David O’Connell is director of Scientific and Technical Affairs for PCI Pharma Services.

David O’Connell

Abstract luminous DNA molecule. Doctor using tablet and check with analysis chromosome DNA genetic of human on virtual interface. Medicine. Medical science and biotechnology. | Image Credit: ©ipopba -stock.adobe.com

Rare medical conditions can do more than substantially affect wellbeing. They can also make sufferers feel discouraged or even hopeless about their prospects for successful treatments. Because some of these diseases may only impact a handful of people worldwide, rare diseases bring an inherent lack of scale—a dearth of established research and infrastructure that make journeys to effective treatments that much longer and more arduous.

Their sheer diversity only exacerbates this difficult dynamic. True to their categorization, rare diseases are as inconsistent as they are infrequent. Typically genetic and often severe, such conditions span a wide spectrum of therapeutic areas, from oncology and neurology to immunology and metabolic disease. The result is a “broad but not deep” scenario that, unfortunately, can leave treatment resources as scarce as the diseases themselves.

Worse yet, “rare” is both a formal designation and a subjective, relative term. While some rare conditions may indeed be one-in-a-million misfortunes, others are far more prevalent. Officially, the threshold in the world’s two most developed markets—the United States and Europe—define rare conditions as those presenting in less than 1 in 2000 people. (Europe has an official 2000:1 ratio

, while the US sets a nationwide limit of 200,000

, which creates a comparable ratio given its population of over 340 million.) Considering this, even rare diseases can cause widespread suffering and unmet treatment needs affecting millions of patients worldwide.

Serving this unconventional global community demands a suitably unconventional pharmaceutical model: one that prioritizes precision, integration, and geographic reach rather than scale. Promisingly, these attributes increasingly align with those displayed by modern contract development and manufacturing organizations (CDMOs)—partners that, at their most comprehensive, are equipped to take the highly specialized molecules used to treat rare diseases from early phase clinical trials through commercial reality.

Precision Molecules for Precision Populations

From a development and processing perspective, treatments for rare diseases demand a rarified air of pharmacological prowess. Unlike therapies for more common conditions, which often rely upon well-understood molecules with broader applicability, many rare disease programs involve highly targeted agents tailored to distinct genetic or molecular signatures. Unsurprisingly, a substantial portion of today’s rare disease and targeted therapies are highly potent compounds, reflecting a broader industry trend in which highly potent APIs represent roughly 30% of drug development pipelines,

and are particularly prevalent in precision medicines.

Aligning with this paradigm shift, it isn’t unusual for rare disease investigational pipelines to be dominated by biologics, gene-based modalities, or other specialized molecular classes. Here, biology matters: roughly 80% of rare conditions have a genetic component,

 making them amenable to molecularly directed approaches such as antisense oligonucleotides, enzyme replacements, or targeted inhibitors that modulate specific pathways or proteins. Such modalities often require sophisticated formulation, containment, and dose control far beyond standard therapies. Encouragingly, these elevated requirements are reflected in the pharma industry’s shifting priorities: industry analyses suggest that approximately 35% of all drugs and biologics currently in global R&D pipelines are intended to treat rare diseases.

For developers and their manufacturing partners, molecular intricacy translates into complexity: APIs that are potentially highly potent, bespoke biologic processes, and the need to balance stability, safety, and efficacy in exceedingly small patient populations. It’s a landscape where scientific nuance is inseparable from operational execution.

Structural Considerations for Rare Disease Programs

Rare disease drug development not only operates at smaller scales, but also under differing sets of physical, regulatory, and human constraints. Hard facts speak to the challenges such fragmentation poses: though there are more than 7000 recognized rare diseases worldwide

—collectively affecting approximately 300 million people—fewer than 5% of these conditions have an FDA-approved treatment.

In conventional pharma, large patient populations allow for trial delays, formulation iterations, and wide-scale manufacturing tolerances. With rare diseases, no such leeway exists. A single trial site may represent a significant proportion of the available patient pool, which means missing a shipment can meaningfully delay or derail an entire study. In fact, clinical trial enrollment itself presents a structural challenge, with rare condition studies seeing significantly fewer participants than common disease trials. The rarer the condition, the scarcer investigational evidence can become; many rare diseases have seen fewer than 10 trials, placing a premium on every opportunity to accrue sound research.

Geography can further complicate matters. Rare disease patients are frequently scattered across multiple regions, compelling sponsors to navigate multi-jurisdictional regulatory frameworks and logistics for very small treatment volumes. And because these therapies often involve highly potent, targeted molecules or genetically informed modalities demanding precise formulation and delivery, processing and logistical fragmentation becomes another potential pitfall. Successful rare disease treatment development requires the synchronized orchestration of science and supply chain that forgo mere scale in favor of agility, adaptability, and global reach.

Considering this, the central challenge posed by rare disease treatment is not how much medicine can be manufactured, but how exactingly it can be produced, released, and delivered. Volumes are often measured in hundreds or even dozens of units, yet those units must reach patients dispersed across multiple countries under tightly controlled regulatory and quality frameworks. A single clinical or commercial batch may represent a meaningful share of the global supply, leaving no room for deviation in formulation, sterility, or containment.

