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Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats

Author

Listed:
  • David Jakubosky

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

  • Erin N. Smith

    (University of California San Diego)

  • Matteo D’Antonio

    (University of California San Diego)

  • Marc Bonder

    (European Bioinformatics Institute
    Genome Biology Unit)

  • William W. Young Greenwald

    (University of California San Diego)

  • Agnieszka D’Antonio-Chronowska

    (University of California San Diego)

  • Hiroko Matsui

    (University of California San Diego)

  • Oliver Stegle

    (European Bioinformatics Institute
    Genome Biology Unit
    German Cancer Research Center)

  • 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) are important sources of genetic diversity but are not routinely analyzed in genetic studies because they are difficult to accurately identify and genotype. Because SVs and STRs range in size and type, it is necessary to apply multiple algorithms that incorporate different types of evidence from sequencing data and employ complex filtering strategies to discover a comprehensive set of high-quality and reproducible variants. Here we assemble a set of 719 deep whole genome sequencing (WGS) samples (mean 42×) from 477 distinct individuals which we use to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We use 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and develop a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.

Suggested Citation

  • David Jakubosky & Erin N. Smith & Matteo D’Antonio & Marc Bonder & William W. Young Greenwald & Agnieszka D’Antonio-Chronowska & Hiroko Matsui & Oliver Stegle & Stephen B. Montgomery & Christopher DeB, 2020. "Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16481-5
    DOI: 10.1038/s41467-020-16481-5
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    Cited by:

    1. 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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