Screening Potential Alllelle-Frequency Disequilibrium in Data from Affymetrix Gene Expression Arrays

Manhong Dai; Yongjia Wang; Elzbieta Sliwerska; Margit Burmeister; Stanley J. Watson; Huda Akil; Fan Meng
Advances in Bioinformatics and its Applications Series in Mathematical Biology and Medicine. 2005; 8:132-139.


The popular Affymetrix human gene expression analysis arrays contain oligonucleotide probes that overlap with thousands of known single nucleotide polymorphism sites. These allele-specific probes provide the possibility of screening allele-frequency difference in existing GeneChip data. We explored analysis procedures that can detect allele-specific signals of known SNPs in different sample groups. Our analysis results and independent genotyping data show it is feasible to utilize these allele-specific probes to screen potential allele-frequency disequilibrium in large-scale GeneChip-based expression profiling projects.