The effect of SNPs on expression levels in Nimblegen RNA expression microarrays. (2015)

• Record Type: Journal Article
• Authors: Lund, Sigrun Helga; Sigurdsson, Asgeir; Gudjonsson, Sigurjon Axel; Gudmundsson, Julius; Gudbjartsson, Daniel Fannar; Rafnar, Thorunn; Stefansson, Kari; Stefansson, Gunnar
• Is Part Of: International journal of data mining and bioinformatics. Volume 12:Number 1(2015)
• Page Start: 1
• Page End: 13
• Publication Date: 2015
• Subjects: RNA expression microarrays -- SNPs -- single nucleotide polymorphisms -- replicate probes -- Nimblegen microarrays -- mismatch probes -- bioinformatics -- alleles; Data mining -- Periodicals; Bioinformatics -- Periodicals; 006.312
• Languages: English
• ISSNs: 1748-5673

Abstract

In this paper the effect of SNPs on expression levels in Nimblegen RNA expression microarrays is investigated. A vast number of replicates of probe pairs representing both alleles of SNPs on 14 loci allows accurate estimation of the difference in signal intensities both within and between probe pairs. The majority of probe–pairs with sufficiently high expression have significant differences in expression levels within the pair and the difference shows concordance with the genotype of the samples. With two or more replicates of each probe, the allele–to–allele variance dominates the error in estimating the difference within the probe–pair, ten replicates are needed for adequate power in calling a true difference within a single probe–pair. Using the expression level of the probe within the probe–pair that has the higher value gives more accurate estimates. When using probes at loci containing known SNPs one should use probes containing both alleles of the SNP.