Title: Topological Data Analysis-Deep Learning Framework for Predicting Cancer Phenotypes. Abstract: Classification of patient cancer phenotypes from gene expression profiles remains a challenge in the field of transcriptomics. Gene expression data typically suffers from extreme noise and performs poorly on deep learning models alone. We build on recent work by Mandal et al., by incorporating the concept of differential gene expression analysis to pre-select genes that are necessary but not sufficient for disease association in our topological data analysis approach. The outcome is a reduction in computational cost in the calculation of persistent homology. We also test multiple topological representations to optimise prediction. Deep learning with topological features performs better compared to its use on raw data. Thus, topological features offers a new perspective on the difficult-to-unravel non-linear connection between genotype and phenotype