I am think Multiplex is better in terms of optimization and cost but might not be better in terms of ease of doing/handling.
I think Multiplex PCR is better than Singleplex PCR when one is considering optimization and cost but might not be better in terms of ease of handling/doing
It depends on what is happening next to the amplimers and how many samples you are processing and how much dna from each sample that you have. For large numbers of samples and if the positive amplification is all the result you need then it is worth the extra effort in setting up a multiplex pcr. For small numbers of samples and if the product is needed for sequencing then singleplex is appropriate. The answer probably lies in between. If one or 2 pcr primer sets work badly or form dimers with other primers these might have to be run separately. If the primers are dye labelled for genotyping using capillary electrophoresis then I would always try to multiplex
It will depend on your objective, the multiplex will save you time and reagents although it is less sensitive than the monoplex.
Multiplex will save your reagent and time but it is prone to error and it is less sensitive than singleplex. In terms of optimization, from laboratory-based experience, I do not see how better it is beside the time-advantage factor for getting more primers working...In fact, it takes more effort sometimes to optimize for multiplex than optimizing each apart, as the peak of activity of each primer may be different
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