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

Author

Listed:
  • David Jakubosky

    (University of California San Diego
    University of California San Diego)

  • Matteo D’Antonio

    (University of California San Diego)

  • Marc Jan Bonder

    (European Bioinformatics Institute, Hinxton
    European Molecular Biology Laboratory)

  • Craig Smail

    (Stanford University School of Medicine
    Stanford University)

  • Margaret K. R. Donovan

    (University of California San Diego
    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
    European Molecular Biology Laboratory
    German Cancer Research Center)

  • Erin N. Smith

    (University of California San Diego)

  • Stephen B. Montgomery

    (Stanford University
    Stanford University)

  • Christopher DeBoever

    (University of California San Diego)

  • Kelly A. Frazer

    (University of California San Diego
    University of California San Diego)

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.

Suggested Citation

  • 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. Smit, 2020. "Properties of structural variants and short tandem repeats associated with gene expression and complex traits," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16482-4
    DOI: 10.1038/s41467-020-16482-4
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    Cited by:

    1. Timothy D. Arthur & Jennifer P. Nguyen & Agnieszka D’Antonio-Chronowska & Hiroko Matsui & Nayara S. Silva & Isaac N. Joshua & André D. Luchessi & William W. Young Greenwald & Matteo D’Antonio & Martin, 2024. "Complex regulatory networks influence pluripotent cell state transitions in human iPSCs," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    2. Marsha M. Wheeler & Adrienne M. Stilp & Shuquan Rao & Bjarni V. Halldórsson & Doruk Beyter & Jia Wen & Anna V. Mihkaylova & Caitlin P. McHugh & John Lane & Min-Zhi Jiang & Laura M. Raffield & Goo Jun , 2022. "Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    3. Yirong Shi & Yiwei Niu & Peng Zhang & Huaxia Luo & Shuai Liu & Sijia Zhang & Jiajia Wang & Yanyan Li & Xinyue Liu & Tingrui Song & Tao Xu & Shunmin He, 2023. "Characterization of genome-wide STR variation in 6487 human genomes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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