23555882

From SEQwiki
Jump to: navigation, search

This reference describes MultiPSQ.

PMID PMID 23555882
Title MultiPSQ: a software solution for the analysis of diagnostic n-plexed pyrosequencing reactions.
Year 2013
Journal PLoS One
Author Dabrowski PW, Schröder K, Nitsche A
Volume 8
Start page 60055


Error: No contents found at URL http://www.ebi.ac.uk/europepmc/webservices/rest/MED/23555882/citations/4000.

According to Europe PubMed Central, this reference has Error: no local variable "citations" was set. " Error: no local variable "citations" was set. " is not a number. citations.

For reference, you can check Google Scholar, which lacks an API because Google ...


Error: Invalid JSON. According to Almetric, this reference has an Altmetric score of Error: no local variable "altscore" was set. " Error: no local variable "altscore" was set. " is not a number..

Full text description

BACKGROUND: Pyrosequencing can be applied for Single-Nucleotide-Polymorphism (SNP)-based pathogen typing or for providing sequence information of short DNA stretches. However, for some pathogens molecular typing cannot be performed relying on a single SNP or short sequence stretch, necessitating the consideration of several genomic regions. A promising rapid approach is the simultaneous application of multiple sequencing primers, called multiplex pyrosequencing. These primers generate a fingerprint-pyrogram which is constituted by the sum of all individual pyrograms originating from each primer used.

METHODS: To improve pyrosequencing-based pathogen typing, we have developed the software tool MultiPSQ that expedites the analysis and evaluation of multiplex-pyrograms. As a proof of concept, a multiplex pyrosequencing assay for the typing of orthopoxviruses was developed to analyse clinical samples diagnosed in the German Consultant Laboratory for Poxviruses.

RESULTS: The software tool MultiPSQ enabled the analysis of multiplex-pyrograms originating from various pyrosequencing primers. Thus several target regions can be used for pathogen typing based on pyrosequencing. As shown with a proof of concept assay, SNPs present in different orthopoxvirus strains could be identified correctly with two primers by MultiPSQ.

CONCLUSIONS: Software currently available is restricted to a fixed number of SNPs and sequencing primers, severely limiting the usefulness of this technique. In contrast, our novel software MultiPSQ allows analysis of data from multiplex pyrosequencing assays that contain any number of sequencing primers covering any number of polymorphisms.