Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave

BioRxiv : the Preprint Server for Biology
Can KockanCenk Sahinalp


Current practices in collaborative genomic data analysis (e.g. PCAWG) necessitate all involved parties to exchange individual patient data and perform all analysis locally, or use a trusted server for maintaining all data to perform analysis in a single site (e.g. the Cancer Genome Collaboratory). Since both approaches involve sharing genomic sequence data - which is typically not feasible due to privacy issues, collaborative data analysis remains to be a rarity in genomic medicine. In order to facilitate efficient and effective collaborative or remote genomic computation we introduce SkSES (Sketching algorithms for Secure Enclave based genomic data analysiS), a computational framework for performing data analysis and querying on multiple, individually encrypted genomes from several institutions in an untrusted cloud environment. Unlike other techniques for secure/privacy preserving genomic data analysis, which typically rely on sophisticated cryptographic techniques with prohibitively large computational overheads, SkSES utilizes the secure enclaves supported by current generation microprocessor architectures such as Intel's SGX. The key conceptual contribution of SkSES is its use of sketching data structures that can fit in t...Continue Reading

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