Application of FunciSNP tool to search risk regions associated with Ovarian Cancer

• Grant number: 14/11109-6
• Support type: Scholarships in Brazil - Scientific Initiation
• Effective date (Start): October 01, 2014
• Effective date (End): September 30, 2015
• Field of knowledge: Biological Sciences - Genetics - Human and Medical Genetics
• Principal researcher: Houtan Noushmehr
• Grantee: Mikely Fernanda Saraiva da Silva
• Home Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil

Abstract

Ovarian cancer is the most lethal gynecological cancer and the overall survival is less than 40 % in five years. This is primarily because most patients have advanced stage at diagnosis. Thus, it is essential to develop methods and strategies to detect such tumors in their initial stages in order to avoid unnecessary interventions. The single nucleotide polymorphisms (SNPs) are alterations in the DNA sequence where only one base is changed. In some cases, tens of SNPs, called tagSNPs, mark distinct loci in complex diseases such as cancer. Epigenomics studies are revolutionizing the field of cancer genetics, however, the causal relationship between increased genetic risk and onset/progression of disease, as well as the mechanisms by which these polymorphisms exert their functions remain unknown. Therefore, to assist the identification of risk regions, researchers in our laboratory (Omics Lab - FMRP) developed the FunciSNP tool (Functional Identification of SNPs with Phenotype by Coincidence with Chromatin Biofeatures), an R / Bioconductor package, to identify potential SNPs in risk loci, integrating its position with biofeatures. The objective of this proposal is to identify risk regions associated with ovarian cancer, applying the FunciSNPtool in DNA sequencing data of ovarian cell lines. The application of FunciSNP tool in ovarian cancer samples may help the identification of putative causative SNPs or markers of the disease, presenting a valuable resource for understanding the disease.