How crowdsourcing can advance precision medicine programs
Sarah Prezek is a lead associate and project manager at Booz Allen Hamilton. This blog was coauthored with Vishal Thovarai, lead scientist at Booz Allen Hamilton, and Elaine Johanson, director 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. The current one-size-fits-all medical treatments deliver non-uniform results and often perform poorly for those who do not fit the “average patient” health profile.
By considering an individual’s specific health attributes, including genomic, environmental, and lifestyle information, medical professionals can better tailor specific treatments that will deliver more successful outcomes.
What if, for example, doctors could better understand which COVID-19 vaccine would perform best on a particular patient based on their unique health profile, or gain insights into how to address the multitude of symptoms associated with long-term COVID?
Enter precision medicine. Advances in this field 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 tumor.
Many cancer patients already routinely undergo molecular testing as part of patient care so that physicians can better tailor treatments that will improve the 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 outcomes that different groups who respond to precision medicine-related crowdsourcing can achieve. Broadly, crowdsourcing-based outreach is a good method to bring awareness to the public and promote engagement with precision medicine.
Public crowdsourcing can also encourage competition between precision medicine stakeholder organizations (e.g. pharmaceutical and bioinformatics companies as well as academics) to deliver innovative discoveries like new genetic markers of disease and accelerate research that can lead to the development of new products at a low cost.
In turn, crowdsourcing enables these stakeholders to validate and showcase their technology. Further, regulators, such as the FDA, that ensure the safety and efficacy of precision medicine products for the public market, can leverage crowdsourcing to advance precision medicine regulatory science, including encouraging the development of innovative tools and methods for assessing product performance and detecting postmarket safety signals.
What is crowdsourcing in precision medicine?
Crowdsourcing is a process of proactively engaging a large group of dispersed participants to offer ideas, approaches, research, expertise, and other valuable contributions with the goal of solving a problem or challenge. By harnessing a global community of experts and scholars and steering them toward a single, specific goal, crowdsourcing is particularly effective at facilitating new discoveries in science and research – and this has certainly proved to be true in the groundbreaking field of precision medicine. The NCTR Indel Calling from Oncopanel Sequencing Data Challenge embodies this idea by asking participants to develop, validate, and benchmark indel calling 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 advance rapidly. In this environment, the associated challenges 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 the potential for huge advancements at every turn – it sparks a real interest and energy in scientific communities around the world, generating collective energy and passion that leads to revolutionary crowdsourcing solutions.
Traditionally, scientific discoveries are time-consuming and extremely expensive because they require development of a product, clinical trials, and ultimately bringing a product to the market. Crowdsourcing can help accelerate this process. This is especially so during the research phase, which is analogous to open-source software with its relatively unhindered evolution compared to closed/proprietary software counterparts.
Beyond crowdsourcing’s potential for scientific discovery, it also has a practical upside of offering a relatively inexpensive way to harness a sizable pool of talent and expertise through time-boxed events.
Furthermore, this approach democratizes the entire process of innovation, offering a venue for anyone from small businesses and students to research facilities and corporations to compete and demonstrate their capabilities in high-visibility challenges, leading to increased opportunities.
Finally, crowdsourcing is an efficient 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 settings. In this way, crowdsourcing is a great tool for bringing conceptual or theoretical ideas into practice, which further refines and advances our collective knowledge.
Real-life applications of crowdsourcing
As mentioned above, a real-life example of crowdsourcing is the precisionFDA NCTR Indel Calling from Oncopanel Sequencing Data Challenge phase one and phase two. Consider how crowdsourcing can support testing and validating oncopanels, next-generation sequencing tools that provide physicians with a genomic-level view of tumors – insights that can 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 calling on the precision medicine, oncology, and next-generation sequencing communities to help devise benchmarking algorithms and approaches that can advance oncopanel regulatory science.
One specific dimension of this challenge is being 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’s important to identify indels within 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 community of experts who specialize in oncopanels and next-generation sequencing to propose algorithms that can solve for it.
There are labs around the world that have already been working on this and would welcome a chance to demonstrate, evaluate, or validate their solution to see how it compares with others that may be in development. Crowdsourcing enables research centers to evaluate and identify the top 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 significant part of their precision medicine programs. Consider the following as next steps:
Secure host platform and environment with a challenge framework
Methodologies from ideation to top performer announcement, including communication strategies and governance
Diverse organizing team including program/project manager, graphics and communication support, and data scientist(s)
Partners or internal contacts with leading challenges and available data (if applicable) to be assessed and used for challenges.
By institutionalizing crowdsourcing into their precision medicine programs stakeholders like precision medicine developers, regulators, citizen scientists, research teams, small business owners, and healthcare organizations can dramatically widen the aperture of their thinking and approaches to addressing the many challenges in this fast-emerging field of science and technology.