Journal article
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay
ME Ritchie, MS Forrest, AS Dimas, C Daelemans, ET Dermitzakis, P Deloukas, S Tavaré
BMC Bioinformatics | BMC | Published : 2010
Open access
Abstract
Background: High-throughput measurement of allele-specific expression (ASE) is a relatively new and exciting application area for array-based technologies. In this paper, we explore several data sets which make use of Illumina's GoldenGate BeadArray technology to measure ASE. This platform exploits coding SNPs to obtain relative expression measurements for alleles at approximately 1500 positions in the genome.Results: We analyze data from a mixture experiment where genomic DNA samples from pairs of individuals of known genotypes are pooled to create allelic imbalances at varying levels for the majority of SNPs on the array. We observe that GoldenGate has less sensitivity at detecting subtle ..
View full abstractGrants
Awarded by Hutchison Whampoa Limited
Funding Acknowledgements
This work was supported by the Isaac Newton Trust and NHMRC Program grant 406657, NHMRC IRIISS grant 361646 and a Victorian State Government OIS grant (MER) and Cancer Research UK and Hutchison Whampoa Limited (ST). We thank Ana-Teresa Maia, Mark Dunning, Susana Campino and Bert Mohr for helpful discussions, Rachel Uren for facilitating file transfers between institutes and Terry Speed for providing feedback on this manuscript.