Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue.
- Authors
- Innocenti, Federico; Cooper, Gregory M; Stanaway, Ian B; Gamazon, Eric R; Smith, Joshua D; Mirkov, Snezana; Ramirez, Jacqueline; Liu, Wanqing; Lin, Yvonne S; Moloney, Cliona; Aldred, Shelly Force; Trinklein, Nathan D; Schuetz, Erin; Nickerson, Deborah A; Thummel, Ken E; Rieder, Mark J; Rettie, Allan E; Ratain, Mark J; Cox, Nancy J; Brown, Christopher D
- Year
- 2011
- Journal
- PLoS genetics
- PMID
- 21637794
- DOI
- 10.1371/journal.pgen.1002078
- PMCID
- PMC3102751
The discovery of expression quantitative trait loci ("eQTLs") can help to unravel genetic contributions to complex traits. We identified genetic determinants of human liver gene expression variation using two independent collections of primary tissue profiled with Agilent (nβ=β206) and Illumina (nβ=β60) expression arrays and Illumina SNP genotyping (550K), and we also incorporated data from a published study (nβ=β266). We found that βΌ30% of SNP-expression correlations in one study failed to replicate in either of the others, even at thresholds yielding high reproducibility in simulations, and we quantified numerous factors affecting reproducibility. Our data suggest that drug exposure, clinical descriptors, and unknown factors associated with tissue ascertainment and analysis have substantial effects on gene expression and that controlling for hidden confounding variables significantly increases replication rate. Furthermore, we found that reproducible eQTL SNPs were heavily enriched near gene starts and ends, and subsequently resequenced the promoters and 3'UTRs for 14 genes and tested the identified haplotypes using luciferase assays. For three genes, significant haplotype-specific in vitro functional differences correlated directly with expression levels, suggesting that many bona fide eQTLs result from functional variants that can be mechanistically isolated in a high-throughput fashion. Finally, given our study design, we were able to discover and validate hundreds of liver eQTLs. Many of these relate directly to complex traits for which liver-specific analyses are likely to be relevant, and we identified dozens of potential connections with disease-associated loci. These included previously characterized eQTL contributors to diabetes, drug response, and lipid levels, and they suggest novel candidates such as a role for NOD2 expression in leprosy risk and C2orf43 in prostate cancer. In general, the work presented here will be valuable for future efforts to precisely identify and functionally characterize genetic contributions to a variety of complex traits.
Age and sex effect replication.(A,D) Replication panel linear regression t-test p-values for genes with significant Sex (A) and Age (D) effects in the UC panel (<5% FDR) were binned (x-axis) and the number of genes per bin (y-axis) is displayed separately for the UW (red) and Merck (blue) replication sets. (B,E) The replication rate of sex (B) and age (E) associations is depicted as a function of UC p-value for UW (red), Merck (blue), either replication study (green), and for the n = 60 resampled data (purple). Note that, at more stringent significance thresholds, the replication rate increases but fewer genes are included. (C) Genes with significant sex associations are enriched on the X (black) and Y (grey) chromosomes. Hypergeometric test p-values (y-axis, log10 scaled) are plotted as a function of the discovery set effect significance threshold (x-axis, log10-scaled). (F) An example of a gene (TMEM22) whose expression level (y-axis) is associated with age (x-axis). Each point represents the expression level (y-axis), adjusted for surrogate variables, and age (x-axis) of an individual sample.
eQTL characteristics.(A,B) Manhattan plots depicting best associated cis-eQTLs for all gene expression traits in the UC (A) and UW (B) studies. Autosomes are ordered and alternately colored along the x-axis. BF of the SNP-gene pair is plotted on the y-axis. Probes overlapping common polymorphisms are plotted as triangles, probes without known SNPs are plotted as open circles. For display purposes, genes with UC BF>23 that replicate in the UW study are labeled with gene names. (C) Distribution of distances from each gene's best associated SNP to its TSS. Negative and positive values denote SNPs 5β² and 3β² of TSS, respectively. Data are plotted for all significant UC eQTLs (BF>5, black), eQTLs replicated in the UW (red), Merck (blue), and eQTLs replicated in either UW or Merck (green).
eQTL replication.(A) Number of gene expression traits (y-axis, log10 scaled) with best associated cis-eQTLs (black) and trans-eQTLs (blue) as a function of BF (x-axis). Counts at each threshold are plotted separately for all probes (solid) and for probes without known polymorphisms (dashed). (B) cis-eQTL associations were tested in two replication sample sets, UW and Merck. Replication sample linear regression t-test p-values were binned (x-axis) and the number of genes per bin (y-axis) is displayed separately for the UW (red) and Merck (blue) replication sets. Data are plotted for all eQTLs (thin lines) and for significant eQTLs (heavy lines). (C) cis-eQTL replication rate (y-axis) is depicted as a function of UC BF (x-axis) for UW (red), Merck (blue), either replication study (green), and for the n = 60 resampled data (purple). Replication rates are plotted separately for probes overlapping known polymorphisms (solid lines) and for probes not overlapping an annotated polymorphism (dashed). (D) Cis-eQTL replication rate (y-axis) plotted as a function of quantile binned SNP to TSS distance. Per bin mean (points) and standard errors (lines) are plotted separately for associations with UC BF>0 (grey) with UC BF>5 (black), and with UC BF>10 (blue). (E) Trans-eQTL replication p-values were binned (x-axis) and the number of genes per bin (y-axis) is displayed separately for the UW (red) and Merck (blue) replication sets. Data are plotted for all eQTLs (thin lines) and for significant eQTLs (heavy lines). (F) trans-eQTL replication rate (y-axis) is depicted as a function of UC BF (x-axis) for UW (red), Merck (blue), either replication study (green), and for the resampled data (purple).
SVA improves eQTL reproducibility.(A) Surrogate variable regression produces more significant associations. Each point represents the BF for each UC gene expression trait and its best associated SNP. Data are plotted for associations tested after surrogate variable regression (y-axis) and unadjusted for surrogate variables (x-axis). Note that most points fall above the diagonal, indicating increased eQTL significance after surrogate variable correction. (B) Cis-eQTL replication rate (y-axis; UC vs UW or Merck) as a function of UC BF threshold. SVA adjusted associations depicted in black, unadjusted in grey.
Fine-mapping functional results.Functional fine-mapping results for three genes, presented in columns: PRMT6 (A, D, G), LDHC (B, E, H), and IPO8 (C, F, I). (AβC) Cis-eQTL scan results are plotted across each gene region with chromosomal coordinates on the x-axis BF on the y-axis. Genotyped SNPs are plotted in black, imputed SNPs in grey, promoter SNPs in green, and 3β²UTR SNPs in orange. The extent of each gene is plotted in a red rectangle near the X-axis. Association data from the UC study plotted as triangles and from the UW study as circles. (DβF) Putative eQTNs identified by promoter and 3β²UTR resequencing. Microarray expression measurements (residuals after regression against covariates, y-axis) for each sample, plotted by genotype at the best-associated (ranked by p-value) SNP within the resequenced regions. Colors of the points correspond to the luciferase data. (GβI) Luciferase reporter results. Normalized luciferase measurements (y-axis) are plotted for each tested clone corresponding to a given haplotype (indicated by color). Blue and red coloring corresponds to the identity of each haplotype at the most strongly correlated individual SNP (same as in the middle row), while varying shades of red and blue differentiate haplotypes that differ at other SNPs. Vectors for each haplotype were prepared multiple independent times (data for each mini-prep are organized into a single column) and each mini-prep was transfected and measured four times (each open circle indicates one of these 4 measurements). The mean luminescence for each mini-prep is shown as a solid circle.
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