Welcome to Group 1's Final Project Repository for BIS15L!
In this repository there are 4 main folders. Each member of Group 1 has a folder where their individual code is stored. The Cancer Type Overview is the folder which contains all of Anthony's code for the project and respective data sets. The Breast Cancer Analysis contains all of Jiaying's code and data files. The Oncoene Mutations folder contains all of Omar's code and data sets. Finally, included in this repository is a folder called BIS15L Final Project which combines all our work together into one file. Please feel free to look over our individual codes as well as our combined work in the Final Project file!
In this project, we employed a three-pronged approach to analyzing the complexities of cancer. First, we started off with a broad overview of the disease through analysis on publically available clinical data from United Kingdom hospitals (https://www.cancerdata.nhs.uk/getdataout/data). This allowed us to compare and contrast different cancer types and how survivability varies across them. We also analyzed a multitude of factors that can contribute to the prognosis of a patient who has been diagnosed with a certain cancer. In the Shiny App written for this part of the project, please refer to the file GDO_metadata.csv for the full description of the the drop-down menu items. Then, we performed analysis on oncogenes and mutations, employing a more streamlined genetic approach to cancer. This involved plotting a Manhattan graph and analyzing single nucleotide polymorphisms (SNPs). Finally, we concluded the project with a detailed analysis into breast cancer, funneling our project into one specific form of cancer. This allowed us to investigate the survivability prognosis of patients with the focus of breast cancer, and the different factors that can contribute to the patient outlook.
Overall, this project illustrates how complex and multi-faceted the disease of cancer is. Specifically, the prognosis and outlook of a cancer diagnosis is extremely type-specific and person-specific, which is why the early diagnosis of the disease is crucial to increasing survivability. Different types of cancer can have vastly different responses to the same treatment measures, such as chemotherapy. Thus, it is important to identify the specific instance of cancer through early screening as soon as possible to give more time to adapt to the specificity of the tumor, and how it can vary from person-to-person and from type of cancer to another type. In the future, we would like to dive in deeper to the genetic intracacies of the disease and perform analysis on patient DNA and their survivability prognosis to further investigate how cancer differs on a person-to-person basis. Thank you for visitng our respository!
Here is the link to our slides presentation: https://prezi.com/view/5f3SJyWvwfVCsoWYL1Nc