Title: The effect of SNPs on expression levels in Nimblegen RNA expression microarrays

Authors: Sigrun Helga Lund; Asgeir Sigurdsson; Sigurjon Axel Gudjonsson; Julius Gudmundsson; Daniel Fannar Gudbjartsson; Thorunn Rafnar; Kari Stefansson; Gunnar Stefansson

Addresses: Faculty of Physical Sciences, University of Iceland, Reykjavik, Iceland ' deCODE genetics, Reykjavik, Iceland ' deCODE genetics, Reykjavik, Iceland ' deCODE genetics, Reykjavik, Iceland ' deCODE genetics, Reykjavik, Iceland ' deCODE genetics, Reykjavik, Iceland ' deCODE genetics, Reykjavik, Iceland ' Faculty of Physical Sciences, University of Iceland, Reykjavik, Iceland

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.

Keywords: RNA expression microarrays; SNPs; single nucleotide polymorphisms; replicate probes; Nimblegen microarrays; mismatch probes; bioinformatics; alleles.

DOI: 10.1504/IJDMB.2015.068949

International Journal of Data Mining and Bioinformatics, 2015 Vol.12 No.1, pp.1 - 13

Received: 23 Jul 2012
Accepted: 20 Apr 2013

Published online: 22 Apr 2015 *

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