PrecisionFDA is Offering a Brand-New User Experience!
February 11th, 2021
The platform has recently introduced features allowing for the efficient organization and management of files, applications, assets, jobs, and workflows. Not only are users able to access these items more easily, but they can now see what is private, public, or exists in any of their shared spaces. Login or request an account to learn more!
PrecisionFDA is Contributing to the Credibility of Clinical Genomics
January 29th, 2021
In this article, the author discusses the ways in which the scientific community is measuring and assessing the accuracy of clinical genomic sequencing. The precisionFDA “Truth” Challenges are highlighted as an example of efforts within the community to standardize and ensure analytic validity of specific sequencing technologies and processes.
PrecisionFDA Adds Four New Tools!
January 29th, 2021
The precisionFDA team strives to make this platform the best possible computing platform for experts in biomedical research. With that in mind, precisionFDA recently added four new tools to the site. The Maxquant tool allows users to analyze large mass spectrometry datasets (https://www.maxquant.org/); Sierra and Hydra support the annotation of HIV sequence data (https://github.com/phac-nml/quasitools/blob/master/docs/hydra.md, https://github.com/PoonLab/sierra-local); Aspera ASCP allows the transfer of files of any size at maximum speed across any distance (https://www.ibm.com/products/aspera/).
Blog: Can Crowd-Sourcing Help Advance Open Science?
January 29th, 2021
The DREAM Challenge directors recently published a blog discussing the pros and cons of crowdsourcing for the advancement of open science. Use this link (https://network-febs-org.cdn.ampproject.org/c/s/network.febs.org/amp/posts/can-crowd-sourcing-help-advance-open-science) to read more and join in on the insightful discussion!
Sentieon Builds Business on Winning PrecisionFDA Challenges
January 29th, 2021
Sentieon recently published an article in Genome Web discussing how their participation in precisionFDA challenges has helped springboard their business (https://www.genomeweb.com/informatics/sentieon-builds-business-winning-precisionfda-challenges).
Labs on FHIR: Sharing Genetic Test Results
January 14th, 2021
The Office of the National Coordinator for Health Information Technology (ONC) Sync for Genes project has and will continue to advance the standardized sharing of genomics information between laboratories, healthcare providers, patients, and researchers. The first two phases of Sync for Genes focused on bringing genomics to the point-of-care, while making the genomic data available for research simultaneously. Sync for Genes Phase 3 aimed to identify the challenges experienced by testing labs when they adopt health IT standards in order to share genomic results. Phase 4 will focus on improving the electronic exchange of genomic data between organizations with at least one data receiver, such as a patient or caregiver. Learn more about these efforts at https://www.healthit.gov/buzz-blog/interoperability/labs-on-fhir-sharing-genetic-test-results
FDA Scientific Computing Days Talk – Unleashing the Power of Multi-Omics for Precision Medicine
September 30th, 2020
During FDA Scientific Computing Days Dr. Emily Boja, Senior Scientist within the FDA Office of Health Informatics and precisionFDA leader, gave a talk on the power of multi-omoics in which she discussed the NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge and the upcoming COVID-19 Precision Immunology App-a-thon.
FDA Scientific Computing Days Poster – Crowdsourcing Advances Reproducibility Standards and Biomarker Development
September 30th, 2020
A precisionFDA poster, featuring the Brain Cancer Predictive Modeling and Biomarker Discovery Challenge and BCO App-a-thon, was presented at FDA Scientific Computing Days
PrecisionFDA has Launched a Newsletter
September 24th, 2020
Receive the newsletter, including challenge and app-a-thon information, by signing up for the precisionFDA mailing list.
PrecisionFDA Training Session Videos
September 22nd, 2020
The FDA’s Genomic Working Group (GWG) hosted a series of precisionFDA training session. Videos of these session are available on YouTube.
Challenge Framework Updated – Submissions Hidden!
August 1st, 2020
The precisionFDA challenge framework has been updated, now allowing participants to submit to challenges without making their files public before the challenge close.
The GA4GH Benchmarking tool is Available as a PrecisionFDA Comparator App
July 30th, 2020
The Global Alliance for Genomics and Health (GA4GH) benchmarking tool, which enables users to compare variant calls against truth sets and assess variant calling performance, is available on precisionFDA as a comparator app.
Join the COVID-19 EHR DREAM Challenge
July 30th, 2020
Join the COVID-19 EHR DREAM Challenge to help identify risk factors that lead to a positive test. Clinical data sets mapped to the OMOP Common Data Model are provided for analytics development.
FDA Announces Support for BioCompute Objects in Regulatory Submission Filings
July 22nd, 2020
FDA announced support for use in regulatory submissions the current version of the IEEE bioinformatics computations and analyses standard for bioinformatic workflows (BioCompute) and an update to include this standard in the FDA Data Standards Catalog.
