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svaRetro and svaNUMT: Modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data

View ORCID ProfileRuining Dong, View ORCID ProfileDaniel Cameron, View ORCID ProfileJustin Bedo, View ORCID ProfileAnthony T Papenfuss
doi: https://doi.org/10.1101/2021.08.18.456578
Ruining Dong
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
2Department of Medical Biology, University of Melbourne, VIC 3010, Australia
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  • ORCID record for Ruining Dong
Daniel Cameron
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
2Department of Medical Biology, University of Melbourne, VIC 3010, Australia
4Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
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Justin Bedo
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
3School of Computing and Information Systems, University of Melbourne, VIC 3010, Australia
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Anthony T Papenfuss
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
2Department of Medical Biology, University of Melbourne, VIC 3010, Australia
4Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
5Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia
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  • For correspondence: papenfuss@wehi.edu.au
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Abstract

Background The biological significance of structural variation is now more widely recognized. However, due to the lack of available tools for downstream analysis, including processing and annotating, interpretation of structural variant calls remains a challenge.

Findings Here we present svaRetro and svaNUMT, R packages that provide functions for annotating novel genomic events such as non-reference retro-copied transcripts and nuclear integration of mitochondrial DNA. We evaluate the performance of these packages to detect events using simulations and public benchmarking datasets, and annotate processed transcripts in a public structural variant database.

Conclusions svaRetro and svaNUMT provide efficient, modular tools for downstream identification and annotation of structural variant calls.

Competing Interest Statement

The authors have declared no competing interest.

  • List of abbreviations

    SV
    structural variant
    NUMT
    nuclear mitochondrial integration
    RT
    retroposed transcript
    TSD
    target site duplication
    mtDNA
    mitochondrial DNA
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    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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    Posted August 19, 2021.
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    svaRetro and svaNUMT: Modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
    Ruining Dong, Daniel Cameron, Justin Bedo, Anthony T Papenfuss
    bioRxiv 2021.08.18.456578; doi: https://doi.org/10.1101/2021.08.18.456578
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    svaRetro and svaNUMT: Modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
    Ruining Dong, Daniel Cameron, Justin Bedo, Anthony T Papenfuss
    bioRxiv 2021.08.18.456578; doi: https://doi.org/10.1101/2021.08.18.456578

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