An interview with Dr. Manuel Garber on how Via Foundry became the backbone for this longitudinal study.
Autoimmune diseases are complex, often unpredictable conditions that affect millions worldwide. Among these, vitiligo—a disorder causing the immune system to attack pigment cells—affects approximately 1.5-2% of the population. To uncover why some people develop autoimmune diseases and others do not, Dr. Manuel Garber, a professor at UMass Chan Medical School and a co-founder of Via Foundry, has launched the VIGOR project with his team. This longitudinal study tracks both genetic predispositions and environmental triggers over time. Central to this ambitious research effort is Via Foundry, a bioinformatics platform that serves as the backbone of VIGOR, enabling the team to manage vast amounts of data, metadata, run analyses and coordinate efforts across diverse teams.
Below is our recent interview with Dr. Garber, where he discusses the goals, challenges, and groundbreaking role of Via Foundry in making this complex study possible.
Could you start by explaining the VIGOR project—its goals and what sets it apart from other studies on autoimmune diseases?
Dr. Garber: Sure, happy to! The core question driving VIGOR is why people develop autoimmune disorders. Think about it—someone lives a healthy life, and then suddenly, their immune cells begin attacking their own body. Why does that happen? We know there’s a genetic factor, as there’s a strong genetic association between autoimmune diseases and certain variants. But the thing is, genetics alone aren’t predictive. People can carry many of these variants and never develop the disease, so there has to be an environmental component at play, too.
The goal of VIGOR is to understand the interaction between these genetic predispositions and environmental triggers. But to do this, we need to track people over time, monitoring both their molecular markers and life events. This requires tools we haven’t really had until now.
The Complexity of the VIGOR Study
What are the logistical and technical challenges involved in a study like VIGOR?
Dr. Garber: There are a lot! The VIGOR project is a long-term, prospective study, which means we collect samples every six months and questionnaires every three months from around 1,000 participants. These participants are spread across the U.S., and many are family members of those with vitiligo—a common autoimmune disease affecting 1.5-2% of the population. Our aim is to monitor these individuals and their family members who have a higher risk of developing vitiligo over several years to see if we can identify any early markers of the disease and track how environmental factors might influence those markers.
Coordinating all this data across such a dispersed group of participants, each submitting samples and completing questionnaires, is no small feat. We have people from 40 states enrolled, and we’ve already sent kits to about 500 participants, with 400 returned so far. It’s an immense amount of data to manage and process.
The Role of Via Foundry in VIGOR
So how does Via Foundry support the project?
Dr. Garber: Via Foundry is the backbone of our operations. It centralizes everything—from participant information and sample management to data integration and processing. Each participant kit has a barcode, so when we receive a sample, it’s immediately tied to that participant in Via Foundry. This is crucial for maintaining data integrity and allowing our lab and clinical teams to track every detail without losing context.
What Via Foundry provides us is essentially “middleware” that sits between all these systems—participant management, sample storage, and data processing. It links everything together so we can track participant data and samples at every step, keeping everything in sync.
It sounds like Via Foundry simplifies a lot of coordination.
Dr. Garber: Absolutely. Via Foundry allows different teams to interact with the project in the ways they need to. For example, clinicians are using Via Foundry to interact with participants by tracking system reports and handling any health-related questions or compliance issues directly through the Via Foundry Platform. Lab personnel are managing sample intake by logging each sample’s details and tracking its status in real-time, from storage to analysis. Bioinformaticians are accessing these data sets within Via Foundry to run analyses and seamlessly share insights. Via Foundry enables efficient collaboration across teams by providing the only feasible way to coordinate and manage this scale of data, eliminating the need for manual exchanges that would otherwise be overwhelming.
The Technology Behind At-Home Sampling
Tell us more about the sampling process and the devices you use in the VIGOR project.
Dr. Garber: We designed a kit with four main devices that allow participants to collect samples from home:
- Saliva Collection Tube – This is similar to what you’d find in consumer genetic tests, like 23andMe. Participants use it for genotyping, which lets us identify both common and rare variants related to vitiligo.
- Tasso Blood Collection Device – This small, painless device collects a precise volume of blood via a micro-lancet. It’s key for detecting autoantibodies, which might be early indicators of autoimmune activity.
- Tape Strip – Participants use this to collect skin cells. It’s like a small piece of Velcro that they press onto their skin, and it gathers cells for proteomic analysis. These cells contain proteins that could be related to autoimmune disease markers.
- Micropatch – This patch, developed by a colleague at MIT, collects interstitial fluid from the skin. This fluid is rich in cytokines, which provide insights into immune activity within the skin.
We were initially concerned that participants might be uncomfortable with the blood collection, but we’ve seen an impressive return rate—over 90% of kits come back complete with samples. That’s been a huge win for us.
Longitudinal Data Management and the Value of Via Foundry
VIGOR is a longitudinal study, which means you’ll be collecting data for years. How does Via Foundry help manage such long-term data?
Dr. Garber: Longitudinal studies are tough because data accumulates over time, and if it isn’t well-organized, it’s easy to lose track. Via Foundry acts as our central data and metadata repository, storing everything in one place so that we can easily search, find and retrieve any sample, cohort, data element or dimensions, or analysis years later without any hassle.
