Genomic Analysis of inherited Melanoma in a Palestinian family: a Next Generation Sequencing study رسالة ماجستير

Abstract

Cutaneous melanoma is a cancer type that arises from melanocytes, the pigmentproducing cells in our skin. It is the most aggressive skin cancer and is responsible for about 75% of skin cancer deaths. Familial predisposition is among the strongest risk factors for cutaneous melanoma and accounts for around 10% of the cases. About half of these melanoma familial cases can't be explained by mutations in known moderate-tohigh penetrance melanoma genes, thus impairing genetic testing and counseling in families with a predisposition to melanoma. The present study concerns a Palestinian family with melanoma, of which the patient had no pathogenic mutations identified in a previous targeted gene panel analysis of 94 genes. Therefore, the primary objective of this thesis is to identify germline mutations predisposing to melanoma in the family via the application of WES. The secondary objective is to determine family members at high risk of developing the disease. We hypothesize that the underlying genetic cause of melanoma is a rare germline mutation segregating in the family. We used whole exome sequencing approaches to identify candidate mutations from DNA samples of the patient, his brother with a brain tumor, and his unaffected brother. We then analyzed WES data using bioinformatics pipelines to generate variant call format for variant filtration. Afterwards, Sanger sequencing of the candidate variant was applied on DNA samples from the patient and family members for validation and segregation analysis. This is followed by In silico analysis of the candidate variants and genes. WES analysis identified three heterozygous rare missense variants, WRN ( p.L383F and p.A995T) and TYRP1 (p.T262M). Importantly, we identified a pathogenic homozygous missense mutation in ERCC2 (p.R683Q), associated with the rare autosomal recessive xeroderma pigmentosum, which increases the risk of developing melanoma. The pathogenic V mutation cosegregated with the clinical phenotypes presented in the two affected brothers and was confirmed by sanger sequencing analysis. Segregation analysis of this mutation showed its absence in the homozygous state in the unaffected family members. These findings confirm that the homozygous ERCC2 (p.R683Q) mutation is the causative mutation for melanoma in the Palestinian family. In conclusion, this study expands the knowledge of the mutational background of familial melanoma in the Palestinian population, which is valuable to guide the diagnosis, prevention, and treatment of affected patients and their families.