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

Sigrun Helga Lund*, Asgeir Sigurdsson, Sigurjon Axel Gudjonsson, Julius Gudmundsson, Daniel Fannar Gudbjartsson, Thorunn Rafnar, Kari Stefansson, Gunnar Stefansson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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 SNP's one should use probes containing both alleles of the SNP.

Original languageEnglish
Pages (from-to)1-13
Number of pages13
JournalInternational Journal of Data Mining and Bioinformatics
Volume12
Issue number1
DOIs
Publication statusPublished - 2015

Bibliographical note

Publisher Copyright:
Copyright © 2015 Inderscience Enterprises Ltd.

Other keywords

  • Mismatch probes
  • Nimblegen microarrays
  • Replicate probes
  • RNA expression microarrays
  • SNP

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