Additionally, the platform's metadata capabilities are deeply flexible meaning they anticipate and enable evolutionary metadata growth - this means that our metadata data structures can quickly mature and advance as our knowledge, insights and studies evolve through time. Such flexibility is critically important in a multi year longitudinal study such as VIGOR
Other aspects are reproducibility and adaptability. Our methods and understanding evolve over time, so we need to be able to reprocess data to apply new insights. Via Foundry's version-controlled pipelines are crucial in allowing us to know what was done with each sample and track each step in the data processing while also allowing us to update our tools and analysis, both of which are critical for consistency in a study like this.
Cost Efficiency and Via Foundry’s Role
What about cost efficiency? Has Via Foundry helped reduce the overall project costs?
Dr. Garber: Absolutely. Without Via Foundry, we’d need far more personnel and manual processes to keep track of all the moving parts in this study. If we tried to build a similar infrastructure from scratch, it would easily have been 10 to 20 times more expensive. Moreover the temporal costs would have been even greater if we were to try and develop such capabilities ourselves it would easily add at least 2 to 3 years of time.
Via Foundry’s platform has centralized everything, so our teams don’t need to communicate constantly to keep records straight or run around managing sample logistics manually. This translates into hundreds, if not thousands, of hours saved that would have otherwise been spent on administrative tasks instead of scientific tasks.
So yes, Via Foundry has allowed us to run this complex operation with far fewer resources and much less time, which is a huge cost-saving measure.
The Future of Data Analysis and AI
You mentioned earlier the potential for AI in this project. How do you envision using it?
Dr. Garber:
We see AI as an exciting next step. For instance, we believe stress is a trigger for autoimmune diseases, and AI could help us identify stress indicators in participant survey responses. If we train an AI model to detect changes in the language of these surveys, we might pick up early signs of stress that could correlate with disease onset.
Via Foundry’s integration capabilities make it a strong foundation for quickly and easily integrating and orchestrating forward-looking AI models and applications. We’re also interested in using large language models (LLMs) within the Via Foundry Platform to simplify data querying, so we could enter complex questions in natural language instead of predefined fields.
It sounds like there’s room for a lot of innovation!
Dr. Garber: Yes, absolutely. Another idea is using AI for metadata entry. Researchers could dictate what they’re doing in real time, and Via Foundry could automatically fill in the metadata fields. This would be a game-changer for data accuracy and ease of use.
Successes, Challenges, and Via Foundry’s Future
How has the Via Foundry platform held up overall? Would you call VIGOR a success so far?
Dr. Garber: I would absolutely call it a success. Everything we feared would go wrong hasn’t, and Via Foundry has handled the complexity seamlessly. The platform has enabled us to coordinate across diverse teams, including clinicians, lab technicians, and bioinformaticians, without a hitch. Via Foundry has proven itself as a reliable hub that brings everything together.
Do you see any potential challenges down the line, especially with new developments in genome analysis?
Dr. Garber: Definitely. For instance, we’re expecting to move from the linear genome model to a graph genome model in the near future, which will provide more detail and open up previously inaccessible regions of the genome. Via Foundry’s adaptability will be key to integrating such changes smoothly without disrupting ongoing work.
That sounds like a big leap. How often do you find yourself reprocessing data in long-term projects like this?
Dr. Garber: It happens all the time. In long-term studies, reprocessing is part of the game as our knowledge advances. Via Foundry’s pipeline management and version control make this much easier. Reprocessing used to be something no one wanted to tackle due to the amount of work involved. Now, it’s manageable.
Expanding the Model to the CLUE Project
VIGOR isn’t your only project using Via Foundry. Could you briefly tell us about the CLUES project?
Dr. Garber: Certainly. CLUE, or the CLUES study, is another research project we’re launching under the same overall proposal. It focuses on identifying key biomarkers associated with different types of skin lupus, including Subacute Cutaneous Lupus (SCLE) and Chronic Cutaneous Lupus (CCLE), with the goal of predicting individuals who may be at risk of progressing to Systemic Lupus Erythematosus (SLE). While it’s separate from VIGOR, CLUE uses similar methodologies and infrastructure, so we’ve been able to adapt Via Foundry for it with minimal changes.
Since we’re already using Via Foundry for VIGOR, we could extend our infrastructure to CLUE by tweaking some configurations rather than building a new system from scratch. Via Foundry’s flexibility allowed us to do that with minimal coding, which has been incredibly efficient.
Thank you, Manuel, for such an enlightening conversation. It sounds like the VIGOR project is in great hands, and we look forward to seeing how it develops.
Dr. Garber: Thank you! It’s been great sharing the story of VIGOR and how Via Foundry is helping us tackle these challenges. The future holds a lot of promise, and I’m excited to see where this takes us.
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The VIGOR project represents a new frontier in autoimmune research, made possible by the robust support of Via Foundry. With its capabilities, Dr. Garber and his team are not only uncovering insights into diseases like vitiligo but also paving the way for future advancements in understanding and treating autoimmune disorders.
About Dr. Manuel Garber
Dr. Manuel Garber is a bioinformatician and professor at UMass Chan Medical School with a deep commitment to understanding how genetics and environmental factors come together to influence human health. As a co-founder of Via Scientific, the company behind Via Foundry, Dr. Garber has combined his research expertise with a drive to make powerful bioinformatics tools accessible to other scientists. Through projects like VIGOR, he and his team are working to uncover new insights into autoimmune diseases, with the hope of making real strides in research that can impact lives.
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