SecCT: Secure and scalable count query models on encrypted genomic data

Abstract

Recently, due to the continued reduction in DNA sequencing cost, large-scale genetic samples are being gathered for accelerating predispositions to specific diseases, tailoring treatment of efficient drugs and therapies, etc. Massive genetic samples are encrypted-and-then-delegated to a public cloud to both save investment and maintenance costs and prevent the potential leakage of sensitive information. However, such a manner compromises the serviceability of a public cloud, since encryption inevitably breaks the semantic information of genetic samples. Secure count query of single-nucleotide polymorphisms (SNPs), as a kernel component for GWASs and related genomic analysis, is attracting much more attention. Existing methods lack provable security, suffer low efficiency caused by multiple interactions with the cloud, etc. In this paper, a secure virtual CT-Tree (secure vCT-Tree) is carefully constructed to confuse the tree structure by introducing a hash function and a Paillier system. Furthermore, by delegating the secure vCT-Tree to the cloud, concrete models (i.e., SecCT and SecCT+) are presented to resolve secure count query problems on-the-fly. SecCT+ is a solution based on trusted execution environment while SecCT is a pure software solution. Both models advance the provable security of genetic research and are proven to be secure under the adaptive chosen keyword (query) attack (IND-CKA2) model. Furthermore, massive experiments are evaluated on realistic data to show the superiority of SecCT and SecCT+.