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- Title
Properties of structural variants and short tandem repeats associated with gene expression and complex traits.
- Authors
Jakubosky, David; D'Antonio, Matteo; Bonder, Marc Jan; Smail, Craig; Donovan, Margaret K. R.; Young Greenwald, William W.; Matsui, Hiroko; i2QTL Consortium; Bonder, Marc J.; Cai, Na; Carcamo-Orive, Ivan; Frazer, Kelly A.; Young Greenwald, William W.; Knowles, Joshua W.; McCarthy, Davis J.; Mirauta, Bogdan A.; Montgomery, Stephen B.; Quertermous, Thomas; Seaton, Daniel D.; Smith, Erin N.
- 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. Genetic variation associated with gene expression changes has mostly been studied in the context of single nucleotide variants. Here, Jakubosky et al. report eQTL analysis of structural variants and short tandem repeats and find properties, such as length of variation, that affect the association.
- Subjects
MICROSATELLITE repeats; GENE expression; SHORT tandem repeat analysis; LINKAGE disequilibrium
- Publication
Nature Communications, 2020, Vol 11, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-020-16482-4