NIST Mass Spectral Peptide Libraries for Advancing Proteomic Research
July 28th, 2020
Modern mass spectrometry-based proteomics are capable of profiling tens of thousands of peptides in a single experiment. Each of these peptides is fragmented along the peptide bonds to form a mass spectrum, often interpreted against a theoretical in silico-generated mass spectrum as part of the analysis workflow. Since peptide mass spectra represent physical properties of these molecules, standard interpretation of these mass spectra has the potential to improve the success rate of all discovery experiments in proteomics. To this regard, NIST has developed mass spectral libraries of biologically relevant peptides to provide peptide reference data for proteomic laboratories, enabling the discovery and validation of disease-related "biomarkers." Using mass spectral libraries to identify these compounds is more sensitive and robust than interpretation by theoretical methods. These databases are freely available for testing and development of new applications (http://peptide.nist.gov), in a form easily searchable using software tools such as Mascot, and updated and maintained as a reference data resource. To date, several of the libraries developed, including human, yeast and E. coli, represent significant coverage of these proteomes and are suitable for routine uses. An additional NIST resource for proteomics is the monoclonal antibody reference material, RM8671, a recombinant humanized IgG1κ expressed in murine suspension culture. The reference material is intended for use in evaluating the performance of methods for determining physicochemical and biophysical attributes of monoclonal antibodies (https://www.nist.gov/programs-projects/nist-monoclonal-antibody-reference-material-8671). The RM8671 is accompanied by a high-resolution spectral library for enhanced glycosylation characterization using 2D LC-MS/MS approach (https://chemdata.nist.gov/dokuwiki/doku.php?id=%20peptidew:lib:newigghsalib).
Join the R&D Innovation Ecosystem Map Prize Competition!
June 11th, 2020
Help inform the design of a prize competition to inspire tools entrepreneurs can use to navigate the complex innovation ecosystem by 11:59 pm Monday June 15 - https://federallabs.org/t2-toolkit/lab-to-market-l2m-innovation-ecosystem. The COVID-19 pandemic has presented many challenges for entrepreneurs. Finding the resources to help turn a good idea into solutions for global impact shouldn't be one of them. We are looking for input to make sure the competition results in useful tools that support an inclusive innovation environment so that all businesses can find the resources they need, which in turn will help the US economy grow and respond to challenges like how to recover from the pandemic. The Federal government has abundant resources (https://federallabs.org/node/218178) available to support innovators – from funding to IP to entrepreneurial training to equipment – but like any complex environment, the innovation ecosystem is difficult to navigate without a roadmap and guides. Gaining access to these resources will boost innovation, create jobs, and build the nation’s economy. Be part of the innovative roadmap to success by submitting your ideas on tapping and connecting the vast resources of the Federal government with your local communities’ efforts to assist entrepreneurs nationwide. Learn more about the competition and how to submit your suggestions at https://federallabs.org/t2-toolkit/lab-to-market-l2m-innovation-ecosystem
NIST Tools for the COVID-19 Open Research Dataset (CORD-19)
May 6th, 2020
NIST has released four new tools for searching the COVID-19 Open Research Dataset (CORD-19), a collection of scientific literature about coronaviruses. The four tools are: (1) the NIST Scientific Indexing Resource for finding related articles from identified keywords and phrases, (2) the COVID-19 Data Repository for searching the dataset by author, institution, and keyword, (3) The COVID-19 Registry of other COVID-19-related resources, and (4) the cord19-cdcs-nist curated archive of the dataset.
New Apps Added to precisionFDA
May 10th, 2020
A number of bioinformatics tools have been added as precisionFDA apps! The list includes: AMRFinder, FastQC, Cutadapt, MultiQC, Qualimap, STAR, RSEM, ResFinder, StringTie, SKESA, DIAMOND, and snpEff. All of these apps are publicly available, and can be found by going to precision.fda.gov/apps/explore, or by clicking the link above. They may be forked and modified. If you have an app request that you'd like to see developed on precisionFDA, don't hesitate to contact us!
Flattening the Curve: Pandemic Data Room and COVID-19 Data Challenge
April 13th, 2020
The Pandemic Data Room is a comprehensive global COVID-19 data repository, with unique data sets, created by a consortium of partners and led by QED Group, to improve understanding of the impact of physical distancing policies on social behavior, disease rates, hospital utilization, and local/national economies. Data available from the Pandemic Data Room will be used to generate insights that lead to a better understanding of the impact of physical distancing and the outbreak. Play a role in the response by creating a COVID-19-focused data visualization or analysis tool and sharing with the global health and data visualization communities. Everyone can participate in this Challenge, with separate tracks for students and professionals. Submissions from each track are judged separately and prizes awarded for each track.
Call to Action: Develop new text and data mining techniques to help answer high-priority scientific questions related to COVID-19.
