For diagnostic PCRs does the targeting of indels hold more discriminatory power and specificity than targeting SNPs or other base pair variation?

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Filipe Pereira

Hi!

indels might have some advantages. check these papers:

Article Identification of species by multiplex analysis of variable-...

Article Straightforward Inference of Ancestry and Admixture Proporti...

Frank R Burns

Indels of greater than a single base, if available, can be quite useful. If possible use more than one discriminatory site in the assay design. It helps to have some specificity in your primer set as well as in the probe, particularly if you are trying to detect a variant DNA in a background of more abundant wild type.