Abstract 469: Systematic analysis of circulating tumor DNA in melanoma patients to uncover mechanisms of resistance and disease clonality
Authors: Gremel Gabriela , Lee Rebecca J. , Girotti Maria R. , Garner Grace , Mandal Amit K. , Wood Sally , Fusi Alberto , Valpione Sara , Serra-Bellver Patricio , Dhomen Nathalie , Lorigan Paul , Marais Richard 
Published: July 2016

Abstract
Recent advances in targeted and immunotherapies have unlocked potent treatment options for malignant melanoma patients. However, targeted therapies are associated with limited response durations and only a fraction of patients benefit from immunotherapies. The analysis of circulating tumour DNA (ctDNA) provides a powerful tool for the continuous assessment of treatment responses in melanoma patients.
We have established a robust pipeline for the serial, prospective analysis of ctDNA in melanoma patients. By combining next generation sequencing (NGS)- and droplet digital PCR (ddPCR)-based approaches we make ideal use of currently available technologies. To date, plasma samples from over 120 individuals have been collected, with follow-up times surpassing one year in many cases.
For routine monitoring of patients commencing BRAF-mutant targeted therapies, pre-treatment DNA, derived from tumour biopsy or plasma, is tested to confirm the exact BRAF mutation and rule out pre-existing resistance-associated mutations using a custom NGS sequencing panel. Timely follow-up throughout treatment is achieved by measuring mutant BRAF fractions in ctDNA using ddPCR. When increasing BRAF variant allele frequencies are detected, additional ddPCR-based profiling for NRAS mutations and NGS-based re-sequencing for other resistance-associated mutations is initiated. We demonstrate superiority of ctDNA monitoring over LDH measurements and present a strategy to detect emerging resistant disease ahead of clinical scans in a cost-effective, timesaving and low technology way.
In addition to the basic characterization of BRAF-mutant cases undergoing targeted therapy, we have used the analysis of ctDNA to uncover clonally distinct tumour sub-populations resulting in complex responses to treatment. For instance, we monitored a case of metastatic vaginal mucosal melanoma undergoing sequential targeted, immuno- and chemotherapy. Despite the presence of a KIT mutation in the primary tumour, response to KIT inhibitor imatinib was mixed. In the absence of tumour biopsies, we used whole exome-wide NGS of ctDNA to study the underlying mechanisms. This strategy revealed a KIT-mutant tumour sub-clone that responded to imatinib and a second sub-clone including an SF3B1 mutation that did not respond. The sub-clones also responded differentially to immunotherapies, but both responded to chemotherapy.
The analysis of ctDNA is a powerful approach to monitor responses to systemic therapies in melanoma. By providing early warning of resistance and crucial information of clonal composition/evolution of the disease, ctDNA analysis has the potential to revolutionize the implementation of precision medicine.
Citation Format: Gabriela Gremel, Rebecca J. Lee, Maria R. Girotti, Grace Garner, Amit K. Mandal, Sally Wood, Alberto Fusi, Sara Valpione, Patricio Serra-Bellver, Nathalie Dhomen, Paul Lorigan, Richard Marais. Systematic analysis of circulating tumor DNA in melanoma patients to uncover mechanisms of resistance and disease clonality. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 469.