Abstract 3418: Rare germline copy number variations in hereditary cutaneous melanoma

Abstract

Abstract Background: Melanoma is a highly aggressive skin cancer; approximately 10% of melanomas are caused by germline mutations, mainly affecting the p16 isoform of the CDKN2A gene (responsible for up to 40% of the familial melanoma). Although other genes exhibiting moderate to high penetrant mutations have been recently associated with melanoma susceptibility, such as CDK4, PALB2, MITF, and TERT promoter, the majority of the melanoma susceptibility remains without a clear genetic etiology. Copy number variations (CNVs) are a common class of structural variants of the human genome, mainly impacting genes that mediate the interaction with environment. However, many rare germline CNVs have been causally associated with diseases, including mental impairment and cancer predisposition. Objective: Aiming to identify new genes potentially related to melanoma predisposition, 34 melanoma-prone patients negative for CDKN2A/CDK4 mutations were investigated for rare germline CNVs. Material and Methods: Patients - patients were ascertained at the A. C. Camargo Cancer Center, Sao Paulo, Brazil; signed informed consents were obtained from all patients. DNA samples from peripheral blood were extracted from 34 unrelated probands fulfilling either the classical criteria for familial melanoma syndrome or based on evidence of a strong genetic predisposition (occurrence of ≥2 primary melanomas). These patients had been previously tested negative for CDKN2A and CDK4 genes. Methods - we performed evaluation of germline CNVs using the CytoSNP-850K (Illumina), analyzing data in the BlueFuse Multi Software v3.2. Selected CNVs were validated by real-time quantitative PCR (qPCR). Results: Among the 34 patients, we detected rare CNVs in 9 of them, mainly large duplications (>230kb) at 4q26-q27, 6p22.1, 8q23.1, 9p24.2, 10q22.3, 12p12.3 and 20p12.1, and deletions affecting 6p24.3 and 19p13.3. Four of these changes in DNA copy number were validated by qPCR using probes for genes mapped within affected regions (ANXA11, ESF1, MGST1 and ANGPT1 genes). Conclusion: We found 26% of the melanoma-prone patients carrying rare germline CNVs that encompass genes potentially associated with melanoma predisposition. Our data suggest that melanoma susceptibility could be originated by a broad spectrum of no recurrent genomic alterations, and part of the genetic etiology of the hereditary melanoma might reside in rare germline copy number changes. In addition to the well-known melanoma genes, germline CNVs, here reported, disclosed other candidate genes to melanoma predisposition deserving further investigation. Funding: This work was supported by grants from FAPESP (2012/21932-6) and the Brazilian National Institute of Science and Technology in Oncogenomics (FAPESP 2008/57887-9, CNPq 573589/08-9). Citation Format: Felipe Fidalgo, Tatiane Rodrigues, Amanda Gonçalves Silva, Luciana Facure, Amanda Nóbrega, Bianca Sá, João Pereira Duprat, Maria Isabel Achatz, Carla Rosenberg, Dirce Maria Carraro, Ana Cristina Krepischi. Rare germline copy number variations in hereditary cutaneous melanoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3418. doi:10.1158/1538-7445.AM2014-3418