Cis-acting expression quantitative trait loci in mice

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Abstract
We previously reported the analysis of genome-wide expression profiles and various diabetes-related traits in a segregating cross between inbred mouse strains C57BL/6J (B6) and DBA/2J (DBA). By considering transcript levels as quantitative traits, we identified several thousand expression quantitative trait loci (eQTL) with LOD score >4.3. We now experimentally address the problem of multiple comparisons by estimating the fraction of false-positive eQTL that are undercis-acting regulation. For this, we have utilized a classiccis–transtest with (B6 × DBA)F1mice to determine the relative levels of transcripts from the B6 and DBA alleles. The results suggest that at least 64% ofcis-acting eQTL with LOD >4.3 are true positives, while the remaining 36% could not be confirmed as trulycis-acting. Moreover, we find that >96% of apparentcis-acting eQTL occur in regions that do not share SNP haplotypes.Cis-acting eQTL serve as an important new resource for the identification of positional candidates in QTL studies in mice. Also, we use the analysis of the correlation structures between genotypes, gene expression traits, and phenotypic traits to further characterize genes expressed in liver that are undercis-acting control, and highlight the advantages and disadvantages of integrating genetics and gene expression data in segregating populations.