What are the steps involved in multiplex PCR?

What are the steps involved in multiplex PCR?

Multiplex assays run on the Luminex platform typically consist of three major steps: nucleic acid amplification by PCR, target-specific extension, and liquid bead array decoding (Merante et al., 2007). After PCR amplification, the amplicons are mixed with a second set of tagged primers specific for each target.

How do you perform PCR optimization?

Four Tips for Optimizing Your PCR Amplification

  1. Avoid sequence complexity.
  2. Check for primer homology.
  3. Match primer Tm.
  4. End with a G or C.
  5. Remember to add spacers for restriction enzyme cloning/isothermal assembly.
  6. Maintain proper primer concentrations.

How can I increase my multiplex PCR?

In multiplex PCR, choose an annealing temperature that allows all the single-plex reactions to give specific products. If you cannot perform temperature-gradient PCR reactions, 60°C is a good starting point. If some bands are missing, lower annealing temperature in 1.5°C steps.

What are the critical factors while designing a multiplex PCR?

Especially important for a successful multiplex PCR assay are the relative concentrations of the primers at the various loci, the concentration of the PCR buffer, the cycling temperatures and the balance between the magnesium chloride and deoxynucleotide concentrations.

What is multiplex PCR panel?

Panel tests for a comprehensive set of 20 upper respiratory viral and identifies the most common viral and bacterial pathogens that cause indistinguishable symptoms. The rapid and accurate identification of chooses to treat an upper respiratory tract infection.

How do you optimize primers?

The two main approaches are optimization of primer concentration and/or annealing temperatures. One approach to optimizing primer concentrations is to create a matrix of reactions. This is used to test a range of concentrations for each primer against different concentrations of the partner primer.

What is the importance of optimizing each PCR step?

Optimising PCR requires a delicate balance between the amplification of specific products and avoiding the production of non-specific products. Each step, from DNA template extraction to cycling times and temperatures, needs to be considered carefully.

What challenges may be faced by optimizing a multiplexed assay?

Two important challenges associated with multiplex PCR technologies include laborious, time-consuming optimization procedures and unsuitability of traditional separation technologies (such as agarose slab gels) for separation of multiplex PCR products, especially if these products only differ by a few base pairs.

Why is optimization important in PCR?

Lack of optimization often results in problems, such as no detectable PCR product or low efficiency amplification of the chosen template; the presence of nonspecific bands or smeary background; the formation of “primer-dimers” that compete with the chosen template/primer set for amplification; or mutations caused by …

How do you optimize primer concentration in PCR?

What is optimal annealing temperature?

The annealing temperature of a standard PCR protocol is either 55°C [2, 3] or 60°C [4]. The chosen temperature depends on the strand-melting temperature of the primers and the desired specificity. For greater stringency higher temperatures are recommended [2].

What are the advantages of multiplex PCR?

Advantages of Multiplex PCR Higher throughput. Cost effective — fewer dNTPs, enzymes, and other consumables. Time saving. Less input material required.

How is multiplex PCR different from standard PCR?

In conventional singleplex PCR, a single target is amplified in a single reaction tube. In contrast, multiplex PCR allows for simultaneous amplification of multiple target sequences in a single tube using specific primer sets in combination with probes labeled with spectrally distinct fluorophores.

Why MgSO4 is used in PCR?

Mg2+ in general stabilizes primer-template complexes. PCR buffers for Taq DNA Polymerase are supplemented with Mg2+, while in PCR with Pfu DNA Polymerase MgSO4 is a preferable component. Due to the binding of Mg2+ to dNTPs, primers and DNA templates, Mg2+ concentration needs to be optimized for maximal PCR yield.

What is assay optimization?

During the assay optimization phase, it is expected that the investigator has detailed understanding of a variety of parameters for their assay. For example, for enzyme inhibition assays, it is critical that the duration of the assay is linear with time and that substrate is not limiting at this time.

How to design a primer for multiplex PCR assays?

Multiplex PCR assays involve designing of large number of primers, hence it is required that the designed primer should be of appropriate length. Usually, primers of short length, in the range of 18-22 bases are used. 2. Melting Temperature Primers with similar Tm, preferably between 55°C-60°C are used.

What is multiplex PCR and how does it increase diagnostic capacity?

To overcome these shortcomings and also to increase the diagnostic capacity of PCR, a variant termed multiplex PCR has been described. In multiplex PCR more than one target sequence can be amplified by including more than one pair of primers in the reaction.

What is the process of multiplex qPCR?

The process of multiplex qPCR test is similar to the conventional multiplex PCR, and needs a few extra reagents. However, it quantifies various templates present in a sample and therefore has great utility in infectivity and diagnostic studies. Primer designing, assay planning and primer ordering steps are completed earlier before doing the assay.

What is the multi-template multiplex PCR principle?

The multi-template multiplex PCR principle relies on the amplification of different templates in a single reaction. Meaning, it amplifies various templates present in a single sample using different primer sets. Each set of primers is unique to each template.