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Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits

Stephanie Feupe Fotsing, Catherine Wang, Shubham Saini, Sharona Shleizer-Burko, View ORCID ProfileAlon Goren, Melissa Gymrek
doi: https://doi.org/10.1101/495226
Stephanie Feupe Fotsing
Biomedical Informatics and Systems Biology, University of California, San Diego, La Jolla, CA, USABioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA USA
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Catherine Wang
Department of Bioengineering, University of California San Diego, La Jolla, CA USA
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Shubham Saini
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
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Sharona Shleizer-Burko
Department of Medicine, University of California San Diego, La Jolla, CA USA
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Alon Goren
Department of Medicine, University of California San Diego, La Jolla, CA USA
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  • ORCID record for Alon Goren
  • For correspondence: mgymrek@ucsd.edu agoren@ucsd.edu
Melissa Gymrek
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USADepartment of Medicine, University of California San Diego, La Jolla, CA USA
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  • For correspondence: mgymrek@ucsd.edu agoren@ucsd.edu
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Abstract

Short tandem repeats (STRs) have been implicated in a variety of complex traits in humans. However, genome-wide studies of the effects of STRs on gene expression thus far have had limited power to detect associations and elucidate the underlying biological mechanisms. Here, we leverage whole genome sequencing and expression data for 17 tissues from GTEx to identify STRs whose repeat lengths are associated with expression of nearby genes (eSTRs). Our analysis reveals more than 3,000 high-confidence eSTRs, which are enriched in known or predicted regulatory regions. We show eSTRs may act through a variety of mechanisms. We further identify hundreds of eSTRs that potentially drive published GWAS signals and implicate specific eSTRs in height and schizophrenia. Overall, our results demonstrate that eSTRs potentially contribute to a range of human phenotypes. We expect that our comprehensive eSTR catalog will serve as a valuable resource for future studies of complex traits.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted December 13, 2018.
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Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits
Stephanie Feupe Fotsing, Catherine Wang, Shubham Saini, Sharona Shleizer-Burko, Alon Goren, Melissa Gymrek
bioRxiv 495226; doi: https://doi.org/10.1101/495226
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Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits
Stephanie Feupe Fotsing, Catherine Wang, Shubham Saini, Sharona Shleizer-Burko, Alon Goren, Melissa Gymrek
bioRxiv 495226; doi: https://doi.org/10.1101/495226

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