Abstract 2413: Rapid, automated BRAF mutation testing of cell-free DNA from plasma of patients with advanced cancers using the novel Idylla platform
Authors: Janku Filip , Huang Helen J. , Claes Bart , Falchook Gerald S. , Fu Siqing , Tsimberidou Apostolia M. , Hong David S. , Naing Aung , Wheler Jennifer J. , Piha-Paul Sarina A. , Karp Daniel D. , Subbiah Vivek , Zinner Ralph G. , Ramzanali Nishma , Luthra Rajyalakshmi , Patel Sapna P. , Kopetz E. Scott , Sablon Erwin , Maertens Geert , Kurzrock Razelle , Meric-Bernstam Funda 
Published: August 2015

Background: BRAF V600 mutations are prevalent in diverse cancers and can be targeted with BRAF inhibitors. Cell-free (cf) DNA from plasma offers an easily obtainable material for BRAF mutation analysis.

Methods: cfDNA from plasma samples of patients with advanced cancers or malignant histiocytosis with known BRAF V600 status from formalin-fixed paraffin-embedded (FFPE) tumor samples, who progressed on systemic therapy was purified and 50-100ng were used for BRAF V600 mutations testing using the Idylla fully integrated real-time PCR-based platform (Biocartis, Mechelen, Belgium) with a quick turnaround time (&lt; 60 minutes). Results were compared to mutation analysis of FFPE primary or metastatic tumor tissue obtained at different points of clinical care from a CLIA-certified laboratory.

Results: cfDNA was extracted from plasma samples of 160 patients with advanced cancers (colorectal, n = 62; melanoma, n = 36; non-small cell lung, n = 13; breast, n = 10; thyroid, n = 10; appendiceal, n = 5; ovarian, n = 4; endometrial, n = 4; other cancers, n = 16). BRAF mutations were detected in 29% (47/160) of plasma samples and in 39% (62/160) of FFPE tumor samples, resulting in concordance in 141 cases (88%, kappa = 0.74, 95% confidence interval [CI] 0.63- 0.85) with sensitivity 73%, specificity 98%, positive and negative predictive value 96% and 85%, respectively. In addition, 35 (22%) patients had sequential plasma samples collection while on therapy including 9 of 17 patients, who had BRAF V600 mutation in FFPE but not in plasma at baseline. Of interest, in 3 of these 9 patients BRAF V600 mutation emerged in plasma later in the course of disease. If these 3 patients are included in the concordance analysis the overall agreement between testing modalities is 144 cases (90%, kappa 0.78, SE 0.05, 95% CI 0.68-0.88) with sensitivity 77%, specificity 98%, positive and predictive value 96% and 87%, respectively. In 15 of 19 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 with the Idylla. Longitudinally collected plasma samples were available in 16 patients with plasma and FFPE BRAF V600 mutations treated with predominantly BRAF targeting combinations. Changes in the amount of BRAF-mutant cfDNA corresponded with changes in serum tumor markers and disease burden visualized via imaging.

Conclusions: Detecting BRAF V600 mutations in plasma cfDNA using the Idylla platform is a fast and noninvasive alternative to mutation testing of tumor tissue with an acceptable level of concordance and should be investigated further for testing and monitoring of BRAF mutation status in patients with cancer.

Citation Format: Filip Janku, Helen J. Huang, Bart Claes, Gerald S. Falchook, Siqing Fu, Apostolia M. Tsimberidou, David S. Hong, Aung Naing, Jennifer J. Wheler, Sarina A. Piha-Paul, Daniel D. Karp, Vivek Subbiah, Ralph G. Zinner, Nishma Ramzanali, Rajyalakshmi Luthra, Sapna P. Patel, E. Scott Kopetz, Erwin Sablon, Geert Maertens, Razelle Kurzrock, Funda Meric-Bernstam. Rapid, automated BRAF mutation testing of cell-free DNA from plasma of patients with advanced cancers using the novel Idylla platform. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2413. doi:10.1158/1538-7445.AM2015-2413