Privacy in the Genomic Era

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward

Routes for breaching and protecting genetic privacy

We are entering the era of ubiquitous genetic information for research, clinical care, and personal curiosity. Sharing these datasets is vital for rapid progress in understanding the genetic basis of human diseases. However, one growing concern is the ability to protect the genetic privacy of the data originators. Here, we technically map threats to genetic privacy and discuss potential mitigation strategies for privacy-preserving dissemination of genetic data.Comment: Draft for comment

SANNS: Scaling Up Secure Approximate k-Nearest Neighbors Search

The $k$-Nearest Neighbor Search ($k$-NNS) is the backbone of several cloud-based services such as recommender systems, face recognition, and database search on text and images. In these services, the client sends the query to the cloud server and receives the response in which case the query and response are revealed to the service provider. Such data disclosures are unacceptable in several scenarios due to the sensitivity of data and/or privacy laws. In this paper, we introduce SANNS, a system for secure $k$-NNS that keeps client's query and the search result confidential. SANNS comprises two protocols: an optimized linear scan and a protocol based on a novel sublinear time clustering-based algorithm. We prove the security of both protocols in the standard semi-honest model. The protocols are built upon several state-of-the-art cryptographic primitives such as lattice-based additively homomorphic encryption, distributed oblivious RAM, and garbled circuits. We provide several contributions to each of these primitives which are applicable to other secure computation tasks. Both of our protocols rely on a new circuit for the approximate top-$k$ selection from $n$ numbers that is built from $O(n + k^2)$ comparators. We have implemented our proposed system and performed extensive experimental results on four datasets in two different computation environments, demonstrating more than $18-31\times$ faster response time compared to optimally implemented protocols from the prior work. Moreover, SANNS is the first work that scales to the database of 10 million entries, pushing the limit by more than two orders of magnitude.Comment: 18 pages, to appear at USENIX Security Symposium 202

PrivGenDB: Efficient and privacy-preserving query executions over encrypted SNP-Phenotype database

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 86.4{\mu}s, respectively, that outperforms the existing schemes

Algorithms that Remember: Model Inversion Attacks and Data Protection Law

Many individuals are concerned about the governance of machine learning systems and the prevention of algorithmic harms. The EU's recent General Data Protection Regulation (GDPR) has been seen as a core tool for achieving better governance of this area. While the GDPR does apply to the use of models in some limited situations, most of its provisions relate to the governance of personal data, while models have traditionally been seen as intellectual property. We present recent work from the information security literature around `model inversion' and `membership inference' attacks, which indicate that the process of turning training data into machine learned systems is not one-way, and demonstrate how this could lead some models to be legally classified as personal data. Taking this as a probing experiment, we explore the different rights and obligations this would trigger and their utility, and posit future directions for algorithmic governance and regulation.Comment: 15 pages, 1 figur

Anonymization and Risk

Perfect anonymization of data sets that contain personal information has failed. But the process of protecting data subjects in shared information remains integral to privacy practice and policy. While the deidentification debate has been vigorous and productive, there is no clear direction for policy. As a result, the law has been slow to adapt a holistic approach to protecting data subjects when data sets are released to others. Currently, the law is focused on whether an individual can be identified within a given set. We argue that the best way to move data release policy past the alleged failures of anonymization is to focus on the process of minimizing risk of reidentification and sensitive attribute disclosure, not preventing harm. Process-based data release policy, which resembles the law of data security, will help us move past the limitations of focusing on whether data sets have been “anonymized.” It draws upon different tactics to protect the privacy of data subjects, including accurate deidentification rhetoric, contracts prohibiting reidentification and sensitive attribute disclosure, data enclaves, and query-based strategies to match required protections with the level of risk. By focusing on process, data release policy can better balance privacy and utility where nearly all data exchanges carry some risk

Lower Bounds for Oblivious Near-Neighbor Search

We prove an $\Omega(d \lg n/ (\lg\lg n)^2)$ lower bound on the dynamic cell-probe complexity of statistically $\mathit{oblivious}$ approximate-near-neighbor search ($\mathsf{ANN}$) over the $d$-dimensional Hamming cube. For the natural setting of $d = \Theta(\log n)$, our result implies an $\tilde{\Omega}(\lg^2 n)$ lower bound, which is a quadratic improvement over the highest (non-oblivious) cell-probe lower bound for $\mathsf{ANN}$. This is the first super-logarithmic $\mathit{unconditional}$ lower bound for $\mathsf{ANN}$ against general (non black-box) data structures. We also show that any oblivious $\mathit{static}$ data structure for decomposable search problems (like $\mathsf{ANN}$) can be obliviously dynamized with $O(\log n)$ overhead in update and query time, strengthening a classic result of Bentley and Saxe (Algorithmica, 1980).Comment: 28 page