The Genom of Homo sapiens.pdf

430 ANTONARAKIS ET AL.POPULATION VARIATION IN GENEEXPRESSIONThe allele-specific gene-dosage effect mainly relies onthe hypothesis that there are allelic differences in normalgene expression. Some initial studies confirmed that (1)there are differences in the allelic expression of genes indifferent mouse strains and humans (Schadt et al. 2003),and (2) there are differences in allelic gene expression inlymphoblastoid cell lines from individuals of the CEPHfamilies (Cheung et al. 2003). Both studies furthershowed that some of this variation is genetically determined.However, these studies used oligonucleotide microarrayanalysis, which is not ideal to detect small differencesfrom genes producing less than ~5 RNA copiesper cell. Real-time quantitative PCR (RT-qPCR) is moresensitive than microarray hybridization, and the dynamicrange of gene expression detection is much larger. Therefore,RT-qPCR can reveal subtle differences in gene expressionthat cannot be detected with microarrays, butcould still be causative for phenotypic variation. In a preliminaryanalysis, we used RT-qPCR to determinewhether there is natural variation in gene expression. Wetested 15 genes in lymphoblastoid cell lines from 8 differentnormal individuals. Each measurement was donein 12 replicates. Figure 5 shows an example of the RTqPCRconfirming the accuracy and reproducibility of theassay. Figure 6 shows the normalized relative expressionlevels of all the genes tested in all individuals. There is indeedwide variation of transcript amount among these individuals;this variation was statistically significant in 10(66%) of these genes (Table 1).These results may serve as a basis for association andlinkage studies between genomic variation cis or transand gene expression variation. Thus, the genomic variationthat controls transcript variation could be identified.This in turn may lead to a better understanding of genomicvariation that confirms susceptibility to commondisorders, to the identification of a plethora of regulatoryelements, and to the characterization of genes and allelesthat contribute to the different phenotypes of Down syndrome.Table 1. Variation of Transcript Amounts among GenesGenep value aABCG1