Abstract: Various mutations have been shown to correlate with prognosis of High-Grade Glioma (Glioblastoma). Overall prognostic assessment requires analysis of multiple modalities: imaging, molecular and clinical. To optimize this assessment pipeline, this paper develops the first deep learning-based system that uses MRI data to predict 19/20 co-gain, a mutation that indicates median survival. It addresses two key challenges when dealing with deep learning algorithms and medical data: lack of data and high data imbalance. To tackle these challenges, we propose a unified approach that consists of a Feature Disentanglement based Generative Adversarial Network (FeaD-GAN) for generating synthetic images. FeaD-GAN projects disentangled features into a high dimensional space and re-samples them from a pseudo-large data distribution to generate synthetic images from very limited data. A thorough analysis is performed to (a) characterize aspects of visual manifestation of 19/20 co-gain to demonstrate the effectiveness of FeaD-GAN and (b) demonstrate that not only do the imaging biomarkers of 19/20 co-gain exist, but also that they are reproducible.