Table Omitted - see PDF Table 1 Workshop speakers and presentation titles Speaker Presentation Title David Duewer, NIST Metrology for Identity and Other Nominal Properties Peter Vallone, NIST ...Forensics: Human Identity Testing in the Applied Genetics Group Javier Atencia, University of Maryland Separation of Bacteria from Complex Samples Nathan Olson, NIST Microbial Genomics at NIST Adam Phillippy, National Biodefense Analysis and Countermeasures Center Sequencing and Informatics for Microbial Forensics William Klimke, National Institutes of Health Bacterial Pathogen Genomics at NCBI Rebecca Lindsey, Centers for Disease Control and Prevention Next-Generation Sequencing for Identification and Subtyping of Foodborne Pathogens Eric Brown, Food and Drug Administration (FDA) Validation, Standardization, and Application of the FDA WGS Pipeline for Foodborne Contamination Traceability William Wolfgang, New York State Department of Health The Prospects for Nextgen Surveillance of Pathogens: A View from a Public Health Lab Patrick McDermott, FDA Whole Genome Sequencing and Antibiotic Resistance Surveillance Heike Sichtig, FDA & Luke Tallon, University of Maryland Development of FDA MicroDB: A Regulatory-Grade Microbial Reference Database David Rasko, University of Maryland From Genome to Biomarker: The Path Forward Bart Weimer, University of California, Davis High Throughput Sequencing Pipeline for Diverse Organisms The majority of the second day consisted of small and large group discussions to identify current and future measurement challenges associated with implementation of NGS for pathogen identification and potential solutions for these challenges. In a separate effort, NIST in collaboration with the FDA is developing genomic DNA reference materials for four bacterial strains, Salmonella enterica subsp. enterica serovar Typhimurium strain LT2, Staphylococcus aureus clinical isolate, Pseudomonas aeruginosa clinical isolate, and Clostridium sporogenes PA3679.
The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their ...variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
The Mid-Atlantic Microbiome Meet-up (M
) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, ...M
held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.
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