NEW YORK (GenomeWeb) – Boston-based startup Root plans to unlock the treasure trove of immune genetics data that is hidden in bone marrow donor registries, providing members with their personal HLA data along with interpretations relating to their ancestry and health. In addition, it wants to enable them to participate in "crowd science" research studies of their interest.
Through these offerings, the company, founded in 2016, hopes to grow bone marrow registries worldwide so more patients in need of a transplant can find a matching donor. "We want to grow, engage, and diversify the registries," said Nathaniel Pearson, Root's founder.
Root's services will be free to donor registry members. Those unwilling to join a donor program can get their HLA genes analyzed for a fee. The company, which is currently looking for seed funding, has already partnered with the National Marrow Donor Program (NMDP), a US-based nonprofit organization that operates the world's largest donor registry of almost 16 million members.
Pearson, who gave a presentation about Root at the Precision Medicine World Conference last month, said that both a professional and a personal interest led him to found the company. As senior director of science and research at personal genomics firm Knome, he was involved in the very early days of consumer genomics, helping customers understand their genome and what it might mean for their health. "My career has been helping people understand their own DNA through good software," he said. "This is an extension of that."
At the time, he said, there were not all that many 'life-changing' insights a healthy person could glean from their genome, and results that could have a big impact — for example, mutations in the BRCA1 and 2 genes — did not require an entire genome to be sequenced.
However, one area of the genome that always struck him as particularly interesting was the HLA (human leukocyte antigen) complex, a region on chromosome 6 that contains several genes encoding the MHC (major histocompatibility complex) proteins, which have crucial functions in the immune system.
Besides defending against infectious disease, HLA genes play a role in organ transplant rejection, autoimmune diseases and allergies, and cancer, all areas that "interest big swaths of the public," Pearson said.
In addition, HLA genes are incredibly diverse and can tell much about a person's ancestry. "Human family trees go back deeper there than pretty much anywhere else in our genomes," he said.
On the personal side, Pearson has been a long-standing supporter of bone marrow and tissue donor programs, which type prospective donors' HLA genes to match them to patients in need. His mother, unable to find a matching donor, died of leukemia at the age of 34, "so the idea of tissue transplant has always been important to me, it's always been a societal mission that I understood," he said.
An estimated 30 million volunteers are members of donor registries worldwide. In order to join, individuals need to provide a cheek swab for HLA typing. But they usually do not get their HLA data back, unless they request it. When Pearson decided to ask for his own data, the registry sent it to him several weeks later in an envelope, and in a format that was impossible to decipher, consisting of "totally inscrutable bioinformatics code." Even being an expert, it took him several days to figure out what alleles he carries and to comb through the biomedical literature to understand what implications they might have for his health.
HLA literature, he said, is very compartmentalized, making the analysis even more difficult. "The autoimmune disease researchers don't talk much with the food allergy researchers, and they don't talk much with the infectious disease researchers, and they don't talk with the perinatal health researchers," he said.
Realizing that millions of others also have their HLA data sitting in a registry and might be interested in finding out how it might affect them, Pearson founded Root.
The company will serve as a proxy to help registry members obtain their data and will store it in a HIPAA-compliant environment. It will also provide them with an ancestry analysis, as well as allow them to participate in "crowd science" research studies they are interested in. Further down the line, Root plans to develop a health report that will list drug responses that have been linked to particular HLA types.
Engaging donor program participants in new ways, Pearson said, might help registries stay in touch with their members — who often joined many years ago — and prevent them from losing touch when members move, with the aim to "keep them part of the vital mission to find a well-matched, willing donor for every patient who needs one."
Registry members are already consented for research, Pearson said, and their HLA data is already used in studies, but they do not usually interact much with the researchers. "We want to be the portal for that interaction to make [the data] much more useful," he said, so scientists "can work with people over the course of time in engaging ways." Root members will be able to indicate in their public profile what types of studies they are most interested in participating, so researchers can readily find them. "We want to make it as easy as possible for people to get involved, and importantly, with the data that already exist," he said.
Root also plans to enable registry members who are no longer eligible as donors, because they automatically "age out" at age 60, to continue contributing to research. Many of these older participants are likely to get cancer at some point, he said, and could participate in studies of immunotherapies, for example.
Individuals who are not already members of a donor registry can determine through a questionnaire on Root's website whether they are eligible to join, and in which country. Pearson said he has already spoken with two registries in Europe about possible collaborations, and programs in other countries, including Mexico, India, Nigeria, and South Africa, "could be wonderful partners for Root where we could help to quickly grow those registries," he said.
Finally, people who already have genomic data available that includes the HLA genes — for example, because they had their exome or genome sequenced — can bring it into Root and analyze it through the company's interface. Pearson said the firm is also considering partnering with other companies and platforms, such as Arivale, Viome, or Helix, to provide an analysis of the HLA genes as part of a larger package of results, though he noted that those firms do not provide their services for free.
Since Root launched its website a few weeks ago, people in almost 30 countries have signed up, Pearson said. So far, the firm has mainly reached out to potential members through social media but hopes that the registries themselves will start promoting its services soon.
The company soon plans to roll out account features that will allow it to host its members' HLA data. "We’re ready to proceed quickly on the API front with any registry that is ready on the regulatory front in any given jurisdiction," Pearson said. Root has also been working closely with experts who oversee ontology for HLA, which will be crucial to obtaining well-structured data.
Further, the company wants to systematically curate everything known about HLA variation and "be the expert guide to understanding what a given HLA genotype might mean in various facets of physiology," Pearson said. "We'll start with the basics, ancestry and kinship, and basic drug responses," and continue curation efforts over time.
Root, which counts George Church and Robert Green of Harvard Medical School, Carlos Bustamante of Stanford University, and Elia Stupka of the Dana-Farber Cancer Institute among its advisors, is currently looking for seed funding from angel investors, venture capital firms, or strategic investors. "For $400,000 to $500,000, we could do much of what we plan, both in terms of the interface development and the regulatory and curation efforts we need to get rolling over the next 18 months or so," Pearson said.
Root's business model will be a little different from other consumer genomics companies, he said, in that individuals will not be charged, except for HLA typing if they do not want to join a registry.
Revenues will come from researchers or companies paying for access to the firm's members, or "Rooters," and their data. Pearson said he also would like to give members themselves some monetary compensation for participating in research, but this will likely be on a small scale.