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DNA Microarray-Based Mutation Discovery and Genotyping

  • David GreshamEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 772)

Abstract

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 (Tm) of the probe is the primary determinant of probe sensitivity. An isothermal-melting temperature DNA microarray design, in which the Tm 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.

Key words

DNA microarray Single-nucleotide polymorphisms Isothermal melting temperature SNPscanner Bulk segregant mapping 

Notes

Acknowledgments

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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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkUSA

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