Private DNA Sequencing: Hiding Information in Discrete Noise

Abstract: When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We assume that the genetic content of these samples is known to the individual but unknown to the sequencing laboratory. Thus, these DNA samples act as "noise" to the sequencing laboratory, but still allow the individual to recover their own DNA samples afterward. Motivated by this idea, we study the problem of hiding a binary random variable $X$ (a genetic marker) with the additive noise provided by mixing DNA samples, using mutual information as a privacy metric. This is equivalent to the problem of finding a worst-case noise distribution for recovering $X$ from the noisy observation among a set of feasible discrete distributions. We characterize upper and lower bounds to the solution of this problem, which are empirically shown to be very close. The lower bound is obtained through a convex relaxation of the original discrete optimization problem, and yields a closed-form expression. The upper bound is computed via a greedy algorithm for selecting the mixing proportions.