Membership Privacy in MicroRNA-based Studies

The continuous decrease in cost of molecular profiling tests is revolutionizing medical research and practice, but it also raises new privacy concerns. One of the first attacks against privacy of biological data, proposed by Homer et al. in 2008, showed that, by knowing parts of the genome of a given individual and summary statistics of a genome-based study, it is possible to detect if this individual participated in the study. Since then, a lot of work has been carried out to further study the theoretical limits and to counter the genome-based membership inference attack. However, genomic data are by no means the only or the most influential biological data threatening personal privacy. For instance, whereas the genome informs us about the risk of developing some diseases in the future, epigenetic biomarkers, such as microRNAs, are directly and deterministically affected by our health condition including most common severe diseases. In this paper, we show that the membership inference attack also threatens the privacy of individuals contributing their microRNA expressions to scientific studies. Our results on real and public microRNA expression data demonstrate that disease-specific datasets are especially prone to membership detection, offering a true-positive rate of up to 77% at a false-negative rate of less than 1%. We present two attacks: one relying on the L_1 distance and the other based on the likelihood-ratio test. We show that the likelihood-ratio test provides the highest adversarial success and we derive a theoretical limit on this success. In order to mitigate the membership inference, we propose and evaluate both a differentially private mechanism and a hiding mechanism. We also consider two types of adversarial prior knowledge for the differentially private mechanism and show that, for relatively large datasets, this mechanism can protect the privacy of participants in miRNA-based studies against strong adversaries without degrading the data utility too much. Based on our findings and given the current number of miRNAs, we recommend to only release summary statistics of datasets containing at least a couple of hundred individuals.