Melanoma: Genomic Profiles, Molecular Markers and Therapeutic Implications

In this context, it is aimed to utilize tissue biopsy tests that will focus on specific areas of clinical applications, namely, diagnosis, prognosis and identification of mutations for targeted therapy and assessment of acquiring treatment resistance. Thus, the tissue biopsy Next Generation Sequencing (NGS) panels in development by NIPD Genetics will be used in clinical practice as complementary diagnostics.

For tumor genotyping of the 200 patients with melanoma skin cancer in the present study it will be used the comprehensive tissue biopsy melanoma cancer panel from NIPD Genetics These panels are designed to target clinically actionable and clinically significant mutations that will provide physicians with genetic information regarding a) prediction of the patient's response to targeted therapy, b) prognosis, that is, prediction of clinical outcome, c) diagnosis and molecular classification of melanoma cancer. The panel allows for the detection of single nucleotide (SNVs) and copy number variants (CNVs), as well as gene fusions and indels; it necessitates at least 400ng of appropriate quality DNA template that is achievable from FFPE samples and is validated with molecular standards and controls for the exclusion of artefacts.

Thorough histological evaluation of the Formalin-Fixed-Paraffin-Embedded (FFPE) tumor tissue blocks will be done by an experienced pathologist to evaluate H&E sections for confirmation of diagnosis, histologic type, grade and tumor cell content (TCC%). DNA isolation will be performed from 10 μm whole sections following manual macro-dissection to enrich samples for tumor DNA, whereby TCC will be assessed as an approximate metric for tumor DNA in the extracted samples, corresponding to tumor nuclei vs. all nuclei in the areas marked for macro-dissection.

A total of 200 patients with melanoma skin cancer are expected to be included in the analysis based on the number of patients registered in the Hellenic Cooperative Oncology Group's (HeCOG's) database along with the ability to achieve precision around the primary and secondary endpoints. Primary endpoint will be the evaluation of the prevalence of mutations, while the secondary endpoint will be the assessment of prognostic significance of mutations with respect to overall survival (OS).