In this article, we propose a novel model, PrivGenDB, for securely storing
and efficiently conducting different queries on genomic data outsourced to an
honest-but-curious cloud server. To instantiate PrivGenDB, we use searchable
symmetric encryption (SSE) to ensure confidentiality while providing the
required functionality. To the best of our knowledge, PrivGenDB construction is
the first SSE-based approach ensuring the confidentiality of shared Single
Nucleotide Polymorphism (SNP)-phenotype data through encryption while making
the computation/query process efficient and scalable for biomedical research
and care. It supports a variety of query types on genomic data, including count
queries, Boolean queries, and k’-out-of-k match queries. Finally, the PrivGenDB
model not only can handle the dataset containing both genotype and phenotype,
but it also supports storing and managing other metadata like gender and
ethnicity privately. Computer evaluations on a dataset with 5,000 records and
1,000 SNPs demonstrate that a count/Boolean query and a k’-out-of-k match query
over 40 SNPs take approximately 4.3s and 86.4{mu}s, respectively, that
outperforms the existing schemes.

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