Abstract 5584: BRAF mutation testing in cell-free DNA from plasma of patients with advanced cancers using a novel, rapid, automated molecular diagnostics prototype platform (IdyllaTM)
Authors: Huang Helen J. , Claes Bart , Falchook Gerald S. , Holley Veronica R. , Naing Aung , Piha-Paul Sarina A. , Tsimberidou Apostolia M. , Zinner Ralph G. , Karp Daniel D. , Fu Siqing , Subbiah Vivek , Hong David S. , Wheler Jennifer J. , Stepanek Vanda M. , Cabrilo Goran , Luthra Rajyalakshmi , Bedikian Agop Y. , Kee Bryan K. , Eng Cathy , Overman Michael J. , Kim Kevin B. , Ivens Tania , Sablon Erwin , Maertens Geert , Kurzrock Razelle , Meric-Bernstam Funda , Janku Filip 
Published: May 2015

Abstract
Background: Cell-free (cf) DNA from the plasma of cancer patients offers an easily obtainable, low-risk, inexpensive and repeatedly applicable source of biologic material for mutation analysis of druggable targets and monitoring molecular changes in tumor(s) during and after therapeutic interventions. Novel, fast, and accurate diagnostic systems are needed for further development of plasma cfDNA testing in personalized therapy.
Methods: cfDNA from plasma samples of 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 (IdyllaTM) fully integrated real-time PCR-based prototype platform (Biocartis, Mechelen, Belgium) with a quick turnaround time (&lt; 90 minutes). The IdyllaTM 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 if available.
Results: cfDNA was extracted from plasma samples of 81 patients with advanced cancers (colorectal, n=37; melanoma, n=16; non-small cell lung, n=10; breast, n=4, Erdheim-Chester histiocytosis, n=3; appendiceal, n=3; other cancers, n=8). BRAF mutations were detected in 31% (25/81) of plasma samples and in 42% (30/72) of available archival tumor samples, resulting in concordance for patients who had plasma and tissue tested (N=72) in 90% (65/72) of cases (kappa=0.80, 95% confidence interval 0.65- 0.94). In 6 of 7 discrepant cases identical plasma cfDNA samples were tested using an alternative cfDNA BRAF mutation PCR-based method (BEAMing, Sysmex Inostics, Baltimore, MD), which yielded 100% agreement. Longitudinally collected plasma samples were available in 3 patients (appendiceal, melanoma and papillary thyroid cancer) treated with BRAF targeting combinations and changes in the amount of BRAF-mutant cfDNA corresponded with changes in tumor markers or subsequent responses to therapy visualized via imaging.
Conclusions: Detecting V600 BRAF mutations in cfDNA from plasma using the IdyllaTM 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 Format: Helen J. Huang, Bart Claes, Gerald S. Falchook, Veronica R. Holley, Aung Naing, Sarina A. Piha-Paul, Apostolia M. Tsimberidou, Ralph G. Zinner, Daniel D. Karp, Siqing Fu, Vivek Subbiah, David S. Hong, Jennifer J. Wheler, Vanda M. Stepanek, Goran Cabrilo, Rajyalakshmi Luthra, Agop Y. Bedikian, Bryan K. Kee, Cathy Eng, Michael J. Overman, Kevin B. Kim, Tania Ivens, Erwin Sablon, Geert Maertens, Razelle Kurzrock, Funda Meric-Bernstam, 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 (IdyllaTM). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5584. doi:10.1158/1538-7445.AM2014-5584