How AI Helps Scientists Solve Complex Biological Mysteries

Vitiligo has been a mystery for biologists forever. It is a complex autoimmune disease linked to genetics, but that’s not the whole story.

Genetics alone doesn’t explain the complexity of vitiligo. Studies on identical twins reveal that only one in four pairs both have the condition. The remaining pairs often see only one twin affected, and this indicates that factors beyond genetics, such as stress and trauma like sunburn, also play significant roles.

The VIGOR Project at UMass Chan Medical School

At our medical school, UMass Chan, my colleagues who have been studying vitiligo have recently launched a new project to understand these complexities. VIGOR, or Vitiligo Impact of Family Groups: Observation and Research, is a groundbreaking initiative designed to understand why vitiligo occurs and how it can be treated more effectively.

This ambitious project will span at least five years, potentially more, enrolling 200 people with vitiligo and 800 of their close relatives who do not have the condition. If you have family members with vitiligo, you can also join the study here.

The VIGOR Study: A Comprehensive Approach

Participants will regularly submit saliva, blood, and skin samples, along with surveys about their lifestyle, stress levels, illnesses, and chemical exposures.

These self-collected samples will be sent to UMass Chan labs, where the team will track the data over the years, identifying which individuals without vitiligo eventually develop the condition. This will help them understand the mix of genetic and environmental factors that cause vitiligo.

Stopping Vitiligo Before It Begins

A unique aspect of the VIGOR study is its proactive approach to understanding and preventing vitiligo.

By closely monitoring individuals who are genetically predisposed but have not yet developed the condition, researchers aim to identify early biomarkers and potential triggers. This could lead to preventive strategies, allowing for interventions before vitiligo manifests.

The goal is to develop treatments that can halt the disease in its tracks, providing hope for those at risk and potentially reducing the incidence of vitiligo in future generations.

Addressing Environmental Triggers

Understanding the role of environmental factors is crucial. The VIGOR project not only focuses on genetic predispositions but also examines how external factors like chemical exposures, stress, and trauma can contribute to the onset of vitiligo.

The study collects detailed data on participants’ lifestyles and environments, and this will show us how these factors interact with genetics to cause the disease. As a result of this comprehensive approach, we’ll gain a complete understanding of what triggers vitiligo.

Moving Forward with VIGOR

The VIGOR project is a major effort to understand the complexities of vitiligo. With advanced research methods and extensive data collection, we will uncover the many causes of this condition. This knowledge will eventually lead to new treatments and preventive measures and greatly improve the lives of those with vitiligo and their families.

Challenges in Data Management

Handling such vast amounts of data over an extended period is difficult. Technology evolves rapidly; in five years, many of today’s applications will become obsolete. One or two scientists may have to leave the project for any reason. So data management and consistency is a potential issue.

Additionally, patient anonymity must be maintained, adding another layer of complexity to data handling.

Via Scientific and the Foundry Platform

Foundry: Empowering Biologists with AI and Data Science

Fortunately, our colleagues at UMass Chan have a powerful tool at their disposal: Foundry, which I’m proud to be one of the founders of. Over a decade ago, my team and I started developing what was initially known as DolphinNext. Recently, we rebranded it as Foundry under Via Scientific.

Foundry is now the world’s most comprehensive science platform. As biologists who understand the unique challenges of our field, we designed Foundry to meet these needs precisely.

Key Features of Foundry Enhanced by AI

Foundry simplifies the management of large-scale, long-term studies like VIGOR. It supports the integration and analysis of multi-omics data, eliminating bioinformatics and coding bottlenecks that often slow scientific advancement. Here’s how Foundry, enhanced by AI, excels in supporting the VIGOR study:

• AI-Powered Experiment Design & Management: Foundry enables seamless integration of various data types, including NGS data, third-party datasets, and private research data. It ensures consistent data accumulation and insight generation over the study’s duration.
• Metadata Enhancement: With customizable metadata capabilities, Foundry’s intuitive interface allows for the easy addition of new data dimensions for modeling and analytics.
• AI-Driven Workflows & Pipelines: Scientists can create and customize bioinformatics workflows without writing any code, using a library of verified pipelines or building new ones from scratch, optimized by AI for efficiency and accuracy.
• Data Import: Foundry automates data import and processing, handling samples efficiently, whether they number in the tens or tens of thousands.
• Orchestration: The platform manages complex computing environments, integrating continuous testing and deployment, and ensuring reproducibility of all runs.
• Advanced Analysis Tools: Foundry provides native visualization tools and integrates with RStudio, Jupyter notebooks, and Shiny apps for advanced data interrogation and sharing, all enhanced by AI algorithms for deeper insights.

Transforming Scientific Research with AI

Foundry offers a suite of tools tailored for scientists, bioinformaticians, and computational biologists. It simplifies data integration, workflow creation, and analysis, making it an invaluable asset for complex research projects like VIGOR. Foundry’s key benefits include:

• Accelerated Scientific Discovery: By streamlining the experiment cycle, Foundry, powered by AI, enables deeper, more frequent scientific inquiries.
• Reproducible Science: Foundry maintains an institutional memory of all results and methods, ensuring reproducibility.
• Proven and Trusted: Supporting thousands of scientists and hundreds of labs globally, Foundry is a trusted platform in both academia and industry.
• Collaborative Efficiency: Foundry facilitates secure collaboration across projects and labs, enhancing research outcomes.
• Scalable and Cost-Effective: Foundry adapts to evolving technological landscapes, insulating users from computing complexities and controlling costs.

Conclusion

The VIGOR study represents a monumental effort to unravel the complexities of vitiligo. Supported by the AI-enhanced Foundry platform, this research has the potential to transform our understanding and treatment of this challenging condition.

As part of the Via Scientific team, I am proud to make this study possible. We are confident that the insights gained from this study will not only advance vitiligo research but also set a precedent for using AI to understand other complex autoimmune and genetic disorders. Together, we’re advancing science and technology to solve the mysteries of human health.

(*) Via Scientific, Inc., a new Cambridge-based technology and AI company, has launched Via Foundry, a multi-omics accelerator platform designed to accelerate scientific breakthroughs. Originally developed over a decade at UMass Chan Medical School by scientists, Via Foundry is now exclusively commercialized by Via Scientific. The company was founded by a team of experts including Melissa J. Moore, PhD, Alper Kucukural, PhD, Manuel Garber, PhD, Jim Crowley, and Janet Kosloff.

Via Foundry automates the complex data and analytical tasks involved in multi-omics research with features like a drag-and-drop pipeline, metadata building functionality, and customizable analytics, eliminating the need for coding. This platform ensures data is shareable, reusable, and reproducible, allowing researchers to focus on core scientific insights and therapeutic breakthroughs.

Via Scientific aims to support biotech, pharmaceutical companies, research institutes, and academic universities while enhancing the AI capabilities of the Via Foundry platform.