Sequence polymorphisms cause many false cis eQTLs

Abstract

Many investigations have reported the successful mapping of quantitative trait loci (QTLs) for gene expression phenotypes (eQTLs). Local eQTLs, where expression phenotypes map to the genes themselves, are of especially great interest, because they are direct candidates for previously mapped physiological QTLs. Here we show that many mapped local eQTLs in genetical genomics experiments do not reflect actual expression differences caused by sequence polymorphisms in cis-acting factors changing mRNA levels. Instead they indicate hybridization differences caused by sequence polymorphisms in the mRNA region that is targeted by the microarray probes. Many such polymorphisms can be detected by a sensitive and novel statistical approach that takes the individual probe signals into account. Applying this approach to recent mouse and human eQTL data, we demonstrate that indeed many local eQTLs are falsely reported as "cis-acting" or "cis" and can be successfully detected and eliminated with this approach.

Figure 1. Identification of false cis eQTLs reported in a human association analysis.

(A) Relative probe positions on the mRNA sequence (top) and hybridization signals (bottom) for gene HSD17B12 for which a cis eQTL is reported . Each line represents one individual and is colored according to the allele that the individual carries for the associating SNP marker rs4755741. This marker is located in an intron of the HSD17B12 gene and it is strongly linked with SNP rs1061810 located in probe 8. By discarding the data for probe 8, the significance for a cis eQTL disappears. (B) Similar plot for gene HLA-DQB1 for which a cis eQTL is reported . Lines are colored according to the allele the individual carries for the associated SNP marker rs6928482. One red-line and one blue-line individual have been sequenced for the probe region; the numbers in red and blue indicate the positions of SNPs within the 25-mer probe regions. The number in italic indicates a single nucleotide insertion in probe 2. We observed 23 SNPs (15 new ones) between these mRNA sequences and the 11 probes. (C) Visualization of the probes for gene HSD17B12 in the UCSC Genome Browser. Below the genomic sequence the probes are displayed in blocks. The block labels contain: probe set name, probe number, orientation on the genome (>> or <<) and probe sequence. Probe 8 and SNP rs1061810 are encircled. There is one SNP in probe 8, as was expected from probe signals. The inserted area shows information about this SNP; dbSNP shows the diversity of the SNP in the CEPH population. (D) Similar plot for gene HLA-DQB1. Probes 1-4 that do not perfectly match the genome are displayed in light blue. The current data in Genome Browser show fewer SNPs than we found in our own sequencing effort.