How Aegis Is Solving the Rare Disease Clinical Trial Matching Problem with AI

The Search That Should Never Have to Happen

Imagine your child is diagnosed with a rare mitochondrial disorder. The diagnosis alone takes years — rare diseases average 4.8 years to diagnose correctly, often after a parade of misdiagnoses and specialist referrals. Then comes the next devastating blow: there is no FDA-approved treatment. The neurologist hands you a printout and says something like, "You might want to look into clinical trials."

So you do. You navigate to ClinicalTrials.gov, a government database that lists over 400,000 studies in dense medical and regulatory language. You try to parse inclusion criteria written for physicians and biostatisticians. You email three patient advocacy groups, two of which reply weeks later. You call hospitals in four states. You spend six months becoming an amateur medical researcher — six months your child doesn't have.

This is the reality for most of the 400 million people worldwide living with one of over 7,000 known rare diseases. And it is a problem that doesn't have to exist.

Meet Aegis: The Matching Engine Rare Disease Medicine Has Been Waiting For

Aegis is an AI-powered clinical trial matching platform purpose-built for the rare disease space. Its tagline says it plainly: Rare disease patients deserve more than rare options.

The platform works by ingesting a patient's health records, genetic test results, and diagnosis codes, then matching them against a continuously updated global database of rare disease clinical trials. But Aegis doesn't stop at surface-level matching. Its engine understands the genuinely complex eligibility logic that defines rare disease trials: specific genetic variants (not just disease names), biomarker thresholds, prior treatment history, washout periods, and geographic constraints.

The result is pre-qualification — not just a list of potentially relevant trials, but a ranked, explainable set of matches where the patient or caregiver can immediately see why they qualify, what steps come next, and what questions to bring to their physician. The back-and-forth that currently delays enrollment by months is compressed into days.

Two sides of the same marketplace

Aegis operates as a two-sided platform. On one side are patients and caregivers — people in crisis who need clarity, not complexity. On the other side are pharmaceutical sponsors and biotech companies running rare disease trials, who face an existential recruitment problem: rare diseases are, by definition, rare. Finding enough eligible patients to power a Phase II or Phase III trial can take years beyond projections, burning cash and threatening the viability of programs that represent the only hope for patients with no other options.

For sponsors, Aegis is a recruitment acceleration engine. By connecting trial sites with pre-qualified, genuinely interested patients, Aegis compresses enrollment timelines and reduces the cost and uncertainty that makes rare disease drug development so financially precarious.

Who Aegis Is Built For

Aegis serves two distinct but deeply interconnected audiences:

Patients and Caregivers

• Families navigating pediatric rare diseases — often parents who have become de facto patient advocates overnight, with no medical background and no roadmap
• Adult patients with confirmed diagnoses who have exhausted approved treatments and need trial access as a clinical option, not a last resort found by accident
• Genetic counselors and patient advocates who serve as intermediaries and need professional-grade tools to search, filter, and present trial options
• Rare disease patient advocacy organizations that want to provide structured trial-matching services to their communities without building the infrastructure themselves

Pharmaceutical Sponsors and Research Sites

• Biotech companies running orphan drug programs who face enrollment timelines that routinely run 2-3x over projections
• Clinical research organizations (CROs) managing site activation and patient recruitment for rare disease studies
• Academic medical centers with rare disease centers of excellence that need broader patient referral pipelines than their local catchment area provides

What Makes Aegis Different

The clinical trial matching space has seen attempts before — but most generic platforms were built for common diseases, where eligibility criteria are simpler and patient populations are large enough that rough matching works. Rare disease is a fundamentally different problem, and Aegis was designed from the ground up for its unique constraints.

The key technical differentiation is in the depth of the eligibility logic. Most trial finders match on disease name or ICD code. Aegis matches on the molecular and clinical specifics that actually determine whether a patient will be accepted by a trial coordinator — specific OMIM identifiers, mutation classifications, enzyme activity thresholds, prior therapeutic exposures. This is the difference between a match that wastes everyone's time and a match that leads to enrollment.

The Market Opportunity

The rare disease therapeutics market is one of the fastest-growing segments in all of biopharma. Orphan drugs now account for nearly 50% of all FDA novel drug approvals in recent years, driven by favorable regulatory pathways, premium pricing, and genuine unmet medical need. The global rare disease treatment market is projected to exceed $350 billion by 2030.

But the bottleneck isn't discovery — it's enrollment. Industry data consistently shows that rare disease clinical trials take an average of 30% longer to enroll than planned, and a meaningful proportion never reach enrollment targets at all, resulting in program abandonment. Each month of enrollment delay costs a mid-sized biotech an estimated $800K–$1.2M in extended operational costs, not counting the opportunity cost of delayed approval.

The timing for a platform like Aegis has never been better. Three converging forces are creating the conditions for rapid adoption:

1. Genomics democratization: Whole exome and genome sequencing costs have plummeted, meaning more rare disease patients have actionable genetic data that can power sophisticated matching
2. EHR interoperability: FHIR-based health data standards are making it increasingly feasible to ingest structured clinical data at scale without manual abstraction
3. Biotech investment in rare disease: Record levels of VC and public market investment in orphan drug programs mean the sponsor-side demand for enrollment acceleration tools is at an all-time high

Built with AI, From Day One

Aegis was built on Artha, the AI platform that takes a company concept from idea to launched product. The platform's AI-first approach meant that Aegis could go from mission statement to functioning product infrastructure — brand, web presence, core platform architecture — at a speed that would have been impossible with traditional development approaches.

That AI-native foundation isn't just a development story. It's core to how the matching engine works. Natural language processing allows Aegis to parse the heterogeneous, semi-structured language of clinical trial eligibility criteria — criteria that are often written inconsistently across sponsors, registries, and geographies. Machine learning models trained on rare disease ontologies allow the platform to understand the relationships between genetic variants, phenotypic presentations, and trial-specific requirements in a way that rules-based systems simply cannot.

"The reason fewer than 5% of rare disease patients ever participate in a clinical trial isn't lack of trials — it's that patients can't find them, and trials can't find patients. Aegis exists to solve the matching problem."

What's Next for Aegis

The near-term roadmap for Aegis focuses on deepening the two-sided marketplace: expanding the patient-facing matching interface to support multilingual access (rare disease knows no borders), building richer sponsor dashboards that give trial teams real-time visibility into their pre-qualified patient pipeline, and developing integrations with the major EHR systems and rare disease patient registries that serve as the data backbone of the ecosystem.

Longer term, Aegis is positioned to become the connective tissue of the rare disease clinical development ecosystem — not just matching patients to trials, but supporting the full enrollment journey: site selection guidance, protocol design feedback based on real-world patient population data, and post-trial natural history data that can accelerate the next generation of drug development programs.

In a field where hope is the scarcest resource, Aegis is building the infrastructure to make hope findable.

Build Your Own Company on Artha

Aegis is one example of what becomes possible when a genuinely important problem meets AI-powered company building. The matching problem in rare disease has existed for decades. What changed is the combination of available data, AI capabilities, and a platform like Artha that can take a mission-driven idea and turn it into a launched company — fast.

If you have an idea for a company — in healthcare, in climate, in fintech, in any space where a real problem is going unsolved — Artha can help you build it. One prompt. One platform. Your company, live.

The next Aegis could be yours. Start building at artha.run →