Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.

ABSTRACT: The use of DNA microarrays to identify nucleotide variation is almost 20 years old. A variety of improvements in probe design and experimental conditions have brought this technology to the point that single-nucleotide differences can be efficiently detected in unmixed samples, although developing reliable methods for detection of mixed sequences (e.g., heterozygotes) remains challenging. Surprisingly, a comprehensive study of the probe design parameters and experimental conditions that optimize discrimination of single-nucleotide polymorphisms (SNPs) has yet to be reported, so the limits of this technology remain uncertain. By targeting 24,549 SNPs that differ between two Saccharomyces cerevisiae strains, we studied the effect of SNPs on hybridization efficiency to DNA microarray probes o

SUBMITTER: Gresham D 

PROVIDER: S-EPMC2824413 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature