Data analysis issues for allele-specific expression using Illumina's GoldenGate assay

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.

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Matthew E. Ritchie, Matthew S. Forrest, Antigone S. Dimas, Caroline Daelemans, Emmanouil T. Dermitzakis, Panagiotis Deloukas, Simon Tavaré
• Keywords: BMCBI 2010, Exciting Application Area, GoldenGate BeadArray Technology, Relative Expression Measurements