Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

Erin P Price; J Inman-Bamber; V Thiruvenkataswamy; F Huygens; P M Giffard

doi:10.1186/1471-2105-8-278

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Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

Journal article

Open access

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Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

Erin P Price, J Inman-Bamber, V Thiruvenkataswamy, F Huygens and P M Giffard

BMC Bioinformatics, Vol.8, 278

2007

DOI: https://doi.org/10.1186/1471-2105-8-278

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Abstract

Background: Single nucleotide polymorphisms (SNPs) and genes that exhibit presence/absence variation have provided informative marker sets for bacterial and viral genotyping. Identification of marker sets optimised for these purposes has been based on maximal generalized discriminatory power as measured by Simpson's Index of Diversity, or on the ability to identify specific variants. Here we describe the Not-N algorithm, which is designed to identify small sets of genetic markers diagnostic for user-specified subsets of known genetic variants. The algorithm does not treat the user-specified subset and the remaining genetic variants equally. Rather Not-N analysis is designed to underpin assays that provide 0% false negatives, which is very important for e.g. diagnostic procedures for clinically significant subgroups within microbial species. Results: The Not-N algorithm has been incorporated into the "Minimum SNPs" computer program and used to derive genetic markers diagnostic for multilocus sequence typing-defined clonal complexes, hepatitis C virus (HCV) subtypes, and phylogenetic clades defined by comparative genome hybridization (CGH) data for Campylobacter jejuni, Yersinia enterocolitica and Clostridium difficile. Conclusion: Not-N analysis is effective for identifying small sets of genetic markers diagnostic for microbial sub-groups. The best results to date have been obtained with CGH data from several bacterial species, and HCV sequence data. © 2007 Price et al; licensee BioMed Central Ltd.

Details

Title: Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants
Authors: Erin P Price (Author) - Queensland University of Technology
J Inman-Bamber (Author) - Queensland University of Technology
V Thiruvenkataswamy (Author) - Queensland University of Technology
F Huygens (Author) - Queensland University of Technology
P M Giffard (Author) - Queensland University of Technology
Publication details: BMC Bioinformatics, Vol.8, 278
Publisher: BioMed Central Ltd.
Date published: 2007
DOI: 10.1186/1471-2105-8-278
ISSN: 1471-2105
Copyright note: Copyright © 2007 Price et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Organisation Unit: University of the Sunshine Coast, Queensland; Centre for Bioinnovation
Language: English
Record Identifier: 99450475802621
Output Type: Journal article

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