In this paper, we propose the first deep reinforcement learning framework to estimate the optimal Dynamic Treatment Regimes from observational medical data. This framework is more flexible and adaptive for high dimensional action and state spaces than existing reinforcement learning methods to model real life complexity in heterogeneous disease progression and treatment choices, with the goal to provide doctor and patients the data-driven personalized decision recommendations. The proposed deep reinforcement learning framework contains a supervised learning step to predict the most possible expert actions; and a deep reinforcement learning step to estimate the long term value function of Dynamic Treatment Regimes. We motivated and implemented the proposed framework on a data set from the Center for International Bone Marrow Transplant Research (CIBMTR) registry database, focusing on the sequence of prevention and treatments for acute and chronic graft versus host disease. We showed results of the initial implementation that demonstrates promising accuracy in predicting human expert decisions and initial implementation for the reinforcement learning step.