Sara Jafarbeiki

Sara Jafarbeiki, Raj Gaire, Amin Sakzad et al.

The cost of DNA sequencing has resulted in a surge of genetic data being utilised to improve scientific research, clinical procedures, and healthcare delivery in recent years. Since the human genome can uniquely identify an individual, this characteristic also raises security and privacy concerns. In order to balance the risks and benefits, governance mechanisms including regulatory and ethical controls have been established, which are prone to human errors and create hindrance for collaboration. Over the past decade, technological methods are also catching up that can support critical discoveries responsibly. In this paper, we explore regulations and ethical guidelines and propose our visions of secure/private genomic data storage/processing/sharing platforms. Then, we present some available techniques and a conceptual system model that can support our visions. Finally, we highlight the open issues that need further investigation.

Sara Jafarbeiki, Amin Sakzad, Shabnam Kasra Kermanshahi et al.

Searchable symmetric encryption (SSE) has been used to protect the confidentiality of genomic data while providing substring search and range queries on a sequence of genomic data, but it has not been studied for protecting single nucleotide polymorphism (SNP)-phenotype data. 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 SSE to ensure confidentiality while conducting different types of queries on encrypted genomic data, phenotype and other information of individuals to help analysts/clinicians in their analysis/care. To the best of our knowledge, PrivGenDB construction is the first SSE-based approach ensuring the confidentiality of shared SNP-phenotype data through encryption while making the computation/query process efficient and scalable for biomedical research and care. Furthermore, 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 handles the dataset containing both genotype and phenotype, and 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 86.4μs, respectively, that outperforms the existing schemes.