Large scale analysis of positional effects of single-base mismatches on microarray gene expression data.

ABSTRACT:

Background

Affymetrix GeneChips utilize 25-mer oligonucleotides probes linked to a silica surface to detect targets in solution. Mismatches due to single nucleotide polymorphisms (SNPs) can affect the hybridization between probes and targets. Previous research has indicated that binding between probes and targets strongly depends on the positions of these mismatches. However, there has been substantial variability in the effect of mismatch type across studies.

Methods

By taking advantage of naturally occurring mismatches between rhesus macaque transcripts and human probes from the Affymetrix U133 Plus 2 GeneChip, we collected the largest 25-mer probes dataset with single-base mismatches at each of the 25 positions on the probe ever used in this type of analysis.

Results</

SUBMITTER: Duan F 

PROVIDER: S-EPMC2877042 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature