Transcriptome-wide association studies (TWAS) integrate genome-wide association studies (GWAS) and gene expression datasets to identify gene–trait associations. In this Perspective, we explore properties of TWAS as a potential approach to prioritize causal genes at GWAS loci, by using simulations and case studies of literature-curated candidate causal genes for schizophrenia, low-density-lipoprotein cholesterol and Crohn’s disease. We explore risk loci where TWAS accurately prioritizes the likely causal gene as well as loci where TWAS prioritizes multiple genes, some likely to be non-causal, owing to sharing of expression quantitative trait loci (eQTL). TWAS is especially prone to spurious prioritization with expression data from non-trait-related tissues or cell types, owing to substantial cross-cell-type variation in expression levels and eQTL strengths. Nonetheless, TWAS prioritizes candidate causal genes more accurately than simple baselines. We suggest best practices for causal-gene prioritization with TWAS and discuss future opportunities for improvement. Our results showcase the strengths and limitations of using eQTL datasets to determine causal genes at GWAS loci.
GWAS have robustly associated thousands of genomic loci with complex traits. Despite this success, GWAS loci are often difficult to interpret: linkage disequilibrium (LD) often obscures the causal variants driving the association, and the causal genes mediating variant effects on the trait are rarely ascertainable from GWAS data alone1. This interpretation challenge has motivated the development of methods to prioritize causal genes at GWAS loci.
One such family of methods is TWAS, which leverage expression reference panels (eQTL cohorts with expression and genotype data) to discover gene–trait associations from GWAS datasets2,3,4. First, the expression panel is used to learn per-gene predictive models of expression variation by using allele counts of genetic variants in the gene’s vicinity (typically within 500 kilobases or 1 megabase). These models are used to predict gene expression for each individual in the GWAS cohort. Finally, statistical associations are estimated between predicted gene expression and the trait (Fig. 1a). Expression prediction and association may be performed sequentially with individual-level GWAS data (PrediXcan2) or simultaneously with summary-level GWAS data (Fusion3 and S-PrediXcan4). Closely related methods include SMR/HEIDI5,6,7, which performs Mendelian randomization (MR) from gene expression to trait, and GWAS–eQTL colocalization methods such as Sherlock8, coloc9,10, QTLMatch11, eCaviar12, enloc13 and RTC14, which discover genes whose expression is regulated by the same causal variants that underlie a GWAS hit.
TWAS have garnered substantial interest within genetics and have been conducted for many traits and tissues15,16. Although TWAS methods are statistical tests associating genetically predicted expression and disease risk, with no guarantees of causality, a key reason for their appeal is the promise of prioritizing candidate causal genes (genes mediating the phenotypic effects of causal genetic variants) and tissues underlying GWAS loci. Unfortunately, there is a prevalent misconception that TWAS are causal-gene tests and that TWAS associations represent bona fide causal genes; in the following sections, we provide guidelines for interpreting TWAS results, highlighting scenarios in which TWAS accurately prioritize candidate causal genes and others for which TWAS-prioritized genes are likely to be non-causal.
As a motivating example illustrating both the successes and interpretational challenges of TWAS, consider C4A, a causal gene for schizophrenia. Variants at the C4A locus contribute to schizophrenia risk by increasing the brain expression of C4A17. A TWAS has strongly associated C4A with schizophrenia on the basis of brain expression data from the Genotype-Tissue Expression (GTEx) project18. Notably, C4A is by far the most significantly associated gene within 100 kilobases in brain tissues. C4A is also the most significantly associated gene in any tissue (Supplementary Table 1), even compared with other closely related genes in the complement system (C4B, CFB and C2). However, 8 of the 12 other genes within 100 kilobases are at least marginally significant (P <0.05) in some brain tissue, and 11 of 12 are highly significant (P <5 × 10−5) in at least one tissue. C4A is also more significantly associated with schizophrenia in the pancreas than in any brain tissue.
TWAS-significant loci contain multiple associated genes
GWAS are well known to rarely identify single variant–trait associations but instead to identify blocks of associated variants in LD (Fig. 1b). Analogously, TWAS frequently identify multiple hit genes per locus16 (Fig. 1c).
To explore this phenomenon, we performed TWAS in two traits and two tissues with Fusion and S-PrediXcan, by using GWAS summary statistics for low-density lipoprotein (LDL) cholesterol19 and Crohn’s disease20, and the 522 liver and 447 whole-blood expression samples from the Stockholm–Tartu Atherosclerosis Reverse Networks Engineering Task (STARNET) cohort21 (Supplementary Fig. 2 and Supplementary Note). We grouped hit genes within 2.5 megabases and found some loci with a single hit gene but others with as many as 11 hit genes (Supplementary Fig. 3).
Correlated expression across individuals may cause false hits
We explored the extent to which co-regulation can lead to multi-hit loci. Co-regulation is conventionally measured by correlating the expression of a pair of genes across individuals. Do genes with correlated expression with a strong TWAS hit also tend to be TWAS hits? We analyzed the SORT1 locus in LDL/liver (TWAS P = 1 × 10−243; Fig. 2a), the strongest hit locus across all four Fusion TWAS.
Although SORT1 has strong evidence of causality, its locus contains eight hit genes in addition to SORT1, and their TWAS P values are highly related to their expression correlation with SORT1 (Spearman correlation = 0.75; Fig. 2b). A similar pattern holds for S-PrediXcan (Supplementary Fig. 5). The two most correlated genes, PSRC1 and CELSR2, were previously noted22 to share an eQTL with SORT1 in the liver (rs646776). Given SORT1’s strong evidence of causality and the other genes’ lack of strong literature evidence, the most parsimonious (though certainly not the only) explanation is that most or all other genes are non-causal and are prioritized only because of correlation with SORT1.
Correlated predicted expression may also cause false hits
However, expression correlation is not the whole story: TWAS tests for association with genetically predicted expression, not total expression. Total expression includes genetic, environmental and technical components, and the genetic component includes contributions from common cis eQTLs (the only component reliably detectable in current TWAS methods), rare cis eQTLs and trans eQTLs. Predicted expression represents only a small component of total expression: a large-scale twin study23 has found that common cis eQTLs explain only approximately 10% of genetic variance in expression.
Predicted expression correlations between same-locus genes are generally slightly higher than total expression correlations, sometimes substantially so (Fig. 3a and Supplementary Figs. 4 and 5d). A gene pair can have correlated predicted expression if the same causal eQTL regulates both genes or if two causal eQTLs in LD each regulate one of the genes24. Although only the first case counts as mechanistic co-regulation, we consider both cases together, because they are not designed to be distinguishable by TWAS: the two genes’ TWAS models can rely on distinct variants even in the first case or rely on the same variant even in the second case. For instance, given a causal eQTL in near-perfect LD with another variant, an L1-penalized linear expression model (for example, LASSO or ElasticNet) may place the most weight on only one of the two variants, but which variant is chosen could change depending on statistical fluctuations in the training set.
Predicted expression correlation may lead to non-causal genes being prioritized before causal genes, even if the total expression correlation is low. This type of confounding has also been observed in gene-set analysis25. For instance, SARS is the main outlier in Fig. 2b and is as significant as SORT1 despite having a total expression correlation of only ~0.2, because of its high predicted expression correlation of ~0.9 (Fig. 3a). SARS is also an outlier in PrediXcan for the same reason (Supplementary Fig. 5d).
Another example is the IRF2BP2 locus in LDL/liver (Fig. 3b). IRF2BP2 encodes an inflammation-suppressing regulatory factor with causal evidence from mouse models. RP4-781K5.7 is a largely uncharacterized long non-coding RNA that lacks evidence of function; most long non-coding RNAs are non-essential for cell fitness26, and current evidence is compatible with most non-coding RNAs being non-functional27. Despite a negligible total expression correlation between the two genes (–0.02), IRF2BP2’s Fusion expression model includes GWAS hit rs556107 with a negative weight, whereas RP4-781K5.7’s includes the same variant (plus two linked variants) with a positive weight (Fig. 3c), thus resulting in almost perfectly anti-correlated predicted expression (–0.94) and both genes being TWAS hits. IRF2BP2 and RP4-781K5.7 are also both hits with S-PrediXcan, and both S-PrediXcan and Fusion place the largest weight on rs556107 but with opposite signs (Supplementary Fig. 6).
We simulated expression and trait data (ntrait = 50,000 individuals; nexpression = 500) for 1,000 random genomic loci by using the FOCUS simulation framework24 and conducted TWAS by using L2-penalized linear regression (Supplementary Note). As expected, a larger predicted expression correlation increased the probability of having a larger TWAS z score than that of the causal gene (Supplementary Table 2). However, this probability remained modestly high even when the predicted expression correlation was low, thus implying that predicted expression, though better than true expression, still imperfectly captures co-regulation.
Shared GWAS variants may cause false hits
More generally, pairs of gene models may share variants (or at least LD partners) even if the predicted expression correlation is low, because other variants distinct between the models may ‘dilute’ the correlation. For instance, at the NOD2 locus for Crohn’s disease/whole blood, NOD2 is a known causal gene, but four other genes are also Fusion hits (Fig. 4a), none of which have strong causal evidence (though rare variants in ADCY7 have been associated with ulcerative colitis28). The model for the strongest hit gene, BRD7, places the most weight on rs1872691, the strongest GWAS hit in NOD2’s model (Fig. 4b). However, NOD2’s model places the most weight on two weaker GWAS hits, rs7202124 and rs1981760. Thus, even though co-regulation with NOD2 may explain why BRD7 is a TWAS hit, this co-regulation is not captured by the metrics that we discussed: both the predicted expression (–0.03) and total expression (0.05) correlations are near 0. The same five genes are also S-PrediXcan hits, and NOD2 and BRD7’s models share the same rs1872691 variant, as with Fusion (Supplementary Fig. 7).
Most generally, models need not even share the same GWAS variants (or LD partners) to have spurious hits. For instance, rs4643314, the strongest GWAS hit in BRD7’s Fusion model, is neither shared nor in strong LD with any variants in NOD2’s model, although it is in weak LD with rs1872691 (Fig. 4b). Although the most parsimonious explanation is that BRD7 is also causal, and rs4643314 acts through BRD7, BRD7 lacks evidence of causality. An alternate explanation is that only NOD2 is causal, rs4643314 acts through NOD2 (but also happens to co-regulate BRD7), and NOD2’s model erroneously fails to include it (a false negative). One trivial reason for false negatives is variants outside the 500 kilobase/1 megabase window included in the model, which can be solved by increasing the window. More problematic causes include bias in the expression panel (‘Discussion’) and, for methods using GWAS summary statistics, LD mismatch between the expression panel and GWAS. This scenario might occur even without any false negatives, for example, if a variant in LD with rs4643314 deleteriously affects NOD2’s coding sequence as well as regulating BRD7, because TWAS is not designed to detect coding effects. Figure 5 illustrates the various types of co-regulation that may lead to non-causal TWAS hits.
Bias with expression panels from non-trait-related tissues
Tissues with large expression panels (whole blood or lymphoblastoid) are commonly used to maximize power, even when they are mechanistically less related to the trait. To date, our case studies have used expression from mechanistically related tissues: liver for LDL and whole blood for Crohn’s disease. What if we swap these tissues and use tissues without a clear mechanistic relationship? The architecture of eQTLs differs substantially across tissues: even among strong eQTLs in GTEx (P ≈ 1 × 10−10), one-quarter show a switch in the most significantly associated gene across tissues18.
We curated candidate causal genes from the literature (Supplementary Table 3) at nine LDL/liver and four Crohn’s disease/whole-blood Fusion TWAS loci and examined how the hit strengths changed when we swapped tissues (Fig. 6). Notably, almost every candidate causal gene (9 of 11 for LDL and 5 of 6 for Crohn’s disease) was no longer a hit in the ‘opposite’ tissue, because of either insufficient expression (n = 4: PPARG, LPA, LPIN3 and SLC22A4) or insufficiently heritable cis expression according to Fusion’s likelihood-ratio test (n = 10: SORT1, IRF2BP2, TNKS, FADS3, ALDH2, KPNB1, SLC22A5, IRF1, CARD9, STAT3). This trend held globally, albeit less strongly: genome-wide, 3,085 of 5,858 LDL/liver genes (53%) dropped out after switching to whole blood, and 1,202 of 2,118 Crohn’s disease/whole-blood genes (57%) dropped out after switching to liver. Just because a gene does not drop out, and is present in both tissues as a result of shared cross-tissue regulatory architecture, causality is not necessarily implied.
More problematically, 15 other genes at the same loci were still hits (eight in LDL/whole blood and seven in Crohn’s disease/liver), five with P <1 × 10−20. This result suggests that the strategy of conducting TWAS in a sub-optimal tissue with a large expression panel is especially problematic because even if there are hits at a locus, the causal gene may not be among them.
Combining the whole-blood and liver reference panels by averaging each individual’s expression in the two tissues (equivalent, for L1- and/or L2-penalized regression, to concatenating the two panels) performed more poorly than using the mechanistically related tissue alone but better than using the less related tissue alone (Supplementary Fig. 8).
TWAS improves causal-gene prioritization
We investigated TWAS’s performance at ranking (prioritizing) causal genes at loci from the previous section. We compared Fusion to two simple gene-ranking baselines (Supplementary Table 4): transcription-start-site proximity to the most significant GWAS variant within 2.5 megabases of any gene at the locus (‘proximity’) and median expression across GTEx individuals in the liver (for LDL genes) or whole blood (for Crohn’s disease genes) (‘expression’). Genes with more significant TWAS P values, smaller distances to the lead GWAS variant or higher expression had higher rankings. The mean rank of the 17 candidate causal genes was 3.9 by random per-locus ranking, 2.0 by TWAS, 2.2 by proximity (P = 0.5, two-tailed Wilcoxon signed-rank test) and 2.9 by expression (P = 0.006). Hence, Fusion outperforms both baselines but does not significantly outperform proximity.
Suggested best practices and future opportunities
We highlighted two vulnerabilities—co-regulation and tissue bias—that affect TWAS’s performance in causal-gene prioritization. In this section, we discuss current best practices and future opportunities for their mitigation.
One emerging approach to address co-regulation repurposes GWAS fine-mapping to TWAS, on the basis of the analogy between LD in GWAS and co-regulation in TWAS. Fine-mapping of causal gene sets (FOCUS)24 directly models predicted expression correlations and uses them to assign genes posterior probabilities of causality. At the SORT1 locus, FOCUS includes SORT1, SARS and CELSR2 in the 90%-credible set; at the IRF2BP2 locus, FOCUS includes both IRF2BP2 and RP4-781K5.7 (Fig. 2d). We recommend using fine-mapping methods such as FOCUS or, at a minimum, considering relative association strengths (P values and effect sizes) at a locus when interpreting TWAS results. If individual-level data are available, inferring effects jointly through penalized regression (for example, LASSO or Ridge) offers a flexible alternative (Supplementary Tables 5 and 6). Nonetheless, TWAS fine-mapping is more challenging than GWAS fine-mapping: predicted expression only imperfectly captures cis expression, owing to both variance and bias in the expression modeling (Box 1).
To address tissue bias, we recommend using an expression panel from only the most mechanistically related tissue available, even when it is smaller than other tissues’. However, using a slightly less related tissue (for example, a different region of the brain) would be advisable if the sample size would be substantially increased; the trade-off between tissue bias and sample size should be evaluated on a case-by-case basis. When a trait’s most related tissue is not known a priori, a recent approach based on LD Score regression29 can be used to select among multiple reference panels. Methods to handle cross-tissue pleiotropy and cell-type heterogeneity, discussed above in the context of fine-mapping, can also mitigate tissue bias. If no sufficiently large reference panels from closely related tissues are available, we recommend aggregating information across all available tissues in a tissue-agnostic manner4,30.
When reference panels have highly dissimilar sizes across tissues, the tissue with the most significant TWAS P value cannot necessarily be assumed to be causal, because reference-panel size affects the P value. For this reason, we recommend considering TWAS effect size in addition to P value when investigating causal tissues for TWAS-associated genes. Even when all reference panels are similarly sized, the exact combination of tissue, cell type and context (for example, developmental stage and cellular stress) mediating the causal gene’s effect may not be captured by any panel, and this may be the case even if TWAS finds the correct causal gene (for example, C4A is correctly chosen on the basis of RNA-seq on adult samples even though its causal effect on schizophrenia probably occurs in adolescence). Furthermore, bias may alter the pattern of TWAS P values and effect sizes across tissues in unexpected ways. We caution against over-interpretation.
