Ensuring privacy in the study of pathogen genetics

Abstract

Rapid growth in the genetic sequencing of pathogens in recent years has led to the creation of large sequence databases. This aggregated sequence data can be very useful for tracking and predicting epidemics of infectious diseases. However, the balance between the potential public health benefit and the risk to personal privacy for individuals whose genetic data (personal or pathogen) are included in such work has been difficult to delineate, because neither the true benefit nor the actual risk to participants has been adequately defined. Existing approaches to minimise the risk of privacy loss to participants are based on de-identification of data by removal of a predefined set of identifiers. These approaches neither guarantee privacy nor protect the usefulness of the data. We propose a new approach to privacy protection that will quantify the risk to participants, while still maximising the usefulness of the data to researchers. This emerging standard in privacy protection and disclosure control, which is known as differential privacy, uses a process-driven rather than data-centred approach to protecting privacy.

Reassessing the Ethics of Molecular HIV Surveillance in the Era of Cluster Detection and Response: Toward HIV Data Justice

“…Greater genetic similarity indicates more recent transmission (CDC 2018; Oster 2019). Phylogenetic HIV analysis has been used in multiple ways, such as for retrospective analyses of samples to understand historical transmission patterns, to map rates of antiretroviral resistance, to discern global transmission patterns, and other uses (Crane 2011;Gagnon and Guta 2012;Mehta et al 2014).…”

Perceptions of Molecular Epidemiology Studies of Hiv among Stakeholders

“…In the context of HIV ME research, most scientific journals require that the analysed sequence data be published, information that may be unique to each individual. Coupled with the fact that the study populations are often small, these factors can significantly increase the risk of identification, 11 and may suggest, but never definitively prove, possible sources of transmission. 8 , 9 Furthermore, this information may be used by public health departments in outbreak investigations, and the published reports of these investigations, even when devoid of protected health information, may still provide clues to the identities of individuals involved.…”

Ethical challenges in pathogen sequencing: a systematic scoping review

“…All articles were initially screened by title and abstract and thirty-nine full text articles were assessed for eligibility. Twenty eight articles were included in the final analysis; three ethical guidelines or frameworks 14 – 17 ; seven empirical research studies 1 , 18 – 23 ; eight reviews of the ethics 2 , 17 – 21 ; and ten publications that contained a section on the ethical aspects of pathogen sequencing 24 – 33 . The literature largely originated from the US and other high-income countries (HICs, country determined by lead author institution): nine from the United States (US), five from the United Kingdom (UK), five from The Netherlands, three from Canada, two from Switzerland, one from Australia, and one from Italy.…”