March 16th, 2020
A consortium, led by the White House Office of Science and Technology Policy, has released the COVID-19 Open Research Dataset (CORD-19), a machine-readable dataset of over 29,000 scholarly articles for COVID-19 and the coronavirus family. This consortium now calls on data scientists to develop tools to help scientists extract and synthesize knowledge from this dataset.
Pan-Structural Variation Hackathon in the Cloud
February 28th, 2020
Baylor College of Medicine is hosting a hackathon on April 19-21 to join the fields of structural variation calling and graph genomes. Registration is open until March 15th.
PrecisionFDA mentioned in the publication "Leveraging the health information technology infrastructure to advance federal research priorities"
February 25th, 2020
Ensuring that federally funded health research keeps pace with the explosion of health data depends on better information technology (IT), access to high-quality electronic health data, and supportive policies. Because it prominently funds and conducts health research, the U.S. federal government needs health IT to rapidly evolve and has the ability to drive that evolution. The Office of the National Coordinator for Health Information Technology developed the National Health IT Priorities for Research: A Policy and Development Agenda (the Agenda) that identifies health IT priorities for research in consultation with relevant federal agencies. This article describes support for the Agenda from the Food and Drug Administration, the National Institutes of Health, and the Veterans Health Administration. Advancing the Agenda will benefit these agencies and support their missions as well as the entire ecosystem leveraging the health IT infrastructure or using data from health IT systems for research.
FDA Announces Collaborative Review of Scientific Evidence to Support Associations Between Genetic Information and Specific Medications
February 20th, 2020
On February 20, 2020, the U.S. Food and Drug Administration (FDA) introduced a new web-based resource that describes some of the gene-drug interactions for which FDA believes there is sufficient scientific evidence to support the described associations between certain genetic variants, or genetic variant-inferred phenotypes, and altered drug metabolism, and in certain cases, differential therapeutic effects, including differences in risks of adverse events. This resource represents a collaborative effort between the FDA’s Center for Devices and Radiological Health (CDRH) and Center for Drug Evaluation and Research (CDER) and is intended to provide the FDA’s current view of certain established gene-drug interactions that appear in FDA-approved drug labeling and additional gene-drug interactions that are consistent with the current FDA labeling and are supported by sufficient scientific evidence based on published literature. The FDA will continue to review the science and strength of the scientific evidence and update this resource periodically. The FDA has opened a docket FDA-2020-N-0839 for stakeholders to provide feedback.
FDA Public Meeting: Modernizing FDA’s Data Strategy
January 8th, 2020
If you are interested in learning more about how FDA is modernizing its data strategy, including data quality, data stewardship, data exchange, and data analytics, attend the “Modernizing FDA’s Data Strategy” public meeting on March 27th!
FDA Public Data Challenge: Gaining New Insights by Detecting Adverse Event Anomalies Using FDA Open Data
January 17th, 2020
Join the challenge to advance techniques for surveillance and detection of adverse events associated with FDA products. Submissions are being accepted until February 28th.
FDA’s Technology Modernization Action Plan (TMAP) mentions precisionFDA
September 18th, 2019
FDA’s technology modernization will be informed by direct engagement with stakeholders. As an example of stakeholder engagement, FDA has used PrecisionFDA to provide a community platform for the evaluation of next-generation sequence data and regulatory exploration.
FDA-ARGOS public quality-controlled microbial reference genome database
July 25th, 2019
The precisionFDA CDRH Biothreat Challenge addressed the need for a comprehensive citizen-science benchmarking study of infectious disease NGS diagnostic classification algorithms.
Follow the PrecisionFDA Twitter Account
October 22nd, 2019
Stay up to date on the latest precisionFDA news and challenge information
Brain Cancer Predictive Modeling and Biomarker Discovery Challenge
October 22nd, 2019
PrecisionFDA and Georgetown-ICBI are launching the Brain Cancer Predictive Modeling and Biomarker Discovery Challenge! The goal of this challenge is to advance techniques for the prognosis and treatment of brain tumors by asking participants to develop machine learning and/or artificial intelligence models to identify biomarkers and predict patient outcomes using gene expression, DNA copy number, and clinical data.
FDA Scientific Computing Days PrecisionFDA Poster
September 9th, 2019
Advancing the Regulatory Science of Omics via Crowdsourcing on the precisionFDA Platform
FDA Scientific Computing Days PrecisionFDA Session Recording
September 10th, 2019
Breakout Session: Engaging the Global Community to Support and Inform Regulatory Science
Best practices for benchmarking germline small-variant calls in human genomes
March 11th, 2019
Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Here, as part of the Global Alliance for Genomics and Health (GA4GH), we present a benchmarking framework for variant calling. We provide guidance on how to match variant calls with different representations, define standard performance metrics, and stratify performance by variant type and genome context. Our approach has been piloted in the PrecisionFDA variant-calling challenges to identify the best-in-class variant-calling methods within high-confidence regions. Finally, we recommend a set of best practices for using our tools and evaluating the results.