SPADA Draft Documents

improved’ detection assays in response to discovery of signature erosion and make an impact in 151 the field in a timely manner.

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Hence, there is a heightened impetus for developing robust in silico methods and synthetic 154 biology approaches to reduce the need for live/inactivated pathogen samples. While in silico 155 assay design approaches cannot circumvent the need for experimental testing against actual 156 pathogens in relevant biological samples, in silico methods can be used to direct the 157 experimental testing to those isolates that are most likely to demonstrate assay failure (due to 158 false positives or false negatives). Computational prioritization of testing has the potential to 159 streamline efficiency by providing robust characterization while minimizing the time, cost and 160 sample resources consumed. While this report is not intended to promote specific applications or 161 software, it is intended to describe recommendations and guidelines for modern in silico assay 162 design and evaluation. 163 164 Assay Development Process: Traditional (Low throughput) vs Modern (High 165 throughput) 166 Traditional and proposed modern assay development processes are illustrated in Figure 4. 167 Apart from the initial assay design step, the traditional approach is centered on laboratory wet lab 168 testing. The key objectives of the modern process are: 1) the extensive use of in silico analyses of 169 whole genome sequences to 2) guide and minimize the number of experimental iterations, 3) 170 minimize the inclusivity, exclusivity and environmental panel wet lab testing, and 4) cut down 171 cost and time and address limitations on obtaining reference materials. Essentially, the modern 172 approach is data-driven and requires (a) establishing well-curated sequence databases, and (b) 173

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