Difference Between Consensus PCR and Pan PCR

The key difference between consensus PCR and pan PCR is that consensus PCR always targets conserved regions whereas Pan PCR targets variable regions to identify different strains of a group

Polymerase chain reaction (PCR) is a gene amplification technique that consists of three main steps as denaturation, annealing and extension. This is widely used in diagnostics and molecular identification. Consensus PCR and Pan PCR techniques are based on the primer targets that each PCR type uses.

CONTENTS

1. Overview and Key Difference
2. What is Consensus PCR 
3. What is Pan PCR
4. Similarities Between Consensus PCR and Pan PCR
5. Side by Side Comparison – Consensus PCR vs Pan PCR in Tabular Form
6. Summary

What is Consensus PCR?

Consensus PCR is a PCR technique that targets a conserved region for a particular species or genera. Therefore, highly conserved regions are chosen for amplification. Through this method, organisms can be identified and distinguished based on their consensus. This method identifies a conserved region for a particular species. For example, the 16s rRNA region of bacteria remains a conserved region among bacteria. Therefore, only one primer set is required for amplification. In most instances, a universal primer specific can be used for the conserved region.

By following a consensus PCR method, species characterization and evolutionary relationships can be deduced. Based on the amplification efficiency of the particular sample organism, the consensus of the organism towards the group can also be deduced. Further, conducting a consensus PCR is vital in phylogenetic studies. It allows the identification of a species and interprets the deviation the particular organism shown in terms of the common ancestor.

What is Pan PCR?

A Pan PCR is a multiplexing mode of PCR. In this technique, different strains are amplified using various primer targets. The targets, however, can be common targets for the strain groups. Thus, in Pan PCR, more than two primer sets can be used at a single time. It can take place in a single tube reaction method or as a multi-tube reaction method. Pan PCR is more time consuming and more complex in comparison to a consensus PCR. Due to this reason, the interpretation of the PCR results may also be more complex in Pan PCR.

The main application of Pan PCR is in molecular diagnostics. It enables distinguishing between different strains of a species by target amplification. Pan PCR is an ideal technique to identify different strains of a single species causing a disease. In most instances, the automation of Pan PCR techniques for various health conditions is very important and is a reliable and highly efficient technique.

What are the Similarities Between Consensus PCR and Pan PCR?

• Consensus PCR and Pan PCR are two types of PCR techniques.
• Both procedures follow the general three-step procedure – denaturation, annealing and extension.
• They use primers which are target specific.
• Both reactions take place in a thermal cycler.
• These reactions can be automated.
• Both can be used in molecular diagnostics and identification; however, the accuracy varies.
• These procedures require validation.

What is the Difference Between Consensus PCR and Pan PCR?

Both Consensus and Pan PCR follow the same routine procedure. However, the key difference between consensus PCR and Pan PCR is based on the primer targets each procedure utilizes. While consensus PCR always target conserved regions, a Pan PCR targets variable regions to identify different strains of a group. Due to this difference, the primer designing protocols, the number of primer sets used, and the specific applications vary.

The below infographic summarizes the difference between Consensus PCR and Pan PCR.

Summary – Consensus PCR vs Pan PCR

PCR, introduced by Mulli, plays an important revolutionary role in molecular biology applications. Consensus and Pan PCR are two types of PCR based on their primer target regions. While consensus PCR targets conserved regions, Pan PCR targets variable regions and plays an important role in strain identification. Due to this basic difference between consensus PCR and Pan PCR, the specific functions of each type of PCR also vary from phylogenetic analysis to molecular characterization to molecular diagnostics.

Reference:

1. Merkelbach-Bruse, S, et al. “Consensus Polymerase Chain Reaction and Enzyme-Linked Immunosorbent Assay for Human Papillomavirus Detection and Typing in Cervical Specimens.” Diagnostic Molecular Pathology: the American Journal of Surgical Pathology, Part B, U.S. National Library of Medicine, Mar. 1999, Available here.
2. Yang, Joy Y, et al. “Pan-PCR, a Computational Method for Designing Bacterium-Typing Assays Based on Whole-Genome Sequence Data.” Journal of Clinical Microbiology, American Society for Microbiology, Mar. 2013, Available here.

Image Courtesy:

1. “Polymerase chain reaction” By Enzoklop – Own work (CC BY-SA 3.0) via Commons Wikimedia