Beacon Project Mitigates Privacy Risks While Maximizing Value of Responsible Data Sharing

TORONTO, CANADA — The Beacon Project is one of three data sharing demonstration projects of the Global Alliance for Genomics and Health (GA4GH). It is an effort to enable international sites to share genetic data to improve human health in the simplest of technical contexts. It is based on a yes/no query that tells searchers whether a specific genetic variant is contained in a participating database.

Recent research published in American Journal of Human Genetics by Carlos Bustamante and Suyash Shringarpure of Stanford University demonstrates a potential to use the Beacon Network to determine the presence or absence of an individual’s genome in a particular Beacon database, but only in the currently exceptional scenario in which that genome, or the genome of a very close relative, is already known to the person making the query.

“We welcome the paper and are pleased to now have careful quantitative analysis of this particular risk scenario. We look forward to ongoing interactions with the authors and others to ensure beacons provide maximum value while respecting privacy,” said Peter Goodhand, executive director of the Global Alliance for Genomics and Health.

"Sharing of genomic data is vital for the future of biomedical sciences and genomic medicine. It has been great to work closely with GA4GH to address the issues raised in our paper and execute policy changes as new theory is developed,” said Bustamante. “These are subtle problems and it is only as we begin to engineer and implement that they come to the forefront. The GA4GH Beacon team had already thought about many of the issues we raised and our work helped provide a theoretical framework to guide design."

“A researcher can use the Beacon Network to discover whether or not genetic data relevant to his or her work are present in a Beacon database,” said David Haussler, Vice Chair of the GA4GH Steering Committee. “If they are, that researcher might make further arrangements with the appropriate institution to obtain more information, in compliance with that institution’s privacy policies.” The Beacon approach was carefully chosen both for its ease of use and to not overly expose genomic data to privacy or security risks, as neither entire individual genome sequences nor patient information are currently shared directly through a Beacon.

In most contemporary circumstances, if someone has already obtained a person’s genetic sequence elsewhere, there is not much more information to be gained by learning that this sequence also appears in a Beacon database. However, one can imagine situations in which it is possible to obtain, perhaps illegally, a person’s genome without other information. In those scenarios, learning that the genome is among those present in a specific institutional Beacon database could reveal sensitive information. For example, if a database is almost exclusively associated with a known phenotype, discovering that an individual’s genome is in the database may allow inferences about the individual’s phenotype.

Beacons conform to the technology standards and operational guidelines defined in the GA4GH Security Technology Infrastructure and adhere to the Framework for the Responsible Sharing of Genomic and Health-Related Data. Additionally, the Beacon Project has been working with GA4GH experts, including the paper’s authors, since the project’s inception to mitigate potential privacy concerns directly related to this issue.

Mitigation efforts, which adhere to the best practices outlined in the GA4GH Privacy & Security Policy, include:

  • Aggregating data among multiple Beacons to increase database size and obscure the database of origin;

  • Creating an information budgeting system to track the rate at which information is revealed and to restrict access when the information disclosed exceeds a certain threshold; and

  • Introducing multiple tiers of secured access, including requiring users to be authorised for data access and to agree not to attempt specific risky scenarios.

“GA4GH is committed to enabling genomic data sharing for the betterment of medicine in the most responsible and secure ways possible,” said Thomas Hudson, Chair of the GA4GH Steering Committee. “Our continued work will build the foundation for smarter and more secure data sharing — a critical task as data networks become even more complex and information-rich.”

For more information about the Beacon Project, visit and read a recent profile in Bio-IT World:….


The Global Alliance for Genomics and Health (GA4GH) is an international, non-profit alliance formed to help accelerate the potential of genomic medicine to advance human health. Bringing together over 370 leading organizations working in healthcare, research, disease and patient advocacy, life science, and information technology, partners in GA4GH are working together to create a common framework of standards and harmonized approaches to enable the responsible, voluntary, and secure sharing of genomic and clinical data. Learn more at: