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Integrative approaches for large-scale transcriptome-wide association studies

Abstract

Many genetic variants influence complex traits by modulating gene expression, thus altering the abundance of one or multiple proteins. Here we introduce a powerful strategy that integrates gene expression measurements with summary association statistics from large-scale genome-wide association studies (GWAS) to identify genes whose cis-regulated expression is associated with complex traits. We leverage expression imputation from genetic data to perform a transcriptome-wide association study (TWAS) to identify significant expression-trait associations. We applied our approaches to expression data from blood and adipose tissue measured in 3,000 individuals overall. We imputed gene expression into GWAS data from over 900,000 phenotype measurements to identify 69 new genes significantly associated with obesity-related traits (BMI, lipids and height). Many of these genes are associated with relevant phenotypes in the Hybrid Mouse Diversity Panel. Our results showcase the power of integrating genotype, gene expression and phenotype to gain insights into the genetic basis of complex traits.

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Figure 1: Schematic of the TWAS approach.
Figure 2: Modes of expression causality.
Figure 3: Accuracy of individual-level expression imputation algorithms.
Figure 4: The number of genes with significant cis heritability observed at varying sample sizes.
Figure 5: Power of summary-based expression imputation algorithms.

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Acknowledgements

We thank the individuals who participated in the study. We also acknowledge L. Yang for helpful discussions that have improved the quality of this manuscript. We also thank K. Mohlke, M. Boehnke and F. Collins for help with the METSIM data. This work was funded in part by US National Institutes of Health (NIH) grants F32 GM106584 (A.G.), R01 GM053725 (B.P.), R01 GM105857 (A.L.P., A.G. and G.B.), HL-28481 (P.P., A.J.L. and M.C.) and HL-095056 (P.P. and B.P.) and by the US NIH training grant in Genomic Analysis and Interpretation T32 HG002536 (A.K.).

Author information

Authors and Affiliations

Authors

Contributions

A.G. and B.P. conceived and designed the experiments. A.G., A.K. and H.S. performed the experiments and analyzed the data. G.B., W.C., B.W.J.H.P., R.J., E.J.C.d.G., D.I.B., F.A.W., P.F.S., E.N., M.A., M.C., A.J.L., T.L., E.R., M.K., I.S., O.T.R., J.K. and M.L. generated data, reagents, materials and analysis tools. A.G., A.L.P., P.P. and B.P. wrote the manuscript. All authors reviewed, revised and wrote feedback for the manuscript.

Corresponding authors

Correspondence to Alexander Gusev or Bogdan Pasaniuc.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Distribution of cis and trans SNP-heritability estimates cross three cohorts.

Cis (left) and trans (right) density plots shown for three cohorts investigated. Black line corresponds to all converged genes; red line corresponds to genes with cis-SNP-heritability >> 0 by LRT. Dotted lines show respective means.

Supplementary Figure 2 Scaled Venn Diagram of overlap in genes with significant cis SNP-heritability across the METSIM, NTR and YFS data.

Supplementary Figure 3 Cross-validation prediction accuracy across three expression cohorts.

Using 10-fold cross-validation, prediction R^2 (divided by corresponding cis-h2g) was compuated in the METSIM, YFS and NTR (Wright et al.) cohorts by three methods: best eQTL in the gene, BLUP and BSLMM. Left panels show accuracy as a functino of cis h2g; right panels show accuracy as a function of LRT P-value for non-zero cis-h2g.

Supplementary Figure 4 Histogram of BSLMM prediction gains in three cohorts.

For each of the METSIM, YFS and NTR (Wright et al.), the difference between BSLMM R^2 and eQTL R^2 (computed by cross-validation) is plotted as histogram.

Supplementary Figure 5 Correlation of summary-based TWAS and individual-level association Z scores.

Genes with significant cis-h2g in YFS were directly tested for association with height (Z-score on y-axis) and plotted against corresponding Z-score from TWAS using only height summary association data (x-axis). Left panel shows test of height against total expression on the y-axis (\rho = 0.415); right panel shows test of height against BLUP genetic component of expression on the y-axis (\rho = 0.998). Right panel demonstrates that summary-based TWAS is essentially identical to individual-level TWAS when using in-sample LD.

Supplementary Figure 6 GWAS summary simulations over diverse disease architectures.

Power to detect a genome-wide significant association is shown for three methods (GWAS; eGWAS computed from best eQTL, and TWAS computed from summary statistics) over different disease architectures. Colors represent number of causal variants in each simulated gene. Left/right panels correspond to simulations with causal variants hidden/shown. Top/bottom panels correspond to simulations with each gene explaining 0.001/0.0005 of trait variance. x-axis shows simulations at increasing GWAS sample sizes (with expression panel fixed at 1,000 samples).

Supplementary Figure 7 TWAS power with expression and genetic component of expression.

Power to detect a genome-wide significant association is shown for summary-statistic TWAS using observed expression as well BLUP genetic value of expression. Left/right panels correspond to simulations with causal variants hidden/shown. Top/bottom panels correspond to simulations with each gene explaining 0.001/0.0005 of trait variance. x-axis shows simulations at increasing GWAS sample sizes (with expression panel fixed at 1,000 samples).

Supplementary Figure 8 GWAS summary simulations with heritable expression independent of phenotype.

Expression and trait were simulated as having the same causal variants but independent effect-sizes and power evaluated. For a single causal variant, this model is statistically identical to a true causal model. Colors indicate the method used (see Supplementary Fig. 4). Left/right panels correspond to simulations with causal variants hidden/shown. Top/bottom panels correspond to simulations with each gene explaining 0.001/0.0005 of trait variance. x-axis shows simulations at increasing GWAS sample sizes (with expression panel fixed at 1,000 samples).

Supplementary Figure 9 TWAS/eGWAS power with increased sample reference size.

: Results from simulations matching Supplementary Figure 4 (top left) model with variable reference panel size from 100-2,000 individuals. Phenotype generated under to the untyped, high effect variant model where expression explains 0.001 of trait variance. TWAS matches or outperforms eGWAS at 1,000 samples, with little additional power gained subsequently. GWAS power is unaffected by expression reference panel and not shown (identical to Supplementary Fig. 4).

Supplementary Figure 10 TWAS/COLOC power under causal model.

Single locus power comparison for causal variant hidden (left) and typed (right), high effect model where expression explains 0.001 of trait variance. Unlike other power simulations, results are not adjusted for genome/transcriptome-wide multiple testing. TWAS and COLOC significance thresholds set in a null expression simulation (with realistic heritable GWAS, see Methods) to achieve 5% FDR.

Supplementary Figure 11 GWAS summary simulations using haplotype-copying model of population.

Results from simulations matching Supplementary Figure 4 re-analyzed using HAPGEN2 to generate all GWAS sub-study individuals. After holding out 1,000 samples for the expression reference, SHAPEIT2 was used to phase 5,000 individuals in a cis-block for each of 100 random genes, yielding 100 random reference panels. For each reference panel we used HAPGEN to generate 60 sub-studies of 5,000 individuals using its haplotype-copying model (under neutrality). Phenotypes were generated with the same causal variants and effects for each sub-study, and the corresponding GWAS summary statistics were computed by meta-analyzing across these batches. Default parameters for SHAPEIT and HAPGEN were always used, and the appropriate genetic map was downloaded from the SHAPEIT2 website.

Supplementary Figure 12 TWAS/COLOC power under independent effects model.

Single locus power comparison for model where expression and trait have the same causal variants with independent effects. GWAS generated from high effect model where expression explains 0.001 of trait variance and causal variants are hidden (left) or typed (right). Unlike other power simulations, results are not adjusted for genome/transcriptome-wide multiple testing. TWAS and COLOC significance thresholds set in a null expression simulation (with realistic heritable GWAS, see Methods) to achieve 5% FDR. Single causal variant scenario is statistically identical to the causal expression model and has equivalent power.

Supplementary Figure 13 LD Score regression (LDSC) provides a noisier local estimate than TWAS for quantifying correlation between complex trait and expression.

Left panel shows in-sample and summary-based estimate of association between height and cis genetic component of expression (correlation = 0.998). Right panel shows in-sample estimate of correlation between height and cis genetic component of expression (y-axis) and LDSC estimate of genetic correlation (x-axis); correlation between the two statistics was 0.7.

Supplementary Figure 14 Distribution of TWAS statistics for height as a function of expression panel size in the merged YFS + NTR (blood) cohorts.

To evaluate the effect of expression panel size on power in real data, we re-ran the TWAS for height using the merged YFS+NTR cohort with down-sampling. The histogram of TWAS Z^2 scores is shown for training from randomly sampled half of the cohort (1,200 samples, top) and the full cohort (2,400 samples, bottom). The mean TWAS Z^2 was 5.8 in the combined cohort and 5.6 in the down-sampled cohort, with the overall distribution of Z-scores largely consistent across the two studies. Importantly, there were four genes that were not previously significant in the YFS/NTR cohorts individually and were significant in the combined study, but all four had been detected by the omnibus test. This is consistent with our simulations showing that TWAS power is saturated beyond 1,000 expression samples. Only 652 genes that were significantly cis-heritable in both YFS and NTR were analyzed.

Supplementary Figure 15 Distance between nearby genes and GWAS index SNP at known GWAS risk loci.

Each line shows the histogram of number of GWAS risk loci overlapping a gene as a function of distance from the index SNP. Black line shows the closest gene. Red denotes genes with significant cis SNP heritability. Green shows the TWAS significant gene.

Supplementary Figure 16 Correlation of TWAS Z-scores from summary-level and individual-level data in METSIM.

Joint distribution of summary-level and individual-level TWAS Z-scores shown across all significant genes for four traits in the METSIM GWAS cohort.

Supplementary Figure 17 Evidence for allelic heterogeneity of expression

Novel TWAS genes were evaluated for allelic heterogeneity of expression using three different tests (left SKAT gene-based test; middle conditional analysis; right LASSO model selection). For each test, genes were categorized into those not reaching TWAS significance in a cohort, reaching TWAS significance but failing the permutation test, and reaching TWAS significance and passing the permutation test. The % of genes considered significant (SKAT/conditional) or the average number of associated variants selected (LASSO) are reported by each bar.For each of the 69 genes x 3 expression cohorts we ran the SKAT gene-based test with expression as outcome to look for evidence of allelic heterogeneity. As with TWAS, all SNPs in the 1-Mb locus around the gene were used, and SKAT was run in common+rare mode (Ionita-Laza et al. Am. J. Hum. Genet. 2013), which was most appropriate for array SNP data. Default parameters were used throughout. Genes were considered significant if they surpassed the multiple-testing burden of 69 genes. The conditional test was evaluated by including the top SNP as a covariate and testing for any secondary eQTLs at the locus that were significant after Bonferroni correction for the number of SNPs at the locus. The LASSO was run on all SNPs in the locus, penalized by the cis-h2g of expression.

Supplementary Figure 18 Expression accuracy (by cross-validation) in 100 random genes.

Average of prediction R^2 divided by corresponding gene cis-h2g shown from randomly selected genes for three methods and two cohorts.

Supplementary Figure 19 Correlation of MuTHER TWAS Z-scores using different LD reference samples.

MuTHER expression data was used to train TWAS predictors using LD from 600 METSIM individuals (x-axis) or 6,000 METSIM individuals (y-axis). Joint distribution of TWAS Z-scores and trend are shown.

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Gusev, A., Ko, A., Shi, H. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet 48, 245–252 (2016). https://doi.org/10.1038/ng.3506

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