SPADA Book - April 11, 2017

Technical Assessment: Operational Suitability

Time-consuming multi-step process • May take hours to days • Time dependent on the sample, protocols, selected platform and analysis complexity Protocol Complexity • Multiple step process (e.g., DNA/RNA extraction, nucleic acids fragmented and end-repaired, sequencing, analysis)  Operational suitability for any approach will be assessed with BioWatch laboratories and other SMEs before being considered for operational use

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FOR OFFICIAL USE ONLY

Technical Assessment: Laboratory Suitability  How would we optimize protocols for BioWatch ? • What type of sample prep is needed?

• How can time requirements be minimized? – Example: How much time does it take per run? • How much sample is needed? • What is the depth and quality? • What are the sequencing biases and errors?  Can we trust the analytical results ? • When do I call something present?

– One read? Many? Stacked reads or broad coverage? – Contamination and host cross-interaction? – Determine abundance from read counts? • How do I evaluate the probability that the result is accurate?

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