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DNA Microarray-Based Mutation Discovery and Genotyping

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Molecular Methods for Evolutionary Genetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 772))


DNA microarrays provide an efficient means of identifying single-nucleotide polymorphisms (SNPs) in DNA samples and characterizing their frequencies in individual and mixed samples. We have studied the parameters that determine the sensitivity of DNA probes to SNPs and found that the melting temperature (T m) of the probe is the primary determinant of probe sensitivity. An isothermal-melting temperature DNA microarray design, in which the T m of all probes is tightly distributed, can be implemented by varying the length of DNA probes within a single DNA microarray. I describe guidelines for designing isothermal-melting temperature DNA microarrays and protocols for labeling and hybridizing DNA samples to DNA microarrays for SNP discovery, genotyping, and quantitative determination of allele frequencies in mixed samples.

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I thank the labs of David Botstein, Leonid Kruglyak, Maitreya Dunham, and Justin Borevitz where many of these methods were developed. I also thank Bo Curry, Leonardo Brizuela, and Ben Gordon at Agilent Technologies for participation in the initial study of microarray design.

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Correspondence to David Gresham .

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Gresham, D. (2012). DNA Microarray-Based Mutation Discovery and Genotyping. In: Orgogozo, V., Rockman, M. (eds) Molecular Methods for Evolutionary Genetics. Methods in Molecular Biology, vol 772. Humana Press.

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-227-4

  • Online ISBN: 978-1-61779-228-1

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