SPADA Docs

degrees of primer-hairpin and primer-dimer formation. For the training set, both the PCR inputs 638 and outputs (described above in section 5.2 Assessing Model Accuracy ) would be publicly 639 revealed. For the validation sets, only the PCR inputs would be revealed. Outputs would be used 640 for evaluation of PCR predictions from different research groups by independent referees. The 641 final goal would be to quantitatively evaluate the performance of different in silico PCR methods 642 (i.e. what did different models get right and wrong). To date there has not been an organized 643 effort to provide funding to acquire the needed training and validation PCR datasets, develop an 644 international committee to referee these contests, or recruit groups of scientists to engage in the 645 contests. Successful completion of this effort would drive the field forward and have a dramatic 646 effect on the quality of future PCR-based diagnostics. 651 of the design in wet lab testing using appropriate templates and reagents. Given the increasing 652 genomic diversity represented in genome databases resulting from improved sequencing 653 technology, many diagnostic assays require the incorporation of degenerate primers and/or 654 probes for efficacious species-specific detection. Quantitative assays require additional design 655 considerations depending on the intended use of the assay. Specific genomic locations need to be 656 targeted and methodologies employed if the desired readout is genome copies. The presence of 657 mismatches in either the primer or probe binding locations can affect the PCR kinetics (i.e. the 658 Cq value for a given target concentration) and thus impact the determination of target quantity. 659 Amplification kinetics need to be determined for each new target variant to ensure accurate 660 647 648 6.0 Assay development and characterization 649 6.1 Assay development 650 Once an optimal assay has been designed in silico , the next step is to assess the performance

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