Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays.

ABSTRACT:

Background

High-density oligonucleotide arrays are widely used for analysis of genome-wide expression and genetic variation. Affymetrix GeneChips - common high-density oligonucleotide arrays - contain perfect match (PM) and mismatch (MM) probes generated by changing a single nucleotide of the PMs, to estimate cross-hybridization. However, a fraction of MM probes exhibit larger signal intensities than PMs, when the difference in the amount of target specific hybridization between PM and MM probes is smaller than the variance in the amount of cross-hybridization. Thus, pairs of PM and MM probes with greater specificity for single nucleotide mismatches are desirable for accurate analysis.

Results

To investigate the specificity for single nucleotide mismatches, we designed a cus

SUBMITTER: Suzuki S 

PROVIDER: S-EPMC2180184 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature