Panel Discussion:Reference Databases

Nathan EdwardsGeorgetown University Medical Center

Reference Database Use Cases

Assay design Specific detection in device/kit (microarray) Signal is species specific

Assay detection Non-specific design (next-gen sequencing) Detection by match to a reference database

Assay validation In silico specificity guarantee? Guided specificity testing? In silico validation after update?

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Assay Design

Specificity: requires all sequences, but mislabeled or incorrect sequences may

compromise the design the set of reference genomes will never be

complete or "uniformly" sampled Homology and phylogeny

may be able to compensate for missing sequences

can inform clinical or in silico testing for specificity May lead to overly conservative designs…

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Assay Detection

Non-specific design generates sequence or signal from "any" organism

Specificity by match to reference database Signal/reference may not be DNA sequence! May require instrument error modeling May require statistical or error tolerant matches

Competition for signal generation? Testing with mixed (abundance) samples is

crucial – not a specificity issue, per se4

Updated Assay Validation

Specific assays: Target sequence may change (influenza) Updated reference may invalidate working

designs Non-specific design assays:

Authentication of detection reference Match algorithm changes may affect performance How is instrument/processing software validated

across versions?

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