Several emerging topics in TWAS deserve further mention. Multi-tissue TWAS methods such as UTMOST30 increase power by jointly training expression models across multiple tissues. MulTiXcan31 fits a multivariate regression with phenotype as the outcome and a gene’s expression across multiple tissues or contexts as the inputs to increase power. The adaptive sum of a powered score test32 increases power by adaptively adjusting how much to exponentiate the weighted genotypes (genotypes times expression model weights) in the final expression-trait test, from γ = 1 (for example, Fusion or PrediXcan) or γ = 2 (for example, SKAT33) to γ = ∞ (in which all weight is placed on the most significant GWAS variant, a method more appropriate than standard TWAS when there are few associated variants). Mogil et al.34 have shown that between-population allele-frequency differences worsen cross-ancestry expression predictions, thus underscoring the importance of gathering diverse expression cohorts. Finally, the emerging ability to generate very large expression panels offers the promise of using trans eQTL signals to overcome the co-regulation problem35,36: although all genes at a locus may show GWAS signal at their cis eQTLs, owing to co-regulation, only the true causal genes are expected to show significant GWAS signal at their trans eQTLs as well.
In our case studies, we assumed that the single gene with substantial causal evidence was the sole causal gene at the locus, with some exceptions (FADS1/2/3 and SLC22A4/5–IRF1). Nonetheless, other loci may contain multiple causal genes. Indeed, under an omnigenic model37, every gene may be causal to some degree, although TWAS identification of marginally causal genes as strong hits due to co-regulation (effect size inflation) remains problematic. Furthermore, the expression of a ‘non-causal’ gene may causally influence expression of the causal gene merely by being transcribed, even if the gene is non-coding or its protein product is non-causal38.
Co-regulation and tissue bias affect other methods integrating GWAS and expression data. Testing of gene–trait associations based on MR5,6,7 is vulnerable, because co-regulation, as a form of pleiotropy, violates one of the core assumptions of MR39. Although the HEIDI test5 corrects for the case in which two genes have distinct but linked causal variants, it does not correct for the case in which they share the same causal variant. GWAS–eQTL colocalization methods such as Sherlock8, coloc9,10, QTLMatch11, eCaviar12, enloc13 and RTC14 are also vulnerable. The more tightly a pair of genes is co-regulated in cis, the more difficult it becomes to distinguish causality on the basis of GWAS and expression data alone. Our results underscore the need for computational and experimental methods that move beyond expression variation across individuals to complement TWAS in identifying causal genes at GWAS loci.
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We gratefully acknowledge J. Pritchard, H. Tang and members of the laboratory of N. Zaitlen for helpful discussions. This work was funded in part by the Natural Sciences and Engineering Research Council of Canada (NSERC) (grant PGSD3-476082-2015 to M.W.); a Stanford Bio-X Bowes fellowship (to M.W.); a Stanford Graduate Fellowship (to N.S.-A.); a National Defense Science & Engineering Grant (to N.S.-A.); NIH grants 1DP2OD022870 and U01HG009431 (to A.K.), 1U24HG008956 and 5U01HG009080 (to M.A.R.), R01HG009120 and R01MH115676 (to B.P.), R01MH107666, R01MH101820 and P30DK20595 (to H.K.I.), and R01HL125863 and R21TR001739 (to J.L.M.B.); NHGRI grant R01HG010140 (to M.A.R.); Leducq Foundation grant 12CVD02 (to J.L.M.B.); and American Heart Association grant A14SFRN20840000 (to J.L.M.B.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
The authors declare no competing interests.
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Wainberg, M., Sinnott-Armstrong, N., Mancuso, N. et al. Opportunities and challenges for transcriptome-wide association studies. Nat Genet 51, 592–599 (2019). https://doi.org/10.1038/s41588-019-0385-z
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