Integrative Bioinformatic Analysis of a Greek Epidemiological Cohort Provides Insight into the Pathogenesis of Primary C
Melanoma is the most lethal type of skin cancer. In this study for the first time we analyze a Greek cohort of primary cutaneous melanoma biopsies, subjected to whole exome sequencing, in order to derive their mutational profile landscape. Moreover, in th
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Metabolic Engineering and Bioinformatics Group, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece {gkontogianni,opapadod,achatzi}@eie.gr 2 Department of Digital Systems, School of Information and Communication Technologies, University of Piraeus, Piraeus, Greece [email protected] 3 HistoBio Diagnosis, Athens, Greece [email protected]
Abstract. Melanoma is the most lethal type of skin cancer. In this study for the first time we analyze a Greek cohort of primary cutaneous melanoma biopsies, subjected to whole exome sequencing, in order to derive their mutational profile landscape. Moreover, in the context of big data analytical methodologies, we integrated the results of the exome sequencing analysis with transcriptomic data of cutaneous melanoma from GEO, in an attempt to perform a multi-layered analysis and infer a tentative disease network for primary melanoma pathogenesis. The purpose of this research is to incorporate different levels of molecular data, so as to expand our understanding of cutaneous melanoma and the broader molecular network implicated with this type of cancer. Overall, we showed that the results of the integrative analysis offer deeper insight in the underlying mechanisms affected by melanoma and could potentially contribute to the valuable effective epidemiological characterization of this disease. Keywords: Data integration analysis Skin cancer
Next generation sequencing
Functional
1 Introduction Melanoma is the most dangerous form of skin cancer [1]. Cutaneous melanoma (or melanoma of the skin), the most common type of melanoma, is a complex multi-factorial disease as both environmental and genetic factors are involved in its manifestation [2]. It is often a fatal neoplasm, derived from melanocytes, that accounts for most skin cancer deaths. In the advanced stages of this cancer, therapeutic intervention usually fails to improve survival despite recent advances in immunotherapy. © IFIP International Federation for Information Processing 2016 Published by Springer International Publishing Switzerland 2016. All Rights Reserved L. Iliadis and I. Maglogiannis (Eds.): AIAI 2016, IFIP AICT 475, pp. 39–52, 2016. DOI: 10.1007/978-3-319-44944-9_4
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According to the World Health Organization, 132,000 melanoma skin cancers occur globally each year and the global incidence of melanoma continues to increase, with a main predisposal factor; sun exposure. The complexities of cellular metabolism and regulatory pathways involved have, until recently, obstructed the formulation of a unified description for melanoma [3]. Thus, despite the descent of gene signatures for various cancers, e.g. breast or colon cancer, a similar progress remains elusive for malignant melanoma. This could be attributed to the intricate nature of the molecular basis of cutaneous melanoma, which needs neatly stratified epidemiological cohorts to effectively address the issue of the high heterogeneity of this disease. In any case, genomic
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