Towards Privacy-Preserving Computation on Gene: Construct Covid-19 Phylogenetic Tree using Homomorphic Encryption

ABSTRACT

Constructing a phylogenetic tree is an essential method of analyzing the evolution of the covid-19 virus. In the case of multiple entities holding different coronavirus genetic data, it is simple to aggregate all data into one entity and then calculate the phylogenetic tree. However, such a method is challenging to carry out. Genetic data is susceptible and has high economic value, and it is usually impossible to copy between different entities directly. Also, the direct sharing of genetic data can lead to data leaks or even legal problems. In this paper, we propose a homomorphic-encryption-based solution to tackle this problem, where two participants, A and B, both hold a part of covid-19 genetic data and compute the gene distance matrix calculation of the overall dataset without revealing the genetic data held by both parties. After the computation, participant A can decrypt the final distance matrix from the encrypted result and then use the plain-text result to construct the covid-19 phylogenetic tree. Experiment results show that the proposed method can process the genetic data accurately in a short time, and the phylogenetic tree generated by the proposed solution has no loss of accuracy compared to plain-text calculation. In terms of engineering optimization, we propose an optimized encryption method, which can further shorten the encryption time of the entire dataset without reducing the security level. © 2022 IEEE.