Researchers from CosmosID and the National Center for Scientific Research of France score highest in microbiome community challenge aimed at benchmarking and improving computational methods for microbial analysis
MOUNTAIN VIEW, Calif.--(BUSINESS WIRE)-- DNAnexus, the global leader in biomedical informatics and data management, today announced the winners of the Mosaic Community Challenge: Strains #1. This first of three Mosaic Community Challenges, sponsored by Janssen Research & Development, LLC, through the Janssen Human Microbiome Institute, aims to benchmark and improve computational methods in microbiome characterization at the strain level. The team from CosmosID, a bioinformatics and NGS service laboratory, received the highest score in the strain-level microbial profiling category, and Rayan Chikhi, Ph.D., Computer Scientist at France’s National Center for Scientific Research (CNRS), scored highest in the assembly category. All testing and analysis took place within the secure and collaborative environment that is the Mosaic platform. Detailed results from the Strains #1 Challenge can be found at: https://platform.mosaicbiome.com/challenges/1.
“Profiling a microbiome sample is the fundamental step in any microbiome analysis and an essential part of biotherapeutic drug development,” said Richard Daly, Chief Executive Officer of DNAnexus. “Current state-of-the-art methods based on next-generation sequencing perform well in correctly identifying organisms down to the genera and species level. However, the performance of current computational methods at the strain level is poor. Through this community challenge, we hope to identify innovative new computational methods that can unravel the microbiome at finer, strain-level, resolution.”
The Mosaic microbiome platform was launched in collaboration with Janssen in order to advance this rapidly growing field and serves as a virtual ecosystem and innovation accelerator for the entire microbiome community. The cloud-based platform, powered by DNAnexus, provides a secure environment for scientists around the world to collaborate on research, share data, and develop and advance methods aimed at increasing our understanding of the human microbiome, while accelerating the translation of these insights into clinical applications for the benefit of patients.
“The clinically informative and actionable unit in microbiology is a strain, not a species,” said Nur Hasan, Ph.D., M.B.A., Chief Science Officer of CosmosID. “That is why our team has invested years of curation into the largest, most comprehensive microbial reference database. The database’s structure follows the phylogenetic hierarchy of all represented microorganisms, which enables reliable microbial identification at all taxonomic levels, down to strain level. Participating in the Mosaic Community Challenge provided us with a unique opportunity to test and validate CosmosID bioinformatics on a neutral, unbiased platform, and to compare our results against other technologies around the globe.”
Huai Li, Ph.D., Vice President of Engineering at CosmosID, added, “When we analyze NGS data against the CosmosID database, our algorithms use machine-learning derived filter settings to deliver a maximum sensitivity (recall) without sacrificing precision. We are pleased to see that as a result the CosmosID analysis pipeline has won the challenge achieving the highest cumulative F1-score, a measure of precision and recall. Our hope is that by testing our bioinformatics tools and validating our results through the Mosaic Community Challenge, we are contributing to the microbiome community’s overall efforts to improve computational methods in microbiome characterization at the strain level.”
“Challenges such as the Strains Community Challenge are very valuable because they push researchers to focus on specific questions within a short timeframe and illuminate the gaps we still have in our understanding of the microbiome and its effects on the biology of human health,” said Rayan Chikhi, Ph.D., CNRS and CRIStAL research center, and an advisor at Clarity Genomics. “There are many groups working on metagenome assembly, and being able to see our results in real time through this Challenge was a game changer, allowing us to look across the community to improve our methods of analysis in near, real time.”
Two additional Mosaic Community Challenges are currently open for participation. The Clinical Strain Detection Challenge is open for submissions through 7:59 p.m. Eastern Time on July 25, 2018. This Challenge aims to speed the translation of microbiome science into novel products by tracking the presence of certain known strains in a sample. A total of $17,000 in prizes will be awarded to prize-eligible winners (See Official Rules of Participation.) The Mosaic Community Challenge: Standards is open through Spring 2019, and aims to capture the diversity of protocols for NGS-based microbiome profiling methods and analyses as a first step in understanding their impact on the variability of the taxonomic results.
Learn more and sign up to participate at mosaicbiome.com/challenges. Organizations interested in hosting a Mosaic Community Challenge can email info@mosaicbiome.com.
DNAnexus will present more on the Mosaic platform and the Mosaic Community Challenges during Translation of Microbiome Research into Clinical Applications this Friday, June 22, at 12:00 p.m. Eastern Time at the Microbiome Movement - Drug Development Summit in Boston. More information can be found on our blog.
About DNAnexus
DNAnexus, the global leader in biomedical informatics and data management, has created the global network for genomics and other biomedical data, operating in North America, Europe, Asia-Pacific (including China), South America, and Africa. The secure, scalable, and collaborative DNAnexus Platform helps thousands of researchers across a spectrum of industries – biopharmaceutical, bioagricultural, sequencing services, clinical diagnostics, government, and research consortia – accelerate their genomics programs globally. For more information on DNAnexus, please visit www.dnanexus.com or follow the company @DNAnexus.
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