Properties of structural variants and short tandem repeats associated with gene expression and complex traits

David Jakubosky, Matteo D’Antonio, Marc Jan Bonder, Craig Smail, Margaret K. R. Donovan, William W. Young Greenwald, Hiroko Matsui, Agnieszka D’Antonio-Chronowska, Oliver Stegle, Erin N. Smith, Stephen B. Montgomery, Christopher DeBoever and Kelly A. Frazer ()
Additional contact information
David Jakubosky: University of California San Diego
Matteo D’Antonio: University of California San Diego
Marc Jan Bonder: European Bioinformatics Institute, Hinxton
Craig Smail: Stanford University School of Medicine
Margaret K. R. Donovan: University of California San Diego
William W. Young Greenwald: University of California San Diego
Hiroko Matsui: University of California San Diego
Agnieszka D’Antonio-Chronowska: University of California San Diego
Oliver Stegle: European Bioinformatics Institute, Hinxton
Erin N. Smith: University of California San Diego
Stephen B. Montgomery: Stanford University
Christopher DeBoever: University of California San Diego
Kelly A. Frazer: University of California San Diego

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: 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.

Date: 2020
References: Add references at CitEc
Citations: View citations in EconPapers (4)

Downloads: (external link)
https://www.nature.com/articles/s41467-020-16482-4 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16482-4

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-020-16482-4

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().