High-throughput method for detecting genomic-deletion polymorphisms

Journal of Clinical Microbiology
Yves-Olivier L Goguet de la SalmonierePeter M Small

Abstract

DNA microarrays have been successfully used with different microorganisms, including Mycobacterium tuberculosis, to detect genomic deletions relative to a reference strain. However, the cost and complexity of the microarray system are obstacles to its widespread use in large-scale studies. In order to evaluate the extent and role of large sequence polymorphisms (LSPs) or insertion-deletion events in bacterial populations, we developed a technique, termed deligotyping, which hybridizes multiplex-PCR products to membrane-bound, highly specific oligonucleotide probes. The approach has the benefits of being low cost and capable of simultaneously interrogating more than 40 bacterial strains for the presence of 43 genomic regions. The deletions represented on the membrane were selected from previous comparative genomic studies and ongoing microarray experiments. Highly specific probes for these deletions were designed and attached to a membrane for hybridization with strain-derived targets. The targets were generated by multiplex PCR, allowing simultaneous amplifications of 43 different genomic loci in a single reaction. To validate our approach, 100 strains that had been analyzed with a high-density microarray were analyzed. The mem...Continue Reading

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Citations

Dec 14, 2011·Applied and Environmental Microbiology·Timothy KudinhaGwendolyn L Gilbert
Oct 17, 2006·Clinical Microbiology Reviews·Barun MathemaBarry N Kreiswirth
Nov 8, 2005·Journal of Clinical Microbiology·Robert FreemanGerard A Cangelosi
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Jul 25, 2015·The Indian Journal of Medical Research·Srinidhi Desikan, Sujatha Narayanan
May 18, 2006·Emerging Infectious Diseases·James M ColbornDonald J Krogstad

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