NEW YORK – Genomics England is working with Sano Genetics and Zetta Genomics to develop a new software tool that will allow genomics research project participants with rare diseases to better self-report information and receive updates back.
The tool, set to be introduced next year, could also find application in other indications such as cancer. Sano Genetics aims to eventually make the finished platform available to its customers worldwide.
Innovate UK, a British government funding body, decided to back the project earlier this year with a £450,000 ($560,000) grant. Its aim is to develop a platform to continuously capture data from patients and their families. Data inputs might include wearable devices or digital journals that will give researchers a look at disease progression or reaction to therapies. By collecting such data, Genomics England hopes to foster the creation of new therapies or tests, as well as give participants a vehicle for input and feedback, something they have requested for some time.
"From a participant's point of view, it's something that has always been requested and mindful of, that our participants want to be actively involved in research," said Fiona Maleady-Crowe, head of ethics at Genomics England. "Patients always say they know the most about their condition, because they have it, or they look after someone who has it, so to be able to bridge that kind of gap is something we have always been conscious of and it was time to address that."
To achieve that, Genomics England decided to work with Cambridge, UK-area startups Sano Genetics and Zetta Genomics. Founded in 2017, Sano Genetics has developed a platform for patient engagement in research that can be adopted for population-scale genomics research programs, while two-year-old Zetta has experience in using OpenCB, a widely used, open source software for managing genomic data.
According to Augusto Rendon, chief bioinformatician at Genomics England, the decision to work with two early-stage companies fits in with the organization's purview to support UK genomics companies. "When Genomics England was founded in 2013, there was always an important goal to kickstart development around genomics," said Rendon. "At this point in time though, it's less about commissioning work and more about seeing the synergy between the needs of our participants, the desire from Sano to test its system to create working proof of concept, and from Zetta to provide the back end to support that," he said. "There is more strategic alignment."
According to Sano Genetics CEO Patrick Short, the firm's discussions with Genomics England date back about a year, when its partners were looking to work with Sano to develop a platform for use in large-scale genome sequencing projects like the 100,000 Genomes Project or soon-to-be-launched Genomic Medicine Service in the UK, both of which will feed into the same national database.
"The goal for us is to build a patient interface for these large-scale research programs that allow both the patients to add information about themselves, and understand what their contribution to the research has been, as well as for the researchers to have new mechanisms that allow them to securely recontact patients that might contribute something to their research," said Short.
Rather than just tweaking and deploying its existing platform, Short said the partners decided to turn to Innovate UK for support to develop and roll the platform out properly. "It's definitely a long-term commitment to the patients who end up using it and we want to make sure from a technological perspective, we have all our bases covered in terms of data privacy and all those important pieces," said Short.
Part of the development process has also involved workshops with potential users, and Sano Genetics and Zetta Genomics held workshops in London in April. "It's about getting a feel from participants about what kind of features this platform should include, how it should look, what they should get out of it," noted Shahla Salehi, scientific research manager at Genomics England.
"This is very much a codesign," she said.
Short said the partners' goal is to have the platform in the hands of participants some time in 2021, to "improve the way we collect data on an individual level, especially data that is not collected in an electronic health record and be able to more effectively match researchers with patients and patients with researchers." He noted that people involved in the 100,000 Genomes Project "really want to be involved, trust Genomics England, trust the process, trust how the data is currently being analyzed, and really want to help."
Sano Genetics is also looking to market the platform outside of England. "The goal is to make this available much more widely," said Short. "That's our north star as a company, building software that enables faster and more patient-centric research."
Will Spooner, CEO of Zetta Genomics, similarly sees the project as a launchpad for reaching other clients. Zetta's technology works with an open-source tool called OpenCB and enables the transfer of genomic data from a file system into a database. "It's a great tool for both the clinical [and] research side of the workflow," said Spooner. He noted that the collaboration with Sano Genetics and Genomics England is a "fantastic use case" for Zetta's technology that should support the development of next-generation therapies and tests.
It will also support more participation involvement. "This is something that participants in research are keen to do," noted Spooner. "They don't see themselves as passive participants where they just give data and that's their input and over, they want to be active participants in the research," he said. "Using this sort of model, you can collect additional information for the participants, make the dataset more valuable, accelerate development of new drugs and new diagnostics that will improve patient care."
Spooner estimated that there might be 500 labs worldwide doing large-scale genomic testing today, many of which might like to adopt such a platform. "The data management problems within testing labs are getting more severe as you go to a genomic scale and as the number of tests increases," said Spooner. "The technology that Zetta has developed helps to manage large volumes of information from genomic testing."
Workstreams
According to Genomics England's Maleady-Crowe, the collaboration with Sano Genetics and Zetta Genomics involves two workstreams. One is focused on technical development of the Sano Genetics platform and the OpenCB technology, and involves trialing the systems for scalability and designing capabilities for federated data analysis within the Genomics England research environment.
A second involves patient surveys and workshops to influence the design of the future platform, and includes an ethical, regulatory, and legal working group to meet UK standards. "We are looking at making the information publicly available, and how it would work in our system but also in a wider UK regulatory framework," said Maleady-Crowe. "We want to do this as a co-production with participants," she said.
According to Rendon, the chief bioinformatician, Genomics England believes the new platform could be rolled out to participants with other conditions, such as cancer. "It depends on what the proof-of-concept looks like, but that is the intention," Rendon said.
Another aspect to the new platform is the National Health Service's Genomic Medicine Service. Introduced in 2017, it includes a whole-genomic sequencing provision and supporting informatics infrastructure developed in partnership with Genomics England. While genomic testing has been launched via the service, the whole-genome sequencing service, which will be offered in partnership with Illumina, is in "late-stage testing," Rendon said, and should launch shortly. Once it does, patients who undergo whole-genome sequencing can elect to provide data via the same platform under development with Sano Genetics and Zetta Genomics.
"Those patients who consent will be part of the same dataset," said Rendon. And all of that data will eventually be made accessible to researchers, as well as to Genomics England internally.
"Genomics England has a clinical diagnostics role, where we take whole genomes from standard clinical service and we produce diagnostics," said Rendon. "Then we take those genomic data and clinical data and longitudinal records and make it available for research," he said. "We don't carry out research ourselves. This is a model that has been trialed by some direct-to-consumer companies quite well," Rendon added. "Our difference is we will not sell results to pharma necessarily, but we will support everyone who is part of our community."