A Molecular Diagnostic Assay for Accurately Differentiating Melanoma from Benign Lesions

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Abstract. Melanoma is the third most common form of skin cancer with estimated 87,110 new cases diagnosed in the United States in the year 2017. Current routine diagnostic approaches utilize microscopic evaluation of thinly sectioned patient biopsies, but in certain cases diagnosis can be contentious even among experts. The overall goal of this multi-phase SBIR project is to develop, validate, and commercialize MelanoMap™, Frontier Diagnostics' patented assay for the diagnosis of melanoma using a matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) platform—and to have this assay available to pathologists in the U.S. as a laboratory developed test. MALDI IMS is a state-of-the-art technology that generates molecular images of tens to thousands of biomolecules from tissue sections in a single analysis. The assay uses formalin-fixed paraffin embedded (FFPE) biopsies used in routine histopathological diagnosis. The proposed assay has pathologists select regions of skin biopsies for analysis via a remote web interface. The acquired IMS data from those regions unambiguously identifies malignant melanoma or benign nevus. Phase I of this proposal will demonstrate the feasibility of this technology platform to achieve cost-effective diagnosis of melanoma from patient skin biopsies at sample volumes acceptable for a clinical laboratory. Specific Aim 1 focuses on the development of a scalable and robust analytical protocol in both sample preparation and informatics to accurately diagnose melanoma with MALDI IMS. In specific aim 2, we will test the methodology developed in Specific Aim 1 on a cohort of melanocytic lesions with known clinical outcome and subsequently validate the classification accuracy of the proposed test In Phase II, the protocols developed in Phase I will be integrated into a diagnostic service workflow. This phase will focus on quality control measures, client facing cloud software, clinical diagnostic reporting, and completing the analysis of a 500-patient sample set for final assay validation. Specific Aim 3 of this proposal (initial aim of Phase II) will establish and implement test tissues into standard workflows that will provide performance metrics for standard operation of a test meeting Clinical Laboratory Improvement Amendments (CLIA) standards. Protocols will be developed to monitor reagents, the reproducibility of sample preparation, and mass spectrometer performance on daily basis. Specific Aim 4 will expand software capabilities to include a secure web interface for clients ordering the test and the laboratory performing the test. The software will meet regulatory compliance, perform statistical analysis, and generate and communicate reports of the MALDI IMS analysis. Specific Aim 5 proposes to expand the sample set used in the initial assay from Specific Aim 2 to include a set of 300 patient samples from our clinical collaborators with 5 or more years follow-up data. The test will be independently validated by an additional 200 patient samples with definitive diagnoses.