Efficient Secure Outsourcing of Genome-Wide Association Studies

A genome-wide association study aimed at finding genetic variations associated with a particular disease is a common approach used in genetic epidemiology. We present a new efficient secure outsourcing computation of GWAS using homomorphic encryption based on ring-LWE. Our method works by virtue of the fact that integer vectors can be packed into a single cipher text and a scalar product of integer vectors can be evaluated using a single homomorphic multiplication. We demonstrate by experimentation that secure outsourcing computation of a ?2 test for independence with 5,000 samples can be processed in one second including communication time, which is 250 times faster than an existing FHE solution.