We’re excited to announce that we’ve just been awarded an Amazon Web Services (AWS) in Education Research Grant in support of our cancer biomarker project! This grant will allow us to run our proteogenomic software Peppy on the AWS Cloud, mining proteomic and genomic data for aberrations that may be at the root of breast cancer. Ultimately, this will help with the project’s larger goal of finding blood-based protein biomarkers for the disease. Rather than hunting through the protein data for a proverbial ‘needle in a haystack,’ we are focusing on the DNA mutations that give rise to cancer, then tracing a path outward to the proteins.
We’re in the discovery stage of a five-year project funded by the National Institutes of Health (NIH), as a member of the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our lab’s role in this project is in the computation: to mine the genomes of breast cancer patients for mutations that may be causing their disease. To do this, we use our unique proteogenomic mapping software, Peppy, capable of processing an entire human genome in a single run. By linking mass spectrometry data from proteins to an in silico translation and digestion of genomes, Peppy can pinpoint the genomic regions of breast cancer patients where aberrations may be causing cancer-related proteins to be over-expressed. Peppy requires a lot of computer memory and processing power to handle entire genomes, so running the program on the AWS Cloud is an obvious choice.
We’re thrilled about the possibilities now open to us by running Peppy on the Cloud, especially in accelerating the tempo of this research. Thank you, AWS!