DNAstack Launches Clinical Evidence Beacons to Drive Crowdsourcing for Genetic Disease Discovery
October 14, 2019
The  Beacon Network , where new Clinical Evidence Beacons can be searched for crowdsourcing classification of genomic variants.
DNAstack today announced the launch of Clinical Evidence Beacons on the Beacon Network, a real-time search engine for finding genetic mutations across a global network of genomic datasets.These additions will enable medical laboratories to crowdsource the interpretation of variants through a secure social network.Accurately interpreting DNA variants identified through genetic testing is essential for patients and clinicians to make informed medical decisions, for a growing number of medical use cases. While some of those variants can be confidently predicted to be pathogenic or benign based on previous studies and data accessible through variant interpretation resources, in many cases evidence is missing or inconsistent, resulting in conflicting evaluations or reporting as “variants of unknown significance” (VUS). Clinical Evidence Beacons facilitate faster and more consistent variant classifications by securely sharing variant interpretation evidence between collaborating organizations, accelerating the exchange of critical knowledge and improving support for patients affected by genetic diseases and carriers of variants that have an impact on medical decision making. The Beacon Network, where new Clinical Evidence Beacons can be searched for crowdsourcing classification of genomic variants.Building upon the Global Alliance for Genomic and Health (GA4GH) Beacon API, an open standard that allows researchers to determine whether a given variant exists within a genomic dataset, Clinical Evidence Beacons are an extension of the protocol being piloted by DNAstack, allowing uncurated knowledge about a variant to be shared and discovered in real time.“The Beacon API 1.0, which was approved as a GA4GH standard last year, validates the international community’s willingness to work together to define standards and engage in data sharing in a meaningful way,” said Miro Cupak, VP Engineering at DNAstack. “The original protocol was intentionally simple. We’ve since been exploring more powerful derivatives, and learned that by integrating clinical data in the payload of the Beacon that we can help solve outstanding issues faced by the clinical genomics community. Clinical Evidence Beacons, while not formally approved as a GA4GH standard, demonstrate one potential application being designed for future versions of the protocol.”
Miro Cupak, VP Engineering at DNAstackThe first Clinical Evidence Beacons to join the Beacon Network come from the Canadian Open Genetics Repository (COGR), a network of over 20 laboratories that have come together to share information about variants and clinical cases. Members of the COGR are now able to search controlled access Clinical Evidence Beacons for variants of interest on the Beacon Network. A national effort to improve the quality of variant classification has been led by the COGR, who previously published that the percentage of variants with discordant classifications dropped from 26.7% to 14.2% as a result of crowdsourcing, demonstrating the power of collaboration between clinical genomics labs.“Our understanding of genetic data continues to evolve and there is often not a one-to-one correlation between genetic variation and disease, so international or global data sharing efforts are vital to moving the field forward,” said Dr. Jordan Lerner-Ellis, principle investigator of the COGR and Head of Advanced Molecular Diagnostics at Toronto’s Mount Sinai Hospital, Sinai Health System and Associate Professor at the University of Toronto. “Systems that allow for easily accessible real-time data sharing will be increasingly important to be able to provide the most up-to-date information and to translate it into patient care.”While the cost of genome sequencing has decreased significantly, it is still costly. Software that enables valuable biomedical data to be shared will enable future healthcare systems to draw on distributed collections of data in real time, unconstrained by traditional institutional silos and long publication cycles. As we move toward personalized healthcare, there is a need for such systems to integrate genomic information, clinical data, and real-world evidence to better inform treatment decisions.“There is an enormous need to share genomic information and we have seen worldwide interest in the application of Beacons in healthcare environments,” said Jordi Rambla, European Genome-phenome Archive (EGA) Team Lead at the Centre for Genomic Regulation (CRG). “Working with the clinical community, we are pioneering ideas to improve upon Beacon 1.0, and using this knowledge and experience to inform the next version of this standard. Ultimately, Clinical Evidence Beacons could make sharing genomic information, as well as phenotypic data, easier, faster, and more securely than is possible today, accelerating knowledge exchange, diagnoses, and improvements to patient care.” 
Miro Cupak, VP Engineering at DNAstack
Jordi Rambla, European Genome-phenome Archive Team Lead at the Centre for Genomic Regulation
Jordi Rambla, European Genome-phenome Archive Team Lead at the Centre for Genomic RegulationWhile DNAstack’s support for clinical use cases has been developed as extensions to the current Beacon version, an international effort coordinated by the GA4GH Discovery Work Stream and lead by the ELIXIR Beacon Project currently prepares a major upgrade of the GA4GH Beacon protocol. Since the roadmap of the next version includes changes supporting a variety of stakeholder defined biomedical use cases, incorporation of the upcoming Beacon protocol into software supported by DNAstack will accelerate future applications for genomic variant research and discovery.About DNAstackDNAstack’s mission is to improve the lives of millions of people affected by genetic disease by breaking down barriers to data sharing and discovery. DNAstack develops standards and technologies for scientists to more efficiently find, access, and analyze the world’s exponentially growing volumes of genomic and biomedical data.Photo CreditsCape Canaveral Air Force Station, United States. Photo Credit: SpaceX