Accelerating Rare Disease Drug Development with AI, Machine Learning, and Real-World Data

The Urgent Need for Innovation in Rare Disease Drug Development

Rare diseases collectively affect over 300 million people worldwide, with more than 7,000 distinct conditions identified. Despite significant advances in drug development, 95% of rare diseases still lack an FDA-approved treatment. Many of these diseases are underdiagnosed or misdiagnosed, with an average diagnostic delay of 5-7 years, preventing early intervention and increasing patient burden.

Developing drugs for rare diseases presents unique hurdles across scientific, clinical, regulatory, and commercial landscapes. While orphan drug incentives have helped drive innovation, small patient populations, high development costs, and complex regulatory pathways remain significant challenges.

For real-world data (RWD) and clinical leaders in Biotech and Life Sciences, the challenge is clear: How can we leverage data-driven strategies to accelerate rare disease identification, optimize trial recruitment, and fast-track regulatory approvals? In part, the answer lies in the strategic use of advanced analytics, artificial intelligence (AI), machine learning (ML), and RWD.

How Real-World Data Is Transforming Rare Disease Identification & Drug Development

Finding patients with rare diseases is a significant challenge for Biotech and Life Sciences companies, as these conditions often have low prevalence, delayed diagnoses, and fragmented data across healthcare systems. RWD has emerged as a powerful tool to identify, recruit, and engage these patients for clinical trials, natural history studies, and commercial treatments.

Patient Identification Challenges

Many rare diseases present with non-specific symptoms, leading to multiple misdiagnoses and treatment delays, and often wait 5 to 7 years for an accurate diagnosis due to non-specific symptoms, limited awareness, and fragmented medical histories. The challenge is to be able to identify individuals earlier in their journey. AI and ML models can be used to analyze RWD (EHR data, claims, lab results, genomics, etc.) to identify undiagnosed patients based on symptom clusters and treatment patterns associated with rare diseases. For example, pattern recognition identifies patients with unusual diagnostic journeys, thereby shortening the time spent on finding a diagnosis and increasing the number of patients who may be eligible for clinical trials and targeted therapies. Because many rare diseases progress silently, and patients often are on the receiving end of symptomatic treatment rather than disease-modifying therapies. AI and ML-powered longitudinal RWD analysis helps track patient progression. These models can identify subtle disease progression markers, allowing early intervention before severe symptoms appear.  Furthermore, because many rare diseases lack well-characterized disease progression models, it is hard to define trial endpoints and measure treatment efficacy. RWD and AI-driven analytics can be used to model disease progression, by integrating biomarker research and genomic insights, improved study design, and stronger evidence generation can lead to shorter regulatory acceptance timelines.

Rare Disease and Clinical Trial Challenges

While getting patients into trials sooner is a positive, rare disease trials struggle with slow recruitment and site selection inefficiencies due to small, geographically dispersed patient populations typical of rare diseases. By using RWD, AI, and ML, patient matching algorithms can look across EHR, claims, and genomic data to identify eligible patients. RWD analytics can help predict where undiagnosed or misdiagnosed patients are located, thereby optimizing trial site selection and outreach. Confounding rare disease clinical trial challenges, many rare disease trials cannot use traditional placebo controls due to ethical concerns or other limitations; it is difficult to prove efficacy with small sample sizes. To combat this, synthetic control arms and external comparators from RWD are being used to evaluate drug effectiveness without requiring additional placebo patients. Data is gathered from sources like EHRs, claims, prior clinical trials, etc., then cleaned, harmonized, and mapped to common data models, like OMOP, for consistency and comparability. Using AI and ML models, patients are selected that closely match the characteristics of trial participants, such as age, gender, disease stage, biomarkers, and treatment history.

RWD also helps overcome other rare disease challenges. Many healthcare providers lack awareness of rare diseases, leading to misdiagnosis, treatment delays, lower adoption of new therapies, and a lack of urgency in enrolling patients into existing trials. By using RWD, Life Science companies can make more effective investments in physician education and make diagnostic algorithms available through EHR integrations. By analyzing claims and treatment patterns, teams can identify hot spots of rare disease diagnoses and identify physicians with rare disease expertise for site expansion.  

Data Fragmentation Challenges

Regulatory agencies require robust real-world evidence (RWE) for orphan drug approvals, but fragmented data hinders evidence generation. Standardizing data from disparate sources has proven to be a major hurdle; however, data standardization, like OMOP, enables RWD from EHRs, claims, and other sources to be linked and aggregated to help ensure regulatory compliance and reproducibility. RWD and AI-driven longitudinal analytics can be used to model disease progression,  treatment outcomes, and safety events, leading to stronger evidence generation and shorter regulatory acceptance timelines.

AI and ML-driven RWD also assist with rare disease identification. Many rare diseases have underlying genetic causes, and RWD from biobanks, genomic databases, and EHRs can help identify novel biomarkers linked to rare diseases. Additionally, many rare disease indicators are buried in unstructured data, like EHR clinical notes, making them difficult to detect. Natural language algorithms can help analyze unstructured data to reveal rare disease symptoms and patterns.

Conclusion

RWD, coupled with AI and ML, is revolutionizing the way rare diseases are identified, studied, and treated. By leveraging RWD, Biotech, and Life Sciences companies can overcome the traditional challenges of patient identification, clinical trial recruitment, and regulatory approval.  As the industry continues to embrace data-driven approaches, the potential to accelerate rare disease drug development and improve patient outcomes has never been greater. By integrating AI, ML, and standardized data frameworks, Life Sciences companies can bridge existing gaps, ensuring that more patients receive timely diagnoses and access to life-changing therapies. The future of rare disease treatment lies in harnessing the power of data—transforming challenges into actionable solutions for both patients and researchers alike. Let's continue the conversation, get in touch or connect with me on LinkedIn.

Accelerating Rare Disease Drug Development with AI, Machine Learning, and Real-World DataLinkedIn

Jeff McDonald

Chief Executive Officer

Jeff is a serial entrepreneur and growth leader who successfully envisioned and developed analytical products and platform technologies to empower growth. He has more than 20 years of experience in the healthcare industry, combining his technology, innovation, and analytic product development experience with his conviction in the power of teamwork to help organizations succeed.
Accelerating Rare Disease Drug Development with AI, Machine Learning, and Real-World DataLinkedIn