The cost of nucleic acid diagnostics can potentially be greatly reduced if multiple reactions can be processed simultaneously in the same tube or well. While simple in concept, successful deep multiplexing of four or more singleplex assays can be extremely difficult. The major difficulty is that assays that perform perfectly well on their own can have major cross-reactions when combined. Vendor-specific software to design multiplex assays is available; the depth of multiplexing possible may vary and some software may be better at checking potential multiplexed assays than at generating them.
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