This reality places unusual demands on manufacturing infrastructure. CDMOs supporting rare diseases must be capable of low-volume, high-mix production, where frequent changeovers, short campaigns, and evolving formulations are the norm rather than the exception. For many rare disease therapies—such as highly potent small molecules and sterile injectables—this painstaking process must unfold within advanced containment systems designed to protect both product integrity and operator safety, often with exposure limits of mere nanograms.

In turn, those exceptionally limited batches must be packaged, labeled, released, and distributed into a multi-region clinical and commercial supply network, supporting trials and patients across North America, Europe, and beyond. Such scenarios are where integration becomes decisive. When development, oral solid dose and sterile manufacturing, quality, and global distribution sit within a single CDMO framework, rare disease sponsors gain something more valuable than scale: continuity of control from first patient to final dose.

Consider a theoretical rare disease therapy entering first-in-human trials with fewer than 20 patients worldwide. The biology is specific, the therapeutic window narrow, and the doses measured in micrograms rather than milligrams. For both the patients and the sponsor, this creates a set of demands that are fundamentally different from conventional pharma production practices. The program must accommodate the following:

A globally dispersed patient population, requiring clinical supply into multiple regions from the very first study

Extremely small cohort sizes, where each dose and batch carry outsized importance

The likelihood of a highly potent, targeted active ingredient demanding advanced containment and precise dose control

A compressed development pathway where early pharmacokinetic and safety data must be generated expediently to avoid impacting characteristically scarce patient enrollment

A need for low-dose first-in-human material, often enabled through micro-dosing platforms such as Xcelodose.

Meeting these demands requires a manufacturing and supply infrastructure built for meticulousness rather than volume. Early clinical material is produced using controlled micro-dosing systems that deliver uniformity at the microgram level, protecting patients while generating reliable data. As the program progresses, the same formulation and containment strategies are carried forward into larger batches, preserving continuity and avoiding disruptive redevelopment.

At the same time, clinical trial supply becomes a global exercise: packaging, multi-language labeling, regulatory release, and distribution into regional depots all must be coordinated for low-volume, high-value shipments. Digital supply platforms track site-level demand and inventory in real time, ensuring that no patient misses a dose due to forecasting error or logistical delay. By the time the therapy reaches late-stage development, the operational framework supporting it is already aligned for commercial reality.

Rare disease medicine now sits at the intersection of scientific possibility and industrial responsibility. The tools to design targeted therapies exist, and the pipelines are increasingly rich with orphan and precision assets. What determines whether these advances translate into real outcomes for patients is no longer discovery alone, but the infrastructure that surrounds it.

Rare disease pipelines eschew pharmaceutical models built around volume and scale, in favor of those prioritizing precision, continuity, and global coordination. Success depends on moving seamlessly from laboratory insight to manufacturable product, from early clinical material to long-term commercial supply, and from fragmented efforts to integrated operational systems.

Of course, these prerequisites are largely invisible to patients. For them, all that matters is whether therapies are viable, effective and available. Behind that sits a complex machinery of formulation science, containment engineering, regulatory alignment, and global distribution—all designed to serve populations too small to benefit from conventional supply-and-demand economics.

In that sense, rarity is no longer just a biological category. It is a measure of how willing the industry is to build systems for those who cannot be served by scale. Not because it is easy, but because the science, the infrastructure, and the ethical imperative have converged. This is a rare moment indeed—one that must be seized by pharma companies and the integrated CDMOs they entrust to help develop, produce, and distribute life-saving rare disease treatments.

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https://www.appliedclinicaltrialsonline.com/view/the-hard-truth-about-rare-disease-and-gene-therapy-drug-development

First-ever rare diseases resolution underscores equity and inclusion.WHO. May 24, 2025, 

https://www.who.int/news/item/24-05-2025-seventy-eighth-world-health-assembly---daily-update--24-may-2025

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David O’Connell, BSc (Hons) is Director of Scientific and Technical Affairs for PCI Pharma Services

a leading CDMO providing integrated end-to-end drug development, manufacturing and packaging capabilities that increase products’ speed to market and opportunities for commercial success. In his current role, O’Connell aids clients with formulation development, technical transfer and scale-up of solid oral, oral liquid and semi-solid products for clinical trials and/or commercialization. 

Articles

Rare diseases, though individually uncommon, collectively affect hundreds of millions and remain largely untreated, with fewer than 5% having FDA-approved therapies. Development increasingly relies on highly potent small molecules, biologics, and gene-based modalities aligned to genetic etiologies and narrow therapeutic windows. The limiting factor is not volume but precision—microgram dosing, stringent containment, and defect-intolerant quality systems—coupled with globally dispersed patients and multi-jurisdictional regulation. Integrated CDMO platforms that unify development, manufacturing, packaging, release, and distribution can de-risk trials and enable seamless commercialization.

Treatment pipelines for rare diseases have never been more promising. Optimizing their impact will require integrated, precision-first CDMO support systems.