SNP Clip: A tool to analyze SNP Mutations to Identify Enrichted Pathways Pertaining to Bladder Cancer Risk

Cancer is a devastating disease affecting millions of people. In simple terms it is caused by cells that grow uncontrollably in the body forming tumors. Bladder cancer is a common cancer being the tenth most diagnosed in 2020 with approximately 570,000 new cases. There are specific risk factors that increase the risk of developing bladder cancer. Some of these include gender, age, smoking and occupational hazards such as aromatic amines exposure. Since there are a variety of different genetic and environmental causes of bladder cancer, further research has been done to try to identify single nucleotide polymorphisms or a SNPs. A SNP is a base pair mutation that occurs in at least 1% of the population. Due to the complexity of DNA, SNP identification is a lengthy and complex process. Therefore, labs conducting this type of research only analyze and identify, at most, a handful of SNPs. There is an abundance of data related to which SNPs could increase the risk of developing bladder cancer. However, the research seems to sto there. Nobody seems to take the next step by looking to find a relationship between the already identified SNPs. Genes work together in combination with each other in what is called a pathway. Consequently, a mutation in an earlier gene in the pathway process may have an obvious phenotypic change. By identifying pathways, we could identify phenotypic characteristics that may indicate an individual is more susceptible to developing bladder cancer without genetic screening. Since the data is so extensive, a computational approach is needed to truly understand what is going on. There are a variety of software that exists that attempt to analyze pathways. One such tool is the WEB-based Gene Set AnLysis Toolkit (WebGestalt). WebGestalt is a “gene set analysis toolkit” that allows user to input SNPs and the most common enriched pathways are produced. However, there is some computer science background that the researcher needs to have to fully understand the process and results. SNP clip will help to bridge the gap between the two fields.