen, Marijke Van der Auwera, Mark Kockx, Isabelle Vanden Bempt, Ina Vandenbroucke, Geert Maertens, Erwin Sablon. BRAF V600 mutation testing on FFPE samples using a novel fully integrated molecular diagnostics platform: A concordance study with reference methods. [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 4213. doi:10.1158/1538-7445.AM2013-4213