Understanding the genetic basis of human variation is a vital goal of biomedical research. Studies in other organisms suggest that differences in gene expression levels account for a major part of the variation within and among species (1, 2). To address this in humans, we developed methods to quantitatively evaluate allelic variation in gene expression.

The analysis of variation in gene expression is complicated by the potentially small differences associated with alterations in a single allele as well as by potential variations between individuals that arise from environmental or physiological rather than genetic factors. To circumvent these analytic problems, we compared the relative expression levels of two alleles of the same gene within the same cellular sample. To make these comparisons, we used a fluorescent dideoxy terminator–based method (3) to distinguish the mRNA products of alleles from normal individuals who were heterozygous for a single nucleotide polymorphism (SNP) in the transcript of interest (fig. S1). We estimated that this approach could confidently identify variations when the differences between expression of the two alleles differed by more than 20%(3).