An increasing number of individuals are turning to Direct-To-Consumer (DTC) genetic testing to learn about their predisposition to diseases, traits, and or ancestry. DTC companies like 23andme and this http URL have started to offer popular and affordable ancestry and genealogy tests, with services allowing users to find unknown relatives and long-distant cousins. Naturally, access and possible dissemination of genetic data prompts serious privacy concerns, thus motivating the need to design efficient primitives supporting private genetic tests. In this paper, we present an effective protocol for privacy-preserving genetic relatedness test (PPGRT), enabling a cloud server to run relatedness tests on input an encrypted genetic database and a test facility's encrypted genetic sample. We reduce the test to a data matching problem and perform it, privately, using searchable encryption. Finally, a performance evaluation of hamming distance based PP-GRT attests to the practicality of our proposals.
Two recent works @cite_21 @cite_14 open a new perspective for privacy-friendly GRT by using fuzzy encryption technique. In these systems, each individual first compresses its haplotype into a 0 1 string, called private genome sketch, and then encrypts'' the sketch by using a random row of a given error correct code matrix. One may detect if user @math is relative by downloading @math 's encrypted sketch, and next decrypting'' the sketch with its own private genome sketch. If the decryption closely leads to a row in the matrix, the haplotypes of both individuals are approximately matched. However, all the aforementioned computation approaches do not really scale well in practice, as they all suffer from an important limitation, i.e., the client is burdened with heavy computation and communication overhead, as it has to download all related encrypted'' results from the server and perform a huge numbers of decryption to identify the relatedness. How to design scalable privacy-preserving GRT that can scale on both server and client side constitutes the main motivation for our work.
@cite_14 @cite_21
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Genomic datasets are often associated with sensitive phenotypes. Therefore, the leak of membership information is a major privacy risk. Genomic beacons aim to provide a secure, easy to implement, and standardized interface for data sharing by only allowing yes no queries on the presence of specific alleles in the dataset. Previously deemed secure against re-identification attacks, beacons were shown to be vulnerable despite their stringent policy. Recent studies have demonstrated that it is possible to determine whether the victim is in the dataset, by repeatedly querying the beacon for his her single nucleotide polymorphisms (SNPs). In this work, we propose a novel re-identification attack and show that the privacy risk is more serious than previously thought. Using the proposed attack, even if the victim systematically hides informative SNPs (i.e., SNPs with very low minor allele frequency -MAF-), it is possible to infer the alleles at positions of interest as well as the beacon query results with very high confidence. Our method is based on the fact that alleles at different loci are not necessarily independent. We use the linkage disequilibrium and a high-order Markov chain-based algorithm for the inference. We show that in a simulated beacon with 65 individuals from the CEU population, we can infer membership of individuals with 95 confidence with only 5 queries, even when SNPs with MAF less than 0.05 are hidden. This means, we need less than 0.5 of the number of queries that existing works require, to determine beacon membership under the same conditions. We further show that countermeasures such as hiding certain parts of the genome or setting a query budget for the user would fail to protect the privacy of the participants under our adversary model. We provide formal definitions and efficient secure techniques for turning noisy information into keys usable for any cryptographic application, and, in particular, reliably and securely authenticating biometric data. Our techniques apply not just to biometric information, but to any keying material that, unlike traditional cryptographic keys, is (1) not reproducible precisely and (2) not distributed uniformly. We propose two primitives: a fuzzy extractor reliably extracts nearly uniform randomness @math from its input; the extraction is error-tolerant in the sense that @math will be the same even if the input changes, as long as it remains reasonably close to the original. Thus, @math can be used as a key in a cryptographic application. A secure sketch produces public information about its input @math that does not reveal @math and yet allows exact recovery of @math given another value that is close to @math . Thus, it can be used to reliably reproduce error-prone biometric inputs without incurring the security risk inherent in storing them. We define the primitives to be both formally secure and versatile, generalizing much prior work. In addition, we provide nearly optimal constructions of both primitives for various measures of “closeness” of input data, such as Hamming distance, edit distance, and set difference. In this paper, we propose privacy-enhancing technologies for medical tests and personalized medicine methods that use patients' genomic data. Focusing on genetic disease-susceptibility tests, we develop a new architecture (between the patient and the medical unit) and propose a "privacy-preserving disease susceptibility test" (PDS) by using homomorphic encryption and proxy re-encryption. Assuming the whole genome sequencing to be done by a certified institution, we propose to store patients' genomic data encrypted by their public keys at a "storage and processing unit" (SPU). Our proposed solution lets the medical unit retrieve the encrypted genomic data from the SPU and process it for medical tests and personalized medicine methods, while preserving the privacy of patients' genomic data. We also quantify the genomic privacy of a patient (from the medical unit's point of view) and show how a patient's genomic privacy decreases with the genetic tests he undergoes due to (i) the nature of the genetic test, and (ii) the characteristics of the genomic data. Furthermore, we show how basic policies and obfuscation methods help to keep the genomic privacy of a patient at a high level. We also implement and show, via a complexity analysis, the practicality of PDS. The human genetics community needs robust protocols that enable secure sharing of genomic data from participants in genetic research. Beacons are web servers that answer allele-presence queries—such as “Do you have a genome that has a specific nucleotide (e.g., A) at a specific genomic position (e.g., position 11,272 on chromosome 1)?”—with either “yes” or “no.” Here, we show that individuals in a beacon are susceptible to re-identification even if the only data shared include presence or absence information about alleles in a beacon. Specifically, we propose a likelihood-ratio test of whether a given individual is present in a given genetic beacon. Our test is not dependent on allele frequencies and is the most powerful test for a specified false-positive rate. Through simulations, we showed that in a beacon with 1,000 individuals, re-identification is possible with just 5,000 queries. Relatives can also be identified in the beacon. Re-identification is possible even in the presence of sequencing errors and variant-calling differences. In a beacon constructed with 65 European individuals from the 1000 Genomes Project, we demonstrated that it is possible to detect membership in the beacon with just 250 SNPs. With just 1,000 SNP queries, we were able to detect the presence of an individual genome from the Personal Genome Project in an existing beacon. Our results show that beacons can disclose membership and implied phenotypic information about participants and do not protect privacy a priori. We discuss risk mitigation through policies and standards such as not allowing anonymous pings of genetic beacons and requiring minimum beacon sizes.