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Channel Glass-based Detection of Human Short Insertion/Deletion Polymorphisms by Tandem Hybridization

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Abstract

The development and critical evaluation of new technologies for identifying genetic polymorphisms will rapidly accelerate the discovery and diagnosis of disease-related genes. We report a novel way for distinguishing a new class of human DNA polymorphisms, short insertion/deletion polymorphisms (indels). A sensor with cylindrical pores named channel glass in combination with tandem hybridization, which uses a 5′-fluorescent labeled stacking probe and microarray-based short allele-specific oligonucleotide (capture probe) was investigated. This methodology allows indels to be detected individually and rapidly with small quantities of target DNA. This establishes a reliable quantitative test. Approaches for simultaneously hybridizing different targets to arrayed probes, designed to detect various indels in parallel, were examined. Five markers were consistently detected in a single hybridization. Possible factors impeding the hybridization reaction process are discussed.

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Acknowledgments

Financial support for this work was provided by PROMEP/103.5/03/1130, Fondo Sectorial Área de Ciencia Básica SEP-CONACYT 2004-C01-46537, PA144B-2007 and by NIH grant R01 HL62681-01.

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Authors and Affiliations

  1. Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Abasolo 600 Pachuca de Soto, Hidalgo, 42000, Mexico

    Gabriel Betanzos-Cabrera

  2. Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA

    Brent W. Harker

  3. Biosciences Division, Oak Ridge National Laboratory, Building 4500-S, MS 6123, Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN, 37831, USA

    Mitchel J. Doktycz & Kenneth L. Beattie

  4. Center for Medical Genetics, Marshfield Clinical Medical Research Foundation, Marshfield, WI, USA

    James L. Weber

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  1. Gabriel Betanzos-Cabrera
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  3. Mitchel J. Doktycz
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  4. James L. Weber
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  5. Kenneth L. Beattie
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Correspondence to Gabriel Betanzos-Cabrera.

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Betanzos-Cabrera, G., Harker, B.W., Doktycz, M.J. et al. Channel Glass-based Detection of Human Short Insertion/Deletion Polymorphisms by Tandem Hybridization. Mol Biotechnol 38, 145–153 (2008). https://doi.org/10.1007/s12033-007-9004-9

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