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  • Perspective
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Opportunities and challenges for transcriptome-wide association studies

Nature Genetics volume 51, pages 592–599 (2019)Cite this article

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Abstract

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.

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Fig. 1: TWAS, like GWAS, frequently has multiple significant associations per locus.
Fig. 2: Co-regulation strongly predicts TWAS hit strength at the SORT1 locus.
Fig. 3: Correlated predicted expression can cause non-causal hits even in the absence of correlated total expression.
Fig. 4: Sharing of GWAS variants between expression models can contribute to non-causal hits even without correlated predicted expression.
Fig. 5: Co-regulation scenarios in TWAS that may lead to non-causal hits, from least to most general.
Fig. 6: Most candidate causal genes drop out after switching to a tissue with a less clear mechanistic relationship to the trait, owing to a lack of sufficient expression or sufficiently heritable expression.

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Acknowledgements

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.

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Authors and Affiliations

  1. Department of Computer Science, Stanford University, Stanford, CA, USA

    Michael Wainberg & Anshul Kundaje

  2. Department of Genetics, Stanford University, Stanford, CA, USA

    Nasa Sinnott-Armstrong, David Golan & Anshul Kundaje

  3. Department of Pathology & Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA

    Nicholas Mancuso & Bogdan Pasaniuc

  4. Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA

    Alvaro N. Barbeira & Hae Kyung Im

  5. New York Genome Center, New York, NY, USA

    David A. Knowles

  6. Department of Computer Science, Columbia University, New York, NY, USA

    David A. Knowles

  7. Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia

    Raili Ermel & Arno Ruusalepp

  8. Clinical Gene Networks AB, Stockholm, Sweden

    Arno Ruusalepp & Johan L. M. Björkegren

  9. Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA

    Thomas Quertermous

  10. Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Ke Hao & Johan L. M. Björkegren

  11. Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia

    Johan L. M. Björkegren

  12. Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden

    Johan L. M. Björkegren

  13. Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA

    Bogdan Pasaniuc

  14. Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA

    Bogdan Pasaniuc

  15. Department of Biomedical Data Science, Stanford University, Stanford, CA, USA

    Manuel A. Rivas

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Contributions

M.W., M.A.R. and A.K. conceived the study. M.W., N.M. and A.N.B. performed analyses. N.S.-A., D.A.K. and D.G. provided intellectual input. R.E., A.R., T.Q., K.H. and J.L.M.B. provided assistance with analysis of the STARNET dataset. H.K.I., B.P., M.A.R. and A.K. supervised the study. M.W., H.K.I., B.P., M.A.R. and A.K. wrote the manuscript. All authors reviewed the manuscript.

Corresponding authors

Correspondence to Johan L. M. Björkegren, Hae Kyung Im, Bogdan Pasaniuc, Manuel A. Rivas or Anshul Kundaje.

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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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