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Seven breast cancer genetic markers were amplified by means of the MLPA reaction, which allows for multiplex amplification of multiple targets with a single primer pair.
The method is quite fast and concludes all the polymorphic STR alleles by multiplex amplification of DNA from the picogram (pg) levels of DNA concentration (Green et al., 2013).
DNA samples are subjected to digestion by a methylation-sensitive restriction endonuclease followed by multiplex amplification of specific genomic targets with fluorescent-labeled primers, capillary electrophoresis of amplification products, and automatic signal analysis by dedicated software, yielding the source tissue of the sample.
In addition, use of clonal emPCR in the 454 system greatly reduces the issue of length bias in multiplex amplification of STRs.
In the second-generation line probe assay, probes targeting the core-coding region were added to the probes targeting the 5'NCR already present in the first-generation assay, and a new PCR reaction was implemented to allow multiplex amplification of both regions.
A nested multiplex amplification of the genomic regions was performed.
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The genus-specific PCR assay, which targets the 223 bp sequence of the gene encoding a 31 kDa Brucella abortus antigen [ 19], and the multiplex amplification for the identification of Brucella to the species level called AMOS PCR for B. abortus, B. melitensis, B. ovis and B. suis[ 20], were carried out on 110 Saudi Arabian serum samples from patients with AFI.
Two 20-cycle multiplex amplification reactions of the regions of interest were performed by using AmpliSeq custom oligos.
To optimize the multiplex amplification, the concentration of MgCl2 and the annealing and extension temperatures were varied (data not shown).
For this subset of markers the possibility of multiplex amplification was tested, as were the variability and allele range of these markers.
We have successfully overcome this problem with a novel combination of two widely used approaches: target-specific multiplex amplification with 15 cycles of polymerase chain reaction (PCR), followed by single-molecule detection of amplicons with atomic force microscopy (AFM).
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