Genome-wide analysis of allele-specific gene expression using oligo microarrays

Human variation is largely caused by deoxyribonucleic acid polymorphism and difference in gene expression. Common disease/common variant hypotheses suggest that quantitative differences among different alleles may be the basis for complex diseases. Quantitative difference in gene expression between alleles may affect most complex diseases. We have developed a gene chip-based method to quantitatively examine allele-specific gene expression of 1063 transcribed single-nucleotide polymorphisms using Affymetrix HuSNP oligo arrays. Among the 602 genes that were heterozygous and expressed in kidney or liver tissues from seven individuals, 326 (54%) showed preferential expression of one allele in at least one individual. The genes that showed allele-specific expression are distributed throughout the genome. We showed that variation of gene expression between alleles is common and that this variation may contribute to human variation. Our studies demonstrate the feasibility to perform genome-wide analysis of allele-specific gene expression.