Serious limitations of the QTL/Microarray approach for QTL gene discovery

Abstract

BackgroundIt has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL). However, the effectiveness of this approach has not been assessed.ResultsThirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons between congenic and background strains. Three studies led to the identification of an underlying QTL gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD) regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of QTL regulated in cis (cis eQTL) showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP).ConclusionsThe literature shows limited successes from the QTL/microarray approach to identify QTL genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select cis-eQTL over trans-eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false cis-eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes that were not tested. Together, our results explain the tendency to report QTL candidates as differentially expressed and indicate that the utility of the QTL/microarray as currently implemented is limited. Alternatives are proposed that make use of microarray data from multiple experiments to overcome the outlined limitations.

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice

“…Second, the large expression differences between the two parental strains or the strong cis -QTL could be due to the presence of a polymorphism at the probe binding site. In our study, we confi rmed that this was not the case for our eight candidate genes, but we cannot exclude the possibility, especially if the cross involved a wild-derived strain ( 37 ).…”

From association to prediction: statistical methods for the dissection and selection of complex traits in plants

“…The technology of choice has changed to direct sequencing of mRNA (i.e. RNA-Seq) due to known problems with the hybridization method of arrays [45,46] and the decrease in cost of RNASeq. Nevertheless the total cost of sequencing mRNA from hundreds to thousands of individuals may still be prohibitive for most agricultural studies and the thousands of genes tested can make it difficult to find true associations among all the false positives [47].…”

Computational Tools for Discovery and Interpretation of Expression Quantitative Trait Loci

“…However, hybridization-based expression technologies are also susceptible to the possibility of false cis -eQTL due to polymorphic probes [41]; therefore, careful prior filtering of expression may be necessary.…”