By Clinical Research Staff 

August 12, 2025 | The clinical research landscape is undergoing a significant transformation, with nonprofit organizations emerging as pivotal players in accelerating drug development for rare diseases. In the most recent episode of the Scope of Things podcast, Annette Bakker, CEO of the Children's Tumor Foundation (CTF), shared insights into how nonprofits are revolutionizing the clinical research ecosystem. 

Bakker highlights a fundamental challenge in drug development: the disconnect between academia and industry. Academia excels at developing research models but prioritizes publications to ensure they can secure funding for their labs. Pharmaceutical companies, on the other hand, focus on drug discovery but keep their data secret and products proprietary. The two fields tend to “stay in their comfort zones,” says Bakker. However, this separation only results in inefficient drug development, with patients ultimately suffering the consequences.  

This is where the nonprofit sector plays a role. Nonprofit organizations can uniquely position themselves as partners in the R&D ecosystem and as nexuses between patients, academia, industry, and regulators, pushing all stakeholders beyond their comfort zones to advance promising treatments. 

The Shelved Asset Issue 

One of the main topics discussed during the conversation was shelved assets.  Pharmaceutical companies frequently shelve drug candidates not because they're ineffective or toxic, but due to strategic or commercial reasons. These shelved assets still have intellectual property (IP) protection and have great potential as treatment options, especially for rare disease patients. But rare diseases are a challenge for pharmaceutical companies. 

“First of all, there are thousands of rare diseases,” explains Bakker. “The second thing is that for [the companies], this ecosystem of specific rare diseases is unknown. There are very few researchers, very few models, and once an asset is shelved, the project team within the company is reassigned to other projects.” 

CTF has pioneered a model where nonprofits function as R&D partners for pharmaceutical companies, helping with resurfacing these shelved assets and redirecting them toward appropriate patient populations. Bakker recalls a success story about a shelved Pfizer drug for neurofibromatosis (NF), where CTF worked directly with Pfizer to assemble a team that would ensure they get the data, find necessary investors, and get the drug to market. The result was a new company called SpringWorks Therapeutics, which received FDA approval in 2023 and was eventually acquired by Merck for $3.5 billion. This experience demonstrated that rescuing shelved assets has significant value for patients and investors.  

Building on this experience, Bakker and colleagues are now developing a centralized "drug vault" to systematically address shelved assets across the industry, making the process more efficient and scalable.  

Prioritizing Patients 

Another topic Bakker mentioned is patient-centric platform trials. Twenty percent of rare disease clinical trials fail because companies and sponsors cannot recruit enough patients in time. A contributing factor is trial designs not considering the practical realities of patients' lives. To combat this issue, CTF has established platform trials for NF that coordinate multiple research centers, standardize endpoints, and—most importantly—involve patients in trial design. This approach has dramatically improved trial efficiency and patient recruitment.  

With approximately 20 clinical centers working together under standardized protocols, the NF clinical trials consortium has conducted 29 trials for approximately $15 million—a fraction of the typical cost. This model is especially valuable for investigating repurposed or off-patent drugs that offer minimal commercial incentive but huge potential benefit to patients. 

“This is where I think the government should be investing their money in things that matter to patients,” Bakker comments. 

“Financial Continuum” 

Bakker envisions a "financial continuum" where non-profit organizations can help biotech companies with promising ideas but insufficient data to attract traditional investment. Non-profits can act as de-risking partners and approach the investment community and bring a non-investable brilliant idea into an investable brilliant idea. “Creating that financial continuum just like we create a research continuum,” as Bakker describes it. A sustainable, de-risking system allows the advancement of rare disease treatments while potentially generating returns that fund future research and more discoveries. 

For rare disease patients and the broader clinical research community, non-profit organizations offer great potential and tremendous hope. By breaking down silos between stakeholders, rescuing shelved assets, designing patient-centric trials, and creating efficient research infrastructures, organizations such as CTF are demonstrating that even the most challenging diseases can benefit from innovative approaches to clinical research and development.