Identifying New SNPs in miRNAs and their Role in Predicting Breast Cancer Risk

DESCRIPTION (provided by applicant): At InterGenetics Incorporated we have developed a prototype multigenic, logistic regression model, called OncoVue(r), to predict sporadic breast cancer risk. This model incorporates polymorphisms in several genes involved in diverse processes implicated in breast carcinogenesis as well as clinical risk factors (such as age) to predict age-specific risk of developing breast cancer. Although this model exceeds the predictive power of the widely used current method of risk assessment (Gail model), the long-term goal of the proposed research is to improve the predictive accuracy of OncoVue(r)by incorporating additional SNPs with a a potential role in breast cancer. miRNAs constitute an important novel and growing class of small ~22nt, non-coding RNAs recently recognized as playing crucial roles in diverse organisms, including humans. Many studies indicate that miRNA expression is deregulated in all human cancers examined so far. Given the important regulatory roles these miRNAs play in diverse biological processes and that they are often deregulated in cancer, it has been hypothesized that polymorphisms in pre-miRNA and/or mature miRNA might alter their processing and/or target selection. More importantly to this project, these sequence variations might alter pre-disposition to cancer. However, to date the existence of polymorphisms in miRNAs has not been studied extensively. Therefore, in order to achieve our long-term goal of improving OncoVue(r) by adding additional informative markers, we propose the following specific aims for this Phase I project: (1) To identify new SNPs in miRNA genes: We will determine the sequence of ~90 miRNA genes in 44 DNAs from ethnically diverse individuals obtained from the Coriell Human Diversity Panel. (2) To examine the relevance of known and newly discovered miRNA SNPs in breast cancer: We will genotype 250 breast cancer cases and 250 cancer-free controls drawn from our existing large case-control breast cancer study. Polymorphisms in the 10 known miRNA single nucleotide polymorphisms (SNPs) and any new SNPs discovered in Aim 1 will be examined using multiplexed, bead-based Allele Specific Primer Extension (ASPE) assays on the Luminex100 flow cytometer platform. The successful completion of these studies will help us discover new polymorphisms in miRNAs, as well as determine if these miRNA polymorphisms are associated with breast cancer risk. In Phase II, we will be poised to examine the association of these newly discovered polymorphism(s) in our large breast cancer case-control study for their ability to predict breast cancer risk and fulfill our ultimate goal of improving our commercialized genetic risk assessment test. 7. PROJECT NARRATIVE At InterGenetics Incorporated we have used multiple, commonly occurring DNA variations to develop a genetic risk assessment model, called OncoVue(r), that predicts breast cancer risk. The proposed research will identify and investigate DNA variation in a newly recognized class of regulatory RNA genes (miRNAs) with the ultimate goal of utilizing them to improve the predictive accuracy of our model. This test, which is applicable to the majority of women without a strong family history of breast cancer, represents a major advancement in breast cancer risk management and cancer prevention.