Comparing Bacterial DNA Microarray Fingerprints

Willse Alan, Chandler Darrell P, White Amanda, Protic Miroslava, Daly Don S and Wunschel Sharon
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Willse Alan: Pacific Northwest National Laboratory
Chandler Darrell P: Biochip Technology Center, Argonne National Laboratory
White Amanda: Pacific Northwest National Laboratory
Protic Miroslava: Biochip Technology Center, Argonne National Laboratory
Daly Don S: Pacific Northwest National Laboratory
Wunschel Sharon: Pacific Northwest National Laboratory

Statistical Applications in Genetics and Molecular Biology, 2005, vol. 4, issue 1, 38

Abstract: Epidemiologic and forensic investigations often require assays to detect subtle genetic differences between closely related microorganisms. Typically, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial samples, where the patterns of DNA fragment sizes are viewed as genotype 'fingerprints'. The limited genomic sample captured on a gel, however, is not always sufficient to discriminate closely related strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if enough independent oligonucleotide probes are used on the microarray, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate a statistical measurement error model to fingerprint 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.

Keywords: microarray fingerprinting; microbial forensics; molecular epidemiology; finite mixture (search for similar items in EconPapers)
Date: 2005
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DOI: 10.2202/1544-6115.1162

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