In this paper, we examine and propose a solution for the challenges of sharing of genome sequence data and of data querying on the genome sequence data on a cloud server in per-sonalized medicine scenarios. We develop a privacy-preserving, a secure and efficient solution for personalized medicine. The solution that we propose making use of stream cipher-based homomorphic transciphering in a cloud server, and to show the effectiveness of transciphering solution in the personalized medicine scenario. This paper also provides the comparative analysis of well-known existing homomorphic encryption solutions BGV and FV schemes combined with the FLIP stream cipher to demonstrate the efficiency and privacy of our solution.