Securing Fieldable Bioinformatics
Daniel Wyschogrod, Steven T. Murphy, Jacob Beal, Allison J. Taggart · 2023
Nanopore sequencing offers promising potential for rapid and target-agnostic sensing and diagnostics in field applications. However, realizing this potential necessitates addressing not only sample collection and processing challenges but also concerns related to information security and privacy when deployed in field devices. We thus introduce the Secure Bloom-Filter Analysis and Compression (SB-FAC) architecture, which breaks bioinformatics computations into a Bloom-filter-based field preprocessing stage that identifies regions of interest in the raw read data and a server-side interpretation stage that combines and interprets these identified regions. Sensitive information encoded in the Bloom filter can be protected from extraction by the use of a cryptographic hash paired with a salt in a Trusted Platform Module (TPM). We experimentally validate the predicted scaling of this approach, confirming that cost per operation linear in salt length, while reverse engineering cost is exponential.