1234P - Hybrid-capture based genomic profiling identifies BRAF V600 and non-V600 alterations in melanoma samples negative by prior testing

Abstract

Background: BRAF and MEK inhibitors are approved for V600-mutated melanoma, and response rates of up to 70% are seen for patients with V600 mutations. Responses to targeted therapies have also been observed for a variety of non-V600 BRAF alterations. Thus, sensitive, accurate, and broad detection of BRAF alterations is critical to match patients with available targeted therapies. Methods: Pathology reports were reviewed for 385 consecutive melanoma cases (Mar 2016 - Mar 2017) with BRAF mutations or rearrangements identified using a hybrid-capture based next generation sequencing (NGS) assay during the course of clinical care. Results: Records of prior BRAF molecular testing were available for 79 (21%) cases, utilizing PCR (n = 30), Sanger sequencing (n = 13), IHC (n = 10), non-hybrid capture based NGS (n = 9), or other or unspecified methodology (n = 17). Of cases with BRAF V600 mutations 11/57 (19%) with available data were negative by prior BRAF testing, including 2/11 (18%) with confirmation that the same biopsy was tested. In cases with BRAF V600 mutations, there was no significant difference in mutant allele frequencies (median 35% vs. 40%, p = 0.25) or percentage of tumor nuclei (median 50% for both, p = 0.97) between samples with prior negative and prior positive results. Prior negative results were also identified in 16/20 (80%) cases with non-V600 mutations, two of which harbored multiple BRAF alterations [K601E (4), D594A/G/N (4), S467L (2), L584F (2), G464V, G466V, G469V, E586K, N581I, L597Q, A589_T599insT]. Two of 2 (100%) cases with activating BRAF fusions also had prior negative BRAF results. Clinical outcomes for a subset of patients will be presented. Conclusions: Despite approved companion diagnostics, significant variability exists in methods for BRAF testing in the clinical setting. Hybrid-capture based NGS identifies diverse activating mutations and fusions, including BRAF V600E, in a significant fraction of cases for which prior BRAF testing returned negative results. Given the proven clinical benefit in patients with BRAF alterations treated with match targeted therapies, hybrid-capture based NGS should be considered for patients with metastatic melanoma, particularly if other testing is negative. Legal entity responsible for the study: Foundation Medicine, Inc. Funding: Foundation Medicine, Inc. Disclosure: A. Wang, J.S. Ross, P.J. Stephens, S.M. Ali, A.B. Schrock, V.A. Miller: Employee with stock ownership in Foundation Medicine, Inc. All other authors have declared no conflicts of interest.