vamos: variable-number tandem repeats annotation using efficient motif sets

Roughly 3% of the human genome is composed of variable-number tandem repeats (VNTRs): arrays of motifs at least six bases. These loci are highly polymorphic, yet current approaches that define and merge variants based on alignment breakpoints do not capture their full diversity. Here we present a me...

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Detalles Bibliográficos
Autores principales: Ren, Jingwen, Gu, Bida, Chaisson, Mark J. P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10373352/
https://www.ncbi.nlm.nih.gov/pubmed/37501141
http://dx.doi.org/10.1186/s13059-023-03010-y
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author Ren, Jingwen
Gu, Bida
Chaisson, Mark J. P.
author_facet Ren, Jingwen
Gu, Bida
Chaisson, Mark