Privacy-preserving Approximate GWAS computation based on Homomorphic Encryption

One of three tasks in a secure genome analysis competition called IDASH 2018 was to develop a solution for privacy-preserving GWAS computation based on homomorphic encryption. The scenario is that a data holder encrypts a number of individual records, each of which consists of several phenotype and genotype data, and provide the encrypted data to an untrusted server. Then, the server performs a GWAS algorithm based on homomorphic encryption without the decryption key and outputs the result in encrypted state so that there is no information leakage on the sensitive data to the server. We develop a privacy-preserving semi-parallel GWAS algorithm by applying an approximate homomorphic encryption scheme HEAAN. Fisher scoring and semi-parallel GWAS algorithms are modified to be efficiently computed over homomorphically encrypted data with several optimization methodologies; substitute matrix inversion by an adjoint matrix, avoid computing a superfluous matrix of super-large size, and transform the algorithm into an approximate version. Our modified semi-parallel GWAS algorithm based on homomorphic encryption which achieves 128-bit security takes $30$--$40$ minutes for $245$ samples containing $10,000$--$15,000$ SNPs. Compared to the true $p$-value from the original semi-parallel GWAS algorithm, the $F_1$ score of our $p$-value result is over $0.99$

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

BLOOM: BLoom filter based oblivious outsourced matchings

Whole genome sequencing has become fast, accurate, and cheap, paving the way towards the large-scale collection and processing of human genome data. Unfortunately, this dawning genome era does not only promise tremendous advances in biomedical research but also causes unprecedented privacy risks for the many. Handling storage and processing of large genome datasets through cloud services greatly aggravates these concerns. Current research efforts thus investigate the use of strong cryptographic methods and protocols to implement privacy-preserving genomic computations

Verifiable Encodings for Secure Homomorphic Analytics

Homomorphic encryption, which enables the execution of arithmetic operations directly on ciphertexts, is a promising solution for protecting privacy of cloud-delegated computations on sensitive data. However, the correctness of the computation result is not ensured. We propose two error detection encodings and build authenticators that enable practical client-verification of cloud-based homomorphic computations under different trade-offs and without compromising on the features of the encryption algorithm. Our authenticators operate on top of trending ring learning with errors based fully homomorphic encryption schemes over the integers. We implement our solution in VERITAS, a ready-to-use system for verification of outsourced computations executed over encrypted data. We show that contrary to prior work VERITAS supports verification of any homomorphic operation and we demonstrate its practicality for various applications, such as ride-hailing, genomic-data analysis, encrypted search, and machine-learning training and inference.Comment: update authors, typos corrected, scheme update