A survey on genomic data by privacy-preserving techniques perspective

Assessing Privacy Vulnerabilities in Genetic Data Sets: Scoping Review

BACKGROUND

Genetic data are widely considered inherently identifiable. However, genetic data sets come in many shapes and sizes, and the feasibility of privacy attacks depends on their specific content. Assessing the reidentification risk of genetic data is complex, yet there is a lack of guidelines or recommendations that support data processors in performing such an evaluation.

OBJECTIVE

This study aims to gain a comprehensive understanding of the privacy vulnerabilities of genetic data and create a summary that can guide data processors in assessing the privacy risk of genetic data sets.

METHODS

We conducted a 2-step search, in which we first identified 21 reviews published between 2017 and 2023 on the topic of genomic privacy and then analyzed all references cited in the reviews (n=1645) to identify 42 unique original research studies that demonstrate a privacy attack on genetic data. We then evaluated the type and components of genetic data exploited for these attacks as well as the effort and resources needed for their implementation and their probability of success.

RESULTS

From our literature review, we derived 9 nonmutually exclusive features of genetic data that are both inherent to any genetic data set and informative about privacy risk: biological modality, experimental assay, data format or level of processing, germline versus somatic variation content, content of single nucleotide polymorphisms, short tandem repeats, aggregated sample measures, structural variants, and rare single nucleotide variants.

CONCLUSIONS

On the basis of our literature review, the evaluation of these 9 features covers the great majority of privacy-critical aspects of genetic data and thus provides a foundation and guidance for assessing genetic data risk.

Future-proofing genomic data and consent management: a comprehensive review of technology innovations

Genomic information is increasingly used to inform medical treatments and manage future disease risks. However, any personal and societal gains must be carefully balanced against the risk to individuals contributing their genomic data. Expanding our understanding of actionable genomic insights requires researchers to access large global datasets to capture the complexity of genomic contribution to diseases. Similarly, clinicians need efficient access to a patient's genome as well as population-representative historical records for evidence-based decisions. Both researchers and clinicians hence rely on participants to consent to the use of their genomic data, which in turn requires trust in the professional and ethical handling of this information. Here, we review existing and emerging solutions for secure and effective genomic information management, including storage, encryption, consent, and authorization that are needed to build participant trust. We discuss recent innovations in cloud computing, quantum-computing-proof encryption, and self-sovereign identity. These innovations can augment key developments from within the genomics community, notably GA4GH Passports and the Crypt4GH file container standard. We also explore how decentralized storage as well as the digital consenting process can offer culturally acceptable processes to encourage data contributions from ethnic minorities. We conclude that the individual and their right for self-determination needs to be put at the center of any genomics framework, because only on an individual level can the received benefits be accurately balanced against the risk of exposing private information.

Balancing Security and Privacy in Genomic Range Queries*

Exciting recent advances in genome sequencing, coupled with greatly reduced storage and computation costs, make genomic testing increasingly accessible to individuals. Already today, one’s digitized DNA can be easily obtained from a sequencing lab and later used to conduct numerous tests by engaging with a testing facility. Due to the inherent sensitivity of genetic material and the often-proprietary nature of genomic tests, privacy is a natural and crucial issue. While genomic privacy received a great deal of attention within and outside the research community, genomic security has not been sufficiently studied. This is surprising since the usage of fake or altered genomes can have grave consequences, such as erroneous drug prescriptions and genetic test outcomes.

Unfortunately, in the genomic domain, privacy and security (as often happens) are at odds with each other. In this paper, we attempt to reconcile security with privacy in genomic testing by designing a novel technique for a secure and private genomic range query protocol between a genomic testing facility and an individual user. The proposed technique ensures authenticity and completeness of user-supplied genomic material while maintaining its privacy by releasing only the minimum thereof. To confirm its broad usability, we show how to apply the proposed technique to a previously proposed genomic private substring matching protocol. Experiments show that the proposed technique offers good performance and is quite practical. Furthermore, we generalize the genomic range query problem to sparse integer sets and discuss potential use cases.