PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens

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Multiplex Detection of Bacteria in Complex Clinical and Environmental Samples using Oligonucleotide-coupled Fluorescent Microspheres
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Multiplex Detection of Bacteria in Complex Clinical and Environmental Samples using Oligonucleotide-coupled Fluorescent Microspheres

Published on: October 23, 2011

Sreedevi Thiyagarajan1, Miloslav Karhanek, Michael Akhras

  • 1Stanford University, Palo Alto, CA, USA. sreedevi@stanford.edu <sreedevi@stanford.edu>

BMC Bioinformatics
|November 16, 2006
PubMed
Abstract

Insights

PathogenMIPer software designs molecular inversion probes (MIPs) for pathogen detection. This tool enables specific probe design for identifying multiple infections from various genomes, enhancing diagnostic capabilities.

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Molecular Inversion Probe (MIP) technology offers a powerful method for pathogen identification and detection.
  • Designing specific and unique MIP oligonucleotides is crucial for accurate microbial genome targeting.
  • Existing methods may not fully leverage genomic variability for detecting multiple co-infections.

Purpose of the Study:

  • To introduce PathogenMIPer, a novel software for designing custom MIP oligonucleotides.
  • To enable the design of specific probes targeting microbial genomes for pathogen detection assays.
  • To facilitate the detection of multiple co-infections within a single assay using MIP technology.

Main Methods:

  • PathogenMIPer utilizes user-provided sequence data (FASTA format) and graphical user interface inputs.
  • The software designs all essential probe components: target-specific sequences, barcodes, primers, and restriction sites.
  • It integrates these components into ready-to-order probes for MIP assays, harnessing genomic variability.

Main Results:

  • PathogenMIPer successfully designed MIPs for pathogen identification and broader genomic analyses.
  • Experimental validation using human papillomavirus (HPV) demonstrated high sensitivity in detecting single and multiple infections, even at low viral loads.
  • The software's capability to design probes for 24 HPV types showed promising results in laboratory sample testing.

Conclusions:

  • PathogenMIPer is an effective software solution for designing MIPs for multiplex DNA target detection.
  • It expands the application of MIP technology for genotyping complex or mixed pathogen infections.
  • The tool supports the detection of difficult-to-amplify pathogens and those with multiple subtypes.

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