How crowdsourcing can advance precision medicine programs

Sarah Prezek is a senior partner and project manager at Booz Allen Hamilton. This blog was co-authored with Vishal Thovarai, Principal Scientist at Booz Allen Hamilton, and Elaine JohansonDirector of Health Informatics Staff in the FDA’s Office of Data, Analytics, and Research and program manager for precisionFDA.

Healthcare organizations understand the enormous potential of precision medicine. Current one-size-fits-all medical treatments yield inconsistent results and often work poorly for those who don’t fit the “average patient” health profile.

By considering an individual’s specific health attributes, including genomic, environmental, and lifestyle information, healthcare professionals can better tailor the specific treatments that will produce better results.

What if, for example, doctors could better understand which COVID-19 vaccine would work best on a particular patient based on their unique health profile, or gain insights into how to treat the myriad of symptoms associated with long-term COVID? term ?

Enter precision medicine. Advances in this field are already giving rise to powerful new discoveries and several new treatments tailored to specific characteristics, such as a person’s genetic makeup or a patient’s tumor genetic profile.

Many cancer patients already routinely undergo molecular testing as part of patient care so doctors can better tailor treatments that will improve chances of survival and minimize adverse effects.

So how can precision medicine developers, regulators, citizen scientists, research teams, small business owners and healthcare organizations advance the regulatory science needed to ensure the safety and efficacy of regulatory tools? Public crowdsourcing challenges are a good first step.

There are unique results that different groups who respond to crowdsourcing related to precision medicine can achieve. Generally speaking, crowdsourcing-based outreach is a good method to raise awareness and promote engagement with precision medicine.

Public crowdsourcing can also encourage competition among precision medicine stakeholder organizations (e.g., pharmaceutical and bioinformatics companies as well as academics) to achieve innovative discoveries such as new genetic markers of diseases and accelerate research which can lead to the development of new products at low cost.

In turn, crowdsourcing allows these players to validate and showcase their technology. Additionally, regulators, such as the FDA, who ensure the safety and efficacy of precision medicine products for the public market, can leverage crowdsourcing to advance the regulatory science of precision medicine, including encouraging the development of innovative tools and methods to assess product performance and detect post-marketing. safety signals.

What is crowdsourcing in precision medicine?

Crowdsourcing is a process of proactively engaging a large group of dispersed participants to come up with ideas, approaches, research, expertise, and other valuable contributions in an effort to solve a problem or challenge. By mobilizing a global community of experts and scholars and directing them towards a single, specific goal, crowdsourcing is particularly effective in facilitating new discoveries in science and research – and it certainly has proven true in the revolutionary field of precision medicine. The NCTR Indel Calling from Oncopanel Sequencing Data Challenge embodies this idea by asking participants to develop, validate, and compare indel calling pipelines to identify indels in oncopanel sequencing datasets (PrecisionFDA, 2022).

Like any new scientific field, precision medicine is constantly evolving and the technologies on which it relies continue to advance rapidly. In this environment, the associated issues are numerous and complex; overcoming these challenges often requires fresh eyes and multiple perspectives. This is precisely what crowdsourcing offers.

And because this field is so new and exciting – with potential for huge advances at every turn – it is generating real interest and energy in scientific communities around the world, generating collective energy and passion that leads to solutions. crowdsourcing revolutionaries.

Traditionally, scientific discoveries are time consuming and extremely expensive as they require product development, clinical trials and ultimately bringing a product to market. Crowdsourcing can help speed up this process. This is especially the case during the research phase, which is analogous to open source software with its relatively free evolution compared to closed/proprietary software counterparts.

Beyond the scientific discovery potential of crowdsourcing, it also has the practical benefit of offering a relatively inexpensive way to tap into a large pool of talent and expertise through time-limited events.

Additionally, this approach democratizes the entire innovation process, providing everyone from small businesses and students to research facilities and corporations a place to compete and demonstrate their capabilities in high-visibility challenges. which increases the opportunities.

Finally, crowdsourcing is an effective way to make hands-on, experiential learning more accessible. By allowing participants to test themselves in a real-world experiment or exercise, they can bridge the gap that often exists between learning in academic and practical contexts. In this way, crowdsourcing is a great tool for putting conceptual or theoretical ideas into practice, which refines and advances our collective knowledge.

Real applications of crowdsourcing

As mentioned above, a concrete example of crowdsourcing is Phase 1 and Phase 2 of the PrecisionFDA NCTR Indel Calling from Oncopanel Sequencing Data Challenge. Consider how crowdsourcing can support the testing and validation of oncopanels, next-generation sequencing tools that provide physicians with a genomic-level view of tumors — information that can translate into better predictive, prognostic, and diagnostic information for patients. cancer patients.

Because oncopanel technology is new, there are few or no benchmarking techniques to verify, test, and compare these tools. This challenge calls on the precision medicine, oncology, and next-generation sequencing communities to help design algorithms and benchmarking approaches that can advance the regulatory science of oncopanels.

A specific dimension of this challenge is to be able to identify insertion/deletion mutations – or “indels” – which is a type of genetic variation in which a specific nucleotide sequence is present (insertion) or absent (deletion).

It is important to identify indels in a genomic sequence because they are often associated with the formation of cancer cells. This is a common next-generation sequencing problem, and crowdsourcing enables the expert community in oncopanels and next-generation sequencing to come up with algorithms that can solve it.

There are labs around the world that have already worked on this topic and would like the opportunity to demonstrate, evaluate, or validate their solution to see how it compares to others that may be in development. Crowdsourcing allows research centers to evaluate and identify the best performing indel call pipelines from a community of leading researchers in the field.

Precision medicine developers, regulators, citizen scientists, research teams, small business owners, and healthcare organizations can and must act now if they want to make crowdsourcing a more integrated and important part of it. of their precision medicine programs. Consider the following as next steps:

• Secure host platform and environment with challenge framework

• Methodologies from ideation to top performance announcement, including communication strategies and governance

• Diverse organizational team including a program/project manager, graphics and communications support and one or more data scientists

• Partners or internal contacts with key challenges and available data (if any) to assess and use for the challenges.

By institutionalizing crowdsourcing into their precision medicine programs, stakeholders such as precision medicine developers, regulators, citizen scientists, research teams, small business owners, and healthcare organizations can significantly broaden the scope of their thinking and their approaches to meet the many challenges in this rapidly emerging field. of science and technology.