title: DNA microarray-based mutation discovery and genotyping.
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 (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.
authors: Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY, USA. dgresham@nyu.edu
authors: David
authors: D
authors: Gresham
mesh_terms: D004247:DNA / Q000235:genetics; D015342:DNA Probes / Q000378:metabolism; D016678:Genome / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D009154:Mutation / Q000235:genetics*; D009711:Nucleotides / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017354:Point Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013194:Staining and Labeling; D013223:Statistics as Topic; D013816:Thermodynamics
chemical_list: D015342:DNA Probes; D009711:Nucleotides; D004247:DNA