August 30, 2016 SPADA Meeting Book

Specificity analysis (cont.):  Environmental aerosol matrix samples: • Method developers should obtain environmental matrix samples that are Variola Working Group SMPR: Tailor Panel to Assay Based on Bioinformatics representative/consistent with the collection method to be used • Considerations include: • Collection medium • Duration of collection • Diversity of geographical areas to be sampled • Climatic/environmental conditions • Seasonal changes • Ensure sufficient replicates to represent environmental condition  Ensure aerosol matrix samples do NOT cross-react  Environmental panel organisms: • Organisms can be pooled (up to 10 per pool) • Method developer must justify exclusion of specific panel organisms  Ensure all organisms are NOT detected at 10X AMDL • If unexpected result, each individual organisms from failed pool must be tested individually at 10X AMDL

Variola Working Group SMPR: Tailor Panel to Assay Based on Bioinformatics

Bioinformatic analysis : • In silico screening on signature sequences • Suggestive of potential performance issues G id dditi t t l b i

l • u e necessary a ons o we a screen ng pane s

• Potential tools for in silico screening:

• http://sourceforge.net/projects/simulatepcr/files/?source=navbar • NCBI tools  Method developer submission should include:  Description of sequence databases used in the in silico analysis  Description of conditions used for in silico analysis  Stringency of in silico analysis must match bench hybridization conditions  Description of tool used for bioinformatics evaluation  Data confirming selected tool performance based on wet-lab testing • Can be generated retrospectively using published assays  List of additional strains to be added to inclusivity or exclusivity panels