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Nat Genet. 2019 Nov;51(11):1652-1659. doi: 10.1038/s41588-019-0521-9. Epub 2019 Nov 1.

The impact of short tandem repeat variation on gene expression.

Author information

1
Biomedical Informatics and Systems Biology, University of California San Diego, La Jolla, CA, USA.
2
Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
3
La Jolla Institute of Immunology, La Jolla, CA, USA.
4
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
5
Department of Medicine, University of California San Diego, La Jolla, CA, USA.
6
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
7
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. mgymrek@ucsd.edu.
8
Department of Medicine, University of California San Diego, La Jolla, CA, USA. mgymrek@ucsd.edu.

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 provide insights into putative mechanisms. Here, we leverage whole-genome sequencing and expression data for 17 tissues from the Genotype-Tissue Expression Project to identify more than 28,000 STRs for which repeat number is associated with expression of nearby genes (eSTRs). We use fine-mapping to quantify the probability that each eSTR is causal and characterize the top 1,400 fine-mapped eSTRs. We identify hundreds of eSTRs linked with published genome-wide association study signals and implicate specific eSTRs in complex traits, including height, schizophrenia, inflammatory bowel disease and intelligence. Overall, our results support the hypothesis that eSTRs contribute to a range of human phenotypes, and our data should serve as a valuable resource for future studies of complex traits.

PMID:
31676866
DOI:
10.1038/s41588-019-0521-9

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