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How crowdsourcing can advance precision medicine programs

Sarah Prezek is a Principal Associate and Project Manager at Booz Allen Hamilton. This blog was written in collaboration with Vishal Thovaraichief scientist at Booz Allen Hamilton, and Elaine Johnsondirector of the health informatics staff under FDA’s Office of Data, Analytics, and Research and program manager of precisionFDA.

Healthcare organizations understand the enormous potential of precision medicine. Current one-size-fits-all medical treatments yield non-uniform results and often perform poorly for those who do not fit the health profile of the “average patient.”

By taking into account an individual’s specific health characteristics, including genomic, environmental, and lifestyle information, medical professionals can better tailor specific treatments that will produce more successful outcomes.

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

Enter precision medicine. Advances in this area are already yielding powerful new discoveries and several new treatments tailored to specific characteristics, such as a person’s genetic makeup or the genetic profile of a patient’s tumour.

Many cancer patients already routinely undergo molecular testing as part of patient care, allowing physicians to better tailor treatments that increase survival rates 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 effectiveness of regulatory tools? Public crowdsourcing challenges are a good first step.

There are unique outcomes that different groups responding to precision medicine crowdsourcing can achieve. Overall, crowdsourced outreach is a good method to raise public awareness and promote engagement in precision medicine.

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

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In turn, crowdsourcing enables these stakeholders to validate and showcase their technology. Furthermore, regulators, such as the FDA, who ensure the safety and efficacy of precision medicine products for the public market can leverage crowdsourcing to advance precision medicine regulatory science, including by encouraging the development of innovative tools and methodologies for assessing of product performance and detecting safety signals.

What is crowdsourcing in precision medicine?

Crowdsourcing is a process that proactively engages a large group of dispersed participants to provide ideas, approaches, research, expertise, and other valuable contributions for the purpose of solving a problem or challenge. By tapping into a global community of experts and scholars and directing them toward one specific goal, crowdsourcing is particularly effective at facilitating new discoveries in science and research – and this has certainly proved true in the pioneering field of precision medicine. Calling the NCTR Indel of Oncopanel Sequencing Data Challenge embodies this idea by asking participants to develop, validate and benchmark indel call pipelines to identify indels in the oncopanel sequencing datasets (PrecisionFDA, 2022).

As with any new field of science, precision medicine is constantly evolving and the technologies it relies on continue to develop rapidly. In this environment, the associated challenges are many and complex; overcoming these challenges often requires fresh eyes and multiple perspectives. That is exactly what crowdsourcing offers.

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

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

Aside from the potential of crowdsourcing for scientific discovery, it also has a practical benefit as it provides a relatively inexpensive way to leverage a significant pool of talent and expertise through time-boxed events.

In addition, this approach democratizes the entire innovation process and provides a place for everyone, from small businesses and students to research facilities and companies, to compete and demonstrate their capabilities in high-visibility challenges, leading to more opportunities.

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

Real-life applications of crowdsourcing

As mentioned above, a realistic example of crowdsourcing is the precisionFDA NCTR Indel Calling of Oncopanel Sequencing Data Challenge phase one and phase two. 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—insights that could translate into improved predictive, prognostic, and diagnostic information for cancer patients.

Because oncopanel technology is new, there are few, if any, benchmarking techniques for verifying, testing, and comparing these tools. This challenge is a call to the precision medicine, oncology, and next-generation sequencing communities to help develop benchmarking algorithms and approaches that can advance copanel regulatory science.

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

It is important to identify indels within a genomic sequence as they are often associated with cancer cell formation. This is a common next-generation sequencing problem, and crowdsourcing enables the community of experts specializing in oncopanels and next-generation sequencing to propose algorithms that can solve this problem.

There are labs around the world that have already worked on this and would love the chance to demonstrate, evaluate or validate their solution to see how it compares to others that may be in development. Crowdsourcing enables research centers to evaluate and identify the best-performing indel-calling pipelines among a community of leading researchers in the field.

Precision medicine developers, regulators, citizen scientists, research teams, small business owners and healthcare organizations can and should act now if they are interested in making crowdsourcing a more integrated and important part of their precision medicine programs. Consider the following as next steps:

  • Secure the host platform and environment with a challenge framework

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

  • Diverse organizing team including program/project manager, graphical and communication support and data scientist(s)

  • Partners or internal contacts with leading challenges and available data (if applicable) to be reviewed and used for challenges.

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

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