Proteogenomics is a recent field that aims to combine multi-omics data from genome sequencing, transcriptome sequencing as well as proteomics for the purpose of identification of novel or variant protein-coding genes. We have developed a proteogenimics pipeline to integrate multi-omcis data from cancer samples.
In our proteogenomics analysis pipeline we process and integrate all three layers of data that are in a cell that is genome, transcriptome, and proteome mainly to identify neoantigens. Identification of neoantigens would allow us to detect novel proteins that are only made in cancer samples that can be used for the purpose of cancer immunotherapy.
Currently, we have multiple cancer cohorts in our lab where we have obtained large amounts of data from whole genome sequencing (WGS), RNA-seq and mass-spectrometry experiments. The objective of this project is to identify neoantigens across different cancer types.