SPADA Docs

Linda Beck , Joint Research and Development, Inc. (JRAD), Suite 209, 50 Tech Pkwy, Stafford, 22 VA 22556 23 The SPADA In Silico Analysis Working Group 2

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Table of Contents

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1.0 Abstract/Objective 2.0 Background and Rationale

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2.1 Additional considerations with the status quo testing of assays against inclusivity/exclusivity panels 7 2.2 Additional considerations with the availability of inclusivity/exclusivity panel reference materials 9 3.0 Assay Development Process: Traditional (Low throughput) vs Modern (High throughput) 11 4.0 Assay Design 12 4.1 Target selection: user defined vs unbiased (in silico) 12 4.2 Traditional primer design paradigm 13 4.3 Modern Primer Design Paradigm 14 4.3.1 Modern sequence databases 14 4.3.2 Inclusivity Databases 15 4.3.3 Exclusivity and Background Databases 19 4.3.4 Target region selection 20 4.3.5 Physical Chemistry Modeling 21 4.3.6 Checking for Specificity and Coverage 22 4.3.7 Probe Design 23 4.3.8 Ranking the Design Results 24 4.3.9 Combining All of the Recommendations into a Coherent Design Pipeline 25 4.3.10 Multiplexing 29 4.3.11 Multiplexing is a complex system 30 5.0 Metrology for In Silico Analysis 31 5.1 Sources of measurement uncertainty 31 5.2 Assessing Model Accuracy 33 5.3 PCR Datasets in Support of Competitions to Spur the Community Forward 34 6.0 Assay development and characterization 35 6.1 Assay development 35 6.2 Assay validation 37 6.3 Assay Stewardship – when new viral or bacterial strains are discovered, will the existing assay work? 39 2 Stakeholder Panel on Agent Detection Assays (SPADA) In Silico Analysis Working Group members: Jessica Appler, Linda Beck, Trevor Brown, Sharon Brunelle, Donald Cronce, Matthew Davenport, Bruce Goodwin, Scott Jackson, Jeffrey Koehler, Nancy Lin, Timothy Minogue, Victoria Olson, Richard Ozanich, Kristian Roth, John SantaLucia, Sanjiv Shah, Ricky Soong, Shanmuga Sozhamannan

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