Secure genomic testing with size- and position-hiding private substring matching

Recent progress in genomics and bioinformatics is bringing complete and on-demand sequencing of human (and other) genomes closer and closer to reality. Despite exciting new opportunities, affordable and ubiquitous genome sequencing prompts some serious privacy and ethical concerns, owing to extreme sensitivity and uniqueness of genomic information. At the same time, new medical applications, such as personalized medicine, require testing genomes for specific markers that themselves represent sensitive (e.g., proprietary) material. This paper focuses on privacy challenges posed by such genetic tests. It presents a secure and efficient protocol called: Size- and Position-Hiding Private Substring Match- ing (SPH-PSM). This protocol allows two parties -- one with a digitized genome and the other with a set of DNA markers -- to conduct a test, such that the result is only learned by the former, and no other information is learned by either party. In particular, the genome owner does not even learn the size or the position of the markers, which makes SPH-PSM the first of its kind. Finally, we report on a prototype of the proposed technique which attests to its practicality.