Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing Article Swipe
Alysha Taylor
,
Dinis Barros
,
Nastassia Gobet
,
Thierry Schuepbach
,
Branduff McAllister
,
Lorène Aeschbach
,
Emma Randall
,
Evgeniya Trofimenko
,
Eleanor R. Heuchan
,
Paula Barszcz
,
Marc Ciosi
,
Joanne Morgan
,
Nathaniel J. Hafford‐Tear
,
Alice E. Davidson
,
Thomas H. Massey
,
Darren G. Monckton
,
Lesley Jones
,
Ioannis Xénarios
,
Vincent Dion
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/2022.03.08.483398
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/2022.03.08.483398
Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and pre-clinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. Interrupted alleles are sometimes present within repeats and can alter disease manifestation. Determining repeat size mosaicism and identifying interruptions in targeted sequencing datasets remains a major challenge. This is in part because standard alignment tools are ill-suited for repetitive and unstable sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington’s disease and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 blood-derived samples from Huntington’s disease individuals and did not require prior knowledge of the flanking sequences. Furthermore, RD can be used to identify alleles with interruptions and provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and the development of novel therapies.
Related Topics
Concepts
Tandem repeat
DNA sequencing
Genetics
Biology
Computational biology
Nanopore sequencing
Trinucleotide repeat expansion
Microsatellite
Allele
DNA
Gene
Genome
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2022.03.08.483398
- https://www.biorxiv.org/content/biorxiv/early/2022/03/09/2022.03.08.483398.full.pdf
- OA Status
- green
- Cited By
- 1
- References
- 59
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4220953334
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4220953334Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2022.03.08.483398Digital Object Identifier
- Title
-
Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencingWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-03-09Full publication date if available
- Authors
-
Alysha Taylor, Dinis Barros, Nastassia Gobet, Thierry Schuepbach, Branduff McAllister, Lorène Aeschbach, Emma Randall, Evgeniya Trofimenko, Eleanor R. Heuchan, Paula Barszcz, Marc Ciosi, Joanne Morgan, Nathaniel J. Hafford‐Tear, Alice E. Davidson, Thomas H. Massey, Darren G. Monckton, Lesley Jones, Ioannis Xénarios, Vincent DionList of authors in order
- Landing page
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https://doi.org/10.1101/2022.03.08.483398Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2022/03/09/2022.03.08.483398.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2022/03/09/2022.03.08.483398.full.pdfDirect OA link when available
- Concepts
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Tandem repeat, DNA sequencing, Genetics, Biology, Computational biology, Nanopore sequencing, Trinucleotide repeat expansion, Microsatellite, Allele, DNA, Gene, GenomeTop concepts (fields/topics) attached by OpenAlex
- Cited by
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1Total citation count in OpenAlex
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2024: 1Per-year citation counts (last 5 years)
- References (count)
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59Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| institutions_distinct_count | 19 |
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