In practise, it makes no difference which way round the labels are used i.e. which label is on the probe, and which one is on the primer. However, for ease of further test development, it may prove useful to put the hapten for the conjugate antibody on the probe (FAM for Milenia, Biotin for PCRD). This way, users who proceed to use a two line strip for multiplexing, can change which line on the strip they detect at by ordering a new labelled primer rather than ordering a new probe.
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