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

Systematizing Genome Privacy Research: A Privacy-Enhancing Technologies Perspective

Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a number of security and privacy concerns stemming from the distinctive characteristics of genomic data. To address them, a new research community has emerged and produced a large number of publications and initiatives. In this paper, we rely on a structured methodology to contextualize and provide a critical analysis of the current knowledge on privacy-enhancing technologies used for testing, storing, and sharing genomic data, using a representative sample of the work published in the past decade. We identify and discuss limitations, technical challenges, and issues faced by the community, focusing in particular on those that are inherently tied to the nature of the problem and are harder for the community alone to address. Finally, we report on the importance and difficulty of the identified challenges based on an online survey of genome data privacy expertsComment: To appear in the Proceedings on Privacy Enhancing Technologies (PoPETs), Vol. 2019, Issue

How Can We Move Clinical Genomics Beyond the Hype?

Examines the debate over increased use of genetic testing, due in part to lax regulation, and its consequences: wasteful spending, patient harm, and health system challenges. Makes recommendations for implementation of and data on promising technologies

The O’Neill Institute for National and Global Health Law: Discovering Innovative Solutions for the Most Pressing Health Problems Facing the Nation and the World

The connection between health and an individual’s ability to function in society, as well as the importance of health to a society’s economic, political, and social wellbeing necessitates finding innovative solutions to the world’s most pressing health problems. The O’Neill Institute for National and Global Health Law at Georgetown University seeks to demonstrate the role that academia can play in addressing complex national and global health problems in a comprehensive, evidence-based, intellectually-rigorous, and nonpartisan manner. The O’Neill Institute currently has three research programs: global health law, national health law, and the center for disease prevention and outcomes. Projects within these programs examine a broad range of health law and policy issues, such as global health governance, global tobacco control, health worker migration, emergency preparedness, national and Chinese health reform, HIV and AIDS issues, food safety, and personalized medicine. These projects merge the scholarly capacity within the institute with the resources of its partners, which include the World Health Organization, World Bank, the Bill & Melinda Gates Foundation, the U.S. Centers for Disease Control and Prevention, and the Campaign for Tobacco Free Kids. Additionally, the faculty and fellows of the O’Neill Institute regularly produce high-level scholarship and engage in teaching offering multi-disciplinary course offerings and innovative graduate degree programs. URL: http://www.law.georgetown.edu/oneillinstitute/documents/2010-03-09_oneill-solutions.pdf; http://mjlst.umn.edu/uploads/Pf/V1/PfV1QhiCT6lUOsv1AqDTCA/111_gostin.pdf

Harnessing Openness to Transform American Health Care

The Digital Connections Council (DCC) of the Committee for Economic Development (CED) has been developing the concept of openness in a series of reports. It has analyzed information and processes to determine their openness based on qualities of "accessibility" and "responsiveness." If information is not available or available only under restrictive conditions it is less accessible and therefore less "open." If information can be modified, repurposed, and redistributed freely it is more responsive, and therefore more "open." This report looks at how "openness" is being or might usefully be employed in the healthcare arena. This area, which now constitutes approximately 16-17 percent of GDP, has long frustrated policymakers, practitioners, and patients. Bringing greater openness to different parts of the healthcare production chain can lead to substantial benefits by stimulating innovation, lowering costs, reducing errors, and closing the gap between discovery and treatment delivery. The report is not exhaustive; it focuses on biomedical research and the disclosure of research findings, processes of evaluating drugs and devices, the emergence of electronic health records, the development and implementation of treatment regimes by caregivers and patients, and the interdependence of the global public health system and data sharing and worldwide collaboration

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Applications of the ACGT Master Ontology on Cancer

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far