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Direct sequencing of products from a multiplex reaction is usually unsuccessful.
Furthermore, the optimal combination of SNPs to produce the highest yield per multiplex reaction is determined.
A successful RT-qPCR multiplex reaction is achieved when multiplex and single assays performed simultaneously on the same run result in similar quantification cycles (Cq) values for the amplification of a particular gene.
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The multiplex reaction was designed to produce four different amplicons of 200, 300, 400, and 480 bp.
Genotypes obtained by the multiplex reaction were in 100% concordance with genotypes obtained using simplex PCR-pyrosequencing (n = 69) and direct DNA sequencing (n = 29).
The hME primers for each multiplex reaction were spotted onto SpectroCHIPs using the Sequenom CCU RoboDesign nanodipenser, detected on the Sequenom MALDI-TOF mass spectrophotometer (MS), and adjusted to normalize MALDI-TOF MS peak height intensities for subsequent multiplexing reactions.
Total amplification of each multiplex reaction was kept below saturation levels to allow the amplifier to remain within the exponential range of the amplification curve and to provide semi-quantitative data.
The multiplex reaction was diluted 1 20; 5 µl were analysed with size standard LIZ600 (Applied Biosystems) on the capillary sequencer.
Ct values obtained for each gene were identical between multiplex and singleplex PCR, indicating that the multiplex reaction was not rate limiting.
Primer compatibility and specificity in the multiplex reaction were checked using OligoAnalyzer 3.1 (IDT) and Primer-BLAST software from NCBI, respectively.
Briefly, multiplex reaction was designed using Assay Designer software version 3.0 (Sequenom) and was processed following standard protocols for iPLEX chemistry.
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