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New methods to analyse microarray data that partially lack a reference signal.

Carpaij, N; Fluit, AC; Lindsay, JA; Bonten, MJ; Willems, RJ (2009) New methods to analyse microarray data that partially lack a reference signal. BMC GENOMICS, 10 (522). ISSN 1471-2164 https://doi.org/10.1186/1471-2164-10-522
SGUL Authors: Lindsay, Jodi Anne

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Abstract

BACKGROUND: Microarray-based Comparative Genomic Hybridisation (CGH) has been used to assess genetic variability between bacterial strains. Crucial for interpretation of microarray data is the availability of a reference to compare signal intensities to reliably determine presence or divergence each DNA fragment. However, the production of a good reference becomes unfeasible when microarrays are based on pan-genomes.When only a single strain is used as a reference for a multistrain array, the accessory gene pool will be partially represented by reference DNA, although these genes represent the genomic repertoire that can explain differences in virulence, pathogenicity or transmissibility between strains. The lack of a reference makes interpretation of the data for these genes difficult and, if the test signal is low, they are often deleted from the analysis. We aimed to develop novel methods to determine the presence or divergence of genes in a Staphylococcus aureus multistrain PCR product microarray-based CGH approach for which reference DNA was not available for some probes. RESULTS: In this study we have developed 6 new methods to predict divergence and presence of all genes spotted on a multistrain Staphylococcus aureus DNA microarray, published previously, including those gene spots that lack reference signals. When considering specificity and PPV (i.e. the false-positive rate) as the most important criteria for evaluating these methods, the method that defined gene presence based on a signal at least twice as high as the background and higher than the reference signal (method 4) had the best test characteristics. For this method specificity was 100% and 82% for MRSA252 (compared to the GACK method) and all spots (compared to sequence data), respectively, and PPV were 100% and 76% for MRSA252 (compared to the GACK method) and all spots (compared to sequence data), respectively. CONCLUSION: A definition of gene presence based on signal at least twice as high as the background and higher than the reference signal (method 4) had the best test characteristics, allowing the analysis of 6-17% more of the genes not present in the reference strain. This method is recommended to analyse microarray data that partially lack a reference signal.

Item Type: Article
Additional Information: © 2009 Carpaij 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.
Keywords: Comparative Genomic Hybridization, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Reference Standards, Staphylococcus aureus, Science & Technology, Life Sciences & Biomedicine, Biotechnology & Applied Microbiology, Genetics & Heredity, COMPARATIVE GENOMIC HYBRIDIZATION, STAPHYLOCOCCUS-AUREUS, DNA MICROARRAY, NORMALIZATION, REVEALS, SINGLE, DIVERSIFICATION, DIVERSITY, INSIGHTS, STRAINS
SGUL Research Institute / Research Centre: Academic Structure > Infection and Immunity Research Institute (INII)
Journal or Publication Title: BMC GENOMICS
ISSN: 1471-2164
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Dates:
DateEvent
13 November 2009Published
Web of Science ID: WOS:000272356900001
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URI: http://openaccess.sgul.ac.uk/id/eprint/677
Publisher's version: https://doi.org/10.1186/1471-2164-10-522

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