Secure Searching of Biomarkers Using Hybrid Homomorphic Encryption Scheme

As genome sequencing technology develops rapidly, there has lately been an increasing need to keep genomic data secure even when stored in the cloud and still used for research. In this paper, we are interested in designing a protocol for the secure outsourcing matching problem on encrypted data. We propose an efficient method to securely search a matching position with the query data and extract some information at the position. After decryption, we only perform a small amount of comparison with the query information in plaintext. We apply this method to find a set of biomarkers in encrypted genomes. The important feature of our method is to encode a genomic database as a single element of polynomial ring. It also requires only a single homomorphic multiplication for query computation. Thus this method has the advantage over the previous methods in parameter size, computational complexity, and communication cost. We evaluate the performance of our method and verify that computation on large-scale personal data can be securely and practically outsourced to a cloud environment during data analysis. It takes about 3.9 seconds to search-and-extract the reference and alternate sequences of the queried position in a database of size 4M.