PrecisionFDA Receives FDA Commissioner’s Award for Outstanding Achievement

Today, the precisionFDA Next Generation Sequencing (NGS) Team received the FDA Commissioner’s Special Citation Award for Outstanding Achievement and Collaboration in the development of the precisionFDA platform promoting innovative regulatory science research to modernize regulation of NGS-based genomic tests. This award recognizes superior achievement of the Agency’s mission through teamwork, partnership, shared responsibility, and fostering collaboration to achieve the FDA goals.

 

PrecisionFDA is an online, cloud-based, virtual research space where members of the genomics community can experiment, share data and tools, collaborate, and define standards for evaluating and validating analytical pipelines. This open-source community platform, which has become a global reference standard for variant comparison, includes members from academia, industry, healthcare, and government, all working together to further innovation and develop regulatory standards for NGS-based drugs and devices. Launched in December 2015, the precisionFDA community includes nearly 5,000 users across 1,200 organizations, with more than 38 terabytes of genomic data stored.

To date, the precisionFDA NGS Team has engaged the genomics community through a series of community challenges:

  • The Consistency Challenge (Feb-Apr 2016): Invited participants to manipulate datasets with their software pipelines and conduct performance comparisons.
  • The Truth Challenge (Apr-May 2016): Gave participants the unique opportunity to test their NGS pipelines on an uncharacterized sample (HG002) and publish results for subsequent evaluation against a newly-revealed ‘truth’ dataset.
  • App-a-thon in a Box (Aug-Dec 2016): Invited the community to contribute NGS software to the precisionFDA app library, enabling the community to explore new tools.
  • Hidden Treasures Competition (Jul-Sep 2017): Participants beta-tested the in-silico analyses of NGS datasets for the purpose of determining the reliability and accuracy of different NGS tests.
  • CFSAN Pathogen Detection Challenge (Feb-Apr 2018): Participants helped to improve bioinformatics pipelines for detecting pathogens in samples sequenced using metagenomics.

We are thrilled that precisionFDA has been recognized for its efforts in fostering shared responsibility for the evaluation and validation of analytical pipelines. PrecisionFDA’s proven success has driven other scientific communities such as St. Jude Cloud to promote pediatric cancer research, and the Mosaic microbiome platform for advancing microbial strains analysis, to establish their own collaborative ecosystem for members to contribute and innovate. DNAnexus is proud to be the platform that powers precisionFDA and other community portals to advance scientific research through a secure and collaborative online environment.

To learn more about DNAnexus community portals please visit: http://go.dnanexus.com/community-portals.

For St. Jude, Advancing Cures for Pediatric Cancer Means Accelerating Genomic Discovery and Collaboration

Angela Blog Author

 

 

 

Historically, cancer research has been slowed by an inability to make genomic data rapidly accessible to research collaborators. Last week, St. Jude Children’s Research Hospital took a big step toward solving this problem with its launch of St. Jude Cloud, an online platform that allows researchers to access the world’s largest public repository of pediatric cancer genomics data. Developed in partnership between St. Jude, Microsoft, and DNAnexus, St. Jude Cloud provides a flexible cloud platform for rapid data mining, analysis and visualization capabilities.

St. Jude has long been a leader in advancing cures for pediatric cancer and other life-threatening diseases, and continues to develop new approaches to revolutionize the way medicine is practice. St. Jude Cloud is the latest unique tool developed in the fight to advance cures for pediatric diseases. DNAnexus is proud to serve as the technology platform that brings together St. Jude researchers and their partners in a secure and collaborative ecosystem.

Collaboration fuels scientific advancements, and St. Jude Cloud is already doing just that. In a paper that was recently published in Nature, St. Jude researchers lead by Jinghui Zhang, PhD, discovered mutations connected to UV damage in a B-cell leukemia. This was a very surprising finding and led the team to ask whether other leukemia samples not included in the original study might have a similar mutational pattern. Scott Newman, PhD, used St. Jude Cloud to reproduce the original experimental findings in just a few days whereas the original research took more than two years to complete.

Using St. Jude Cloud, Newman was able to conduct large-scale data analysis enabling him to identify the same UV-linked mutational signature in pediatric B-Cell leukemia patients over four days. Discovering these additional samples further helped researchers understand the possible link between UV damage and a blood cancer and potentially leads to the development of new therapies. Learn more about the St. Jude Cloud and its research capabilities via Q&A with Newman featured in the St. Jude Progress.

Like St. Jude Cloud, DNAnexus delivers fit-for-purpose community portals to advance scientific research through a secure and collaborative online environment that has been independently audited and certified. DNAnexus community research portals allow members to focus on discovery and innovation, removing the burden of secure data management, distribution, and data analysis. Other community research portals powered by DNAnexus include the FDA’s precisionFDA platform for advancing regulatory standards for NGS-based drug and devices, and the microbiome research platform, Mosaic, which facilitates the translation of microbiome research into clinical applications.

Learn more about DNAnexus community portals and determine which use case is right for you.

Regeneron Genetics Center Identifies Promising Target for Development of New Therapies for Chronic Liver Disease

Angela Blog Author

 

 

 

NEJMLast week a team of researchers at Regeneron Genetics Center published a paper in the New England Journal of Medicine, which identified a new genetic variant that likely protects against chronic liver disease and may reveal new therapeutic targets. Chronic liver disease and cirrhosis are leading causes of illness and death in the United States, affecting more than 3.9 million adults. From 2000 to 2015 the death rate has increased by 31%, according to the Centers for Disease Control and Prevention.

Using exome sequence data and electronic health records (EHRs) from nearly 47,000 participants in the DiscovEHR human genetics study, researchers identified genetic variants associated with serum levels of two proteins (ALT and AST) linked to liver injury. Regeneron validated the ALT and AST association findings by  reproducing the discovery using in three additional cohorts. In addition, researchers were able to confirm chronic liver disease associations in more diverse, multi-ethnic populations. The ability to quickly cross-validate the discovery demonstrates the increasing power of sequencing as cohorts grow is size and diversity.

The impact of this genome-wide association study is huge, and demonstrates the power of genomics to identify targets for therapeutic intervention in an area for which there are currently no approved therapeutics. The substantial protection from the loss-of-function variant in HSD17B13 gene against non-viral liver disease suggests that pharmacological inhibition of this enzyme may slow or prevent the progression of these disorders.  Risk reduction ranged between approximately 30-70% for both alcoholic and nonalcoholic liver disease. In addition, allele frequency in the population was found to be high, around 20% and present in African, Asian, and European populations at frequencies of 10-30%. The fact that such common variants relevant to high-value therapeutic targets remain to be discovered suggests that NGS-based technologies are just beginning to tap into the potential to unlock the human genome to improve health.

Given that finding new targets for drug development remains one of the hardest and most valuable tasks within pharmaceutical R&D, based on these findings, it seems reasonable to believe that these methods can be applied to other disease areas to yield many more high value discoveries. DNAnexus is proud to be the cloud-based translational medicine platform utilized by Regeneron Genetics Center in their large-scale, groundbreaking studies. The exemplary DiscovEHR study is a powerful example of how the DNAnexus Platform is employed as the proven option at scale by organizations and consortia globally to integrate genetic and phenotypic data, enable collaboration, and accelerate discovery.

You can read more about other powerful large-scale GWAS studies by Regeneron Genetics Center and their collaborators here and here.