EPSim-GS: Efficient and Privacy-Preserving Similarity Range Query over Genomic Sequences

Abstract

Similarity query over genomic sequences has played a significant role in personalized medicine and has applications in various fields, including DNA alignment and genomic sequencing. Since handling genomic sequences requires massive storage and considerable computational capacity, service providers prefer to process similarity queries over genomic sequences on cloud servers rather than at the client side. Due to the sensitivity of genomic sequences, preserving the privacy of queries has attracted considerable attention, and as a result, genomic sequences are demanded to be outsourced in an encrypted form. Although many schemes have been proposed for similarity queries over encrypted genomic data, they are either inefficient or have limitations in supporting the dynamic update of the dataset. To address the challenges, we propose an efficient and privacy-preserving similarity range query scheme, namely EPSim-GS. First, we introduce how to build a hash table to index the dataset, and present a similarity range query algorithm based on the hash table. Then, we design two cloud-based privacy-preserving protocols based on the Paillier cryptosystem to support the similarity range query algorithm over the encrypted dataset. After that, we propose EPSim-GS by leveraging the two privacy-preserving protocols. We then analyze the security of EPSim-GS and prove that it is privacy-preserving. Finally, we perform experiments to evaluate the scheme’s performance, and the results indicate that it is computationally efficient.