VNtyper enables accurate alignment-free genotyping of MUC1 coding VNTR using short-read sequencing data in autosomal dominant tubulointerstitial kidney disease Article Swipe
Hassan Saei
,
Vincent Morinière
,
Laurence Heidet
,
Olivier Gribouval
,
Saïd Lebbah
,
Frédéric Torès
,
Manon Mautret‐Godefroy
,
Bertrand Knebelmann
,
Stéphane Burtey
,
Vincent Vuiblet
,
Corinne Antignac
,
Patrick Nitschké
,
Guillaume Dorval
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1016/j.isci.2023.107171
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1016/j.isci.2023.107171
The human genome comprises approximately 3% of tandem repeats with variable length (VNTR), a few of which have been linked to human rare diseases. Autosomal dominant tubulointerstitial kidney disease-MUC1 (ADTKD-MUC1) is caused by specific frameshift variants in the coding VNTR of the MUC1 gene. Calling variants from VNTR using short-read sequencing (SRS) is challenging due to poor read mappability. We developed a computational pipeline, VNtyper, for reliable detection of MUC1 VNTR pathogenic variants and demonstrated its clinical utility in two distinct cohorts: (1) a historical cohort including 108 families with ADTKD and (2) a replication naive cohort comprising 2,910 patients previously tested on a panel of genes involved in monogenic renal diseases. In the historical cohort all cases known to carry pathogenic MUC1 variants were re-identified, and a new 25bp-frameshift insertion in an additional mislaid family was detected. In the replication cohort, we discovered and validated 30 new patients.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1016/j.isci.2023.107171
- http://www.cell.com/article/S2589004223012488/pdf
- OA Status
- gold
- Cited By
- 18
- References
- 42
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4381094049
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4381094049Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1016/j.isci.2023.107171Digital Object Identifier
- Title
-
VNtyper enables accurate alignment-free genotyping of MUC1 coding VNTR using short-read sequencing data in autosomal dominant tubulointerstitial kidney diseaseWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-06-17Full publication date if available
- Authors
-
Hassan Saei, Vincent Morinière, Laurence Heidet, Olivier Gribouval, Saïd Lebbah, Frédéric Torès, Manon Mautret‐Godefroy, Bertrand Knebelmann, Stéphane Burtey, Vincent Vuiblet, Corinne Antignac, Patrick Nitschké, Guillaume DorvalList of authors in order
- Landing page
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https://doi.org/10.1016/j.isci.2023.107171Publisher landing page
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-
https://www.cell.com/article/S2589004223012488/pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://www.cell.com/article/S2589004223012488/pdfDirect OA link when available
- Concepts
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Frameshift mutation, Genetics, Genotyping, Variable number tandem repeat, Tandem repeat, Copy-number variation, Cohort, Computational biology, Biology, Human genome, Gene, Genome, Whole genome sequencing, Medicine, Mutation, Allele, Genotype, PathologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
18Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 9, 2024: 9Per-year citation counts (last 5 years)
- References (count)
-
42Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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