Proteomics Analysis of FLT3-ITD Mutation in Acute Myeloid Leukemia Using Deep Learning Neural Network

Deep Learning can significantly benefit cancer proteomics and genomics. In this study, we attempted to determine a set of critical proteins that were associated with the FLT3-ITD mutation in newly-diagnosed acute myeloid leukemia patients. A Deep Learning network consisting of autoencoders formed a hierarchical model from which high-level features were extracted without labeled training data. Dimensional reduction reduced the number of critical proteins from 231 to 20. Deep Learning found an excellent correlation between FLT3-ITD mutation with the levels of these 20 critical proteins (accuracy 97%, sensitivity 90%, and specificity 100%). Our Deep Learning network could hone in on 20 proteins with the strongest association with FLT3-ITD. The results of this study allow for a novel approach to determine critical protein pathways in the FLT3-ITD mutation, and provide proof-of-concept for an accurate approach to model big data in cancer proteomics and genomics.