Properties of Structural Variants and Short Tandem Repeats Associated with Gene Expression and Complex Traits

Overview

Journal Nat Commun

Specialty Biology

Date 2020 Jun 12

PMID 32522982

Citations 50

Authors

David Jakubosky

Matteo DAntonio

Marc Jan Bonder

Craig Smail

Margaret K R Donovan

William W Young Greenwald

Hiroko Matsui

Agnieszka DAntonio-Chronowska

Oliver Stegle

Erin N Smith

Stephen B Montgomery

Christopher DeBoever

Kelly A Frazer

Affiliations

Soon will be listed here.

Abstract

Structural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we identify genomic features of SV classes and STRs that are associated with gene expression and complex traits, including their locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We identify a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and show that they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits.

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