Abstract A202: BRAF mutation testing in cell-free DNA from plasma of patients with advanced cancers using a novel, rapid, automated molecular diagnostics prototype platform.
Authors: Huang Helen J. , Claes Bart , Falchook Gerald S. , Tsimberidou Apostolia M. , Holley Veronica R. , Subbiah Vivek , Zinner Ralph G. , Naing Aung , Karp Daniel D. , Piha-Paul Sarina A. , Wheler Jennifer J. , Fu Siqing , Hong David S. , Stepanek Vanda M. , Luthra Rajyalakshmi , Meric-Bernstam Funda , Ivens Tania , Sablon Erwin , Maertens Geert , Kee Bryan K. , Kurzrock Razelle , Scherer Stefan , Janku Filip 
Published: August 2014

Abstract
Background: Cell-free (cf) DNA in the plasma of cancer patients offers an easily obtainable, low-risk, and inexpensive and repeatedly applicable source of biologic material for mutation analysis for druggable targets and monitoring of the molecular changes of tumor during and after therapeutic interventions. Novel, fast, and accurate diagnostic systems are needed for further implementation of cfDNA testing in personalized therapy.
Methods: cfDNA in plasma samples from patients with advanced cancers who progressed on systemic therapy was purified and 100 ng was used for testing for V600 BRAF mutations using the prototype molecular diagnostics (MDx) fully integrated real-time PCR-based prototype platform (Biocartis, Mechelen, Belgium) with a quick turnaround time (&lt; 90 minutes). Both the MDx prototype platform and the BRAF V600 mutation prototype assay were used for research purposes only. Results were compared to mutation analysis of archival primary or metastatic tumor tissue from a CLIA-certified laboratory.
Results: cfDNA was extracted from plasma samples of 52 patients with advanced cancers (colorectal, n=23; melanoma, n=14; non-small cell lung cancer, n=6; ovarian, n=2; other cancers, n=7). BRAF mutations were detected in 35% (18/52) of plasma samples and in 48% (25/52) of archival tumor samples, resulting in agreement in 86.5% cases (kappa=0.73, 95% confidence interval 0.55- 0.91). In 7 cases with BRAF mutation in the tumor and wild-type BRAF in cfDNA, cfDNA mutation analysis using an alternative PCR-based method (BEAMing) was requested and results will be presented at the meeting along with detailed patient characteristics, mutation types and treatment outcomes.
Conclusions: Detecting V600 BRAF mutations in cfDNA from plasma with the MDx prototype platform is a fast and noninvasive alternative to mutation testing of tumor tissue with an acceptable level of concordance and sensitivity, and should be investigated further for testing and monitoring of BRAF mutation status in patients with cancer.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A202.
Citation Format: Helen J. Huang, Bart Claes, Gerald S. Falchook, Apostolia M. Tsimberidou, Veronica R. Holley, Vivek Subbiah, Ralph G. Zinner, Aung Naing, Daniel D. Karp, Sarina A. Piha-Paul, Jennifer J. Wheler, Siqing Fu, David S. Hong, Vanda M. Stepanek, Rajyalakshmi Luthra, Funda Meric-Bernstam, Tania Ivens, Erwin Sablon, Geert Maertens, Bryan K. Kee, Razelle Kurzrock, Stefan Scherer, Filip Janku. BRAF mutation testing in cell-free DNA from plasma of patients with advanced cancers using a novel, rapid, 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 A202.