High false sign rates in transcriptome-wide association studies.

Authors

Peter A Gerlach, Nikhil Milind, Jeffrey P Spence, Jonathan K Pritchard

Published in

Nature genetics. Oct 22, 2026. Epub Oct 22, 2026.

Abstract

Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it remains unclear how accurately TWAS recover the true direction of a gene's effect on a trait. Here we estimate the false sign rate of TWAS for plasma proteins, leveraging the expectation that increased gene expression should generally increase protein expression. We then extend this framework to complex traits, where loss-of-function burden tests provide the expected direction of effect. In both analyses, we observe high discordance with expectations, with TWAS showing a false sign rate of 23% for plasma proteins and 33% for complex traits. We propose that much of the sign discordance arises when expression quantitative trait loci in non-trait-relevant tissues tag haplotypes associated with traits in genome-wide association studies via distinct, tightly linked regulatory variants, yielding spurious TWAS associations with the correct genes but with unreliable direction of effect. These findings show that TWAS-based direction-of-effect estimates should be interpreted with caution and raise concerns about the reliability of TWAS more broadly.

PMID:
42918898
Bibliographic data and abstract were imported from PubMed on 24 Oct 2026.

Read full publication at:
Please sign in to see all details.

Stats

1-terrible, 9-excellent. How would you rate this publication? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.