Answering Count Queries for Genomic Data with Perfect Privacy

In this paper, we consider the problem of answering count queries for genomic data subject to perfect privacy constraints. Count queries are often used in applications that collect aggregate (population-wide) information from biomedical Databases (DBs) for analysis, such as Genome-wide association studies. Our goal is to design mechanisms for answering count queries of the following form: How many users in the database have a specific set of genotypes at certain locations in their genome? At the same time, we aim to achieve perfect privacy (zero information leakage) of the sensitive genotypes at a pre-specified set of secret locations. The sensitive genotypes could indicate rare diseases and/or other health traits that one may want to keep private. We present two local count-query mechanisms for the above problem that achieve perfect privacy for sensitive genotypes while minimizing the expected absolute error (or per-user error probability) of the query answer. We also derived a lower bound of the per-user probability of error for an arbitrary query answering mechanism that satisfies perfect privacy. We show that our mechanisms achieve error that is close to the lower bound, and are match the lower bound for some special cases. We numerically show that the performance of each mechanism depends on the data prior distribution, the intersection between the queried and sensitive data, and the strength of the correlation in the genomic data sequence.