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MLVA PCRs were performed in four multiplex reactions in a final volume of 15 μl.
The Mass ARRAY Assay Design 3.1 software was used to design multiplex reactions in which the selected SNPs were included.
One student prepared the samples for the top half of the gel while the other set up the multiplex reactions in the bottom half.
For these individuals, including their parents, it was necessary to analyse the following loci in another two multiplex reactions in order to conclusively resolve their family of origin.
The qPCR reactions (see Table 1 for details) were performed as two multiplex reactions in a Corbett RotorGene 6000 PCR machine (Qiagen, Hilden, Germany) using Qiagen QuantiTect Multiplex Taq polymerase and corresponding buffers as advised by the manufacturer.
We amplified these eight microsatellites in two multiplex reactions in 97 individuals with the QIAGEN Multiplex PCR Kit QIAGENN) in 10-μL final reaction volumes with 0.2 μM of each primer, 4.6 μL of Multiplex Mix, 1.2 μL of DNase-free water, and 5 30 ng of template DNA.
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In this work we described a highly sensitive single nucleotide polymorphisms (SNPs) typing method with detection of 42 mitochondrial DNA (mtDNA) SNPs in a single PCR and SNaPshot multiplex reaction in order to allow haplogroup classification in Latin American admixture population.
Microsatellites were amplified in multiplex PCR reactions, in a final volume of 10 µl, containing 50 ng of genomic DNA, and separated in multiplex reaction in the capillary automatic sequencer MegaBACE 1000 (GE Healthcare).
RT PCR was performed with primers for both CCL2 and β-actin in a multiplex reaction in a total volume of 20 μl incorporating P-labelled dATP using standard PCR cycling conditions with annealing at 60°C.
The above data demonstrate that the concentration of Taq polymerase needs to be optimized based both on the number and the sequences of the primers added to a multiplex reaction, in order to obtain maximal efficiency without mis-priming.
The first set of AIMs consisted of 14 SNPs reported and genotyped in two multiplex reactions as in Da Silva et al. [56] The second set of AIMs included 48 INDELs reported and genotyped in three multiplex reactions as in Santos et al. [57].
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