
How Will FDA’s new precisionFDA Science 2.0 Collaboration Platform Protect Data?
Reporter: Stephen J. Williams, Ph.D.
As reported in MassDevice.com
FDA launches precisionFDA to harness the power of scientific collaboration
By: Taha A. Kass-Hout, M.D., M.S. and Elaine Johanson
Imagine a world where doctors have at their fingertips the information that allows them to individualize a diagnosis, treatment or even a cure for a person based on their genes. That’s what President Obama envisioned when he announced his Precision Medicine Initiative earlier this year. Today, with the launch of FDA’s precisionFDA web platform, we’re a step closer to achieving that vision.
PrecisionFDA is an online, cloud-based, portal that will allow scientists from industry, academia, government and other partners to come together to foster innovation and develop the science behind a method of “reading” DNA known as next-generation sequencing (or NGS). Next Generation Sequencing allows scientists to compile a vast amount of data on a person’s exact order or sequence of DNA. Recognizing that each person’s DNA is slightly different, scientists can look for meaningful differences in DNA that can be used to suggest a person’s risk of disease, possible response to treatment and assess their current state of health. Ultimately, what we learn about these differences could be used to design a treatment tailored to a specific individual.
The precisionFDA platform is a part of this larger effort and through its use we want to help scientists work toward the most accurate and meaningful discoveries. precisionFDA users will have access to a number of important tools to help them do this. These tools include reference genomes, such as “Genome in the Bottle,” a reference sample of DNA for validating human genome sequences developed by the National Institute of Standards and Technology. Users will also be able to compare their results to previously validated reference results as well as share their results with other users, track changes and obtain feedback.
Over the coming months we will engage users in improving the usability, openness and transparency of precisionFDA. One way we’ll achieve that is by placing the code for the precisionFDA portal on the world’s largest open source software repository, GitHub, so the community can further enhance precisionFDA’s features.Through such collaboration we hope to improve the quality and accuracy of genomic tests – work that will ultimately benefit patients.
precisionFDA leverages our experience establishing openFDA, an online community that provides easy access to our public datasets. Since its launch in 2014, openFDA has already resulted in many novel ways to use, integrate and analyze FDA safety information. We’re confident that employing such a collaborative approach to DNA data will yield important advances in our understanding of this fast-growing scientific field, information that will ultimately be used to develop new diagnostics, treatments and even cures for patients.
Taha A. Kass-Hout, M.D., M.S., is FDA’s Chief Health Informatics Officer and Director of FDA’s Office of Health Informatics. Elaine Johanson is the precisionFDA Project Manager.
The opinions expressed in this blog post are the author’s only and do not necessarily reflect those of MassDevice.com or its employees.
So What Are the Other Successes With Such Open Science 2.0 Collaborative Networks?
In the following post there are highlighted examples of these Open Scientific Networks and, as long as
- transparancy
- equal contributions (lack of heirarchy)
exists these networks can flourish and add interesting discourse. Scientists are already relying on these networks to collaborate and share however resistance by certain members of an “elite” can still exist. Social media platforms are now democratizing this new science2.0 effort. In addition the efforts of multiple biocurators (who mainly work for love of science) have organized the plethora of data (both genomic, proteomic, and literature) in order to provide ease of access and analysis.
Science and Curation: The New Practice of Web 2.0
Curation: an Essential Practice to Manage “Open Science”
The web 2.0 gave birth to new practices motivated by the will to have broader and faster cooperation in a more free and transparent environment. We have entered the era of an “open” movement: “open data”, “open software”, etc. In science, expressions like “open access” (to scientific publications and research results) and “open science” are used more and more often.
Curation and Scientific and Technical Culture: Creating Hybrid Networks
Another area, where there are most likely fewer barriers, is scientific and technical culture. This broad term involves different actors such as associations, companies, universities’ communication departments, CCSTI (French centers for scientific, technical and industrial culture), journalists, etc. A number of these actors do not limit their work to popularizing the scientific data; they also consider they have an authentic mission of “culturing” science. The curation practice thus offers a better organization and visibility to the information. The sought-after benefits will be different from one actor to the next.
Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson and others
- Using Curation and Science 2.0 to build Trusted, Expert Networks of Scientists and Clinicians
Given the aforementioned problems of:
I. the complex and rapid deluge of scientific information
II. the need for a collaborative, open environment to produce transformative innovation
III. need for alternative ways to disseminate scientific findings
CURATION MAY OFFER SOLUTIONS
I. Curation exists beyond the review: curation decreases time for assessment of current trends adding multiple insights, analyses WITH an underlying METHODOLOGY (discussed below) while NOT acting as mere reiteration, regurgitation
II. Curation providing insights from WHOLE scientific community on multiple WEB 2.0 platforms
III. Curation makes use of new computational and Web-based tools to provide interoperability of data, reporting of findings (shown in Examples below)
Therefore a discussion is given on methodologies, definitions of best practices, and tools developed to assist the content curation community in this endeavor
which has created a need for more context-driven scientific search and discourse.
However another issue would be Individual Bias if these networks are closed and protocols need to be devised to reduce bias from individual investigators, clinicians. This is where CONSENSUS built from OPEN ACCESS DISCOURSE would be beneficial as discussed in the following post:
Risk of Bias in Translational Science
As per the article
Risk of bias in translational medicine may take one of three forms:
- a systematic error of methodology as it pertains to measurement or sampling (e.g., selection bias),
- a systematic defect of design that leads to estimates of experimental and control groups, and of effect sizes that substantially deviate from true values (e.g., information bias), and
- a systematic distortion of the analytical process, which results in a misrepresentation of the data with consequential errors of inference (e.g., inferential bias).
This post highlights many important points related to bias but in summarry there can be methodologies and protocols devised to eliminate such bias. Risk of bias can seriously adulterate the internal and the external validity of a clinical study, and, unless it is identified and systematically evaluated, can seriously hamper the process of comparative effectiveness and efficacy research and analysis for practice. The Cochrane Group and the Agency for Healthcare Research and Quality have independently developed instruments for assessing the meta-construct of risk of bias. The present article begins to discuss this dialectic.
- Information dissemination to all stakeholders is key to increase their health literacy in order to ensure their full participation
- threats to internal and external validity represent specific aspects of systematic errors (i.e., bias)in design, methodology and analysis
So what about the safety and privacy of Data?
A while back I did a post and some interviews on how doctors in developing countries are using social networks to communicate with patients, either over established networks like Facebook or more private in-house networks. In addition, these doctor-patient relationships in developing countries are remote, using the smartphone to communicate with rural patients who don’t have ready access to their physicians.
Located in the post Can Mobile Health Apps Improve Oral-Chemotherapy Adherence? The Benefit of Gamification.
I discuss some of these problems in the following paragraph and associated posts below:
Mobile Health Applications on Rise in Developing World: Worldwide Opportunity
According to International Telecommunication Union (ITU) statistics, world-wide mobile phone use has expanded tremendously in the past 5 years, reaching almost 6 billion subscriptions. By the end of this year it is estimated that over 95% of the world’s population will have access to mobile phones/devices, including smartphones.
This presents a tremendous and cost-effective opportunity in developing countries, and especially rural areas, for physicians to reach patients using mHealth platforms.
How Social Media, Mobile Are Playing a Bigger Part in Healthcare
E-Medical Records Get A Mobile, Open-Sourced Overhaul By White House Health Design Challenge Winners
In Summary, although there are restrictions here in the US governing what information can be disseminated over social media networks, developing countries appear to have either defined the regulations as they are more dependent on these types of social networks given the difficulties in patient-physician access.
Therefore the question will be Who Will Protect The Data?
For some interesting discourse please see the following post
Atul Butte Talks on Big Data, Open Data and Clinical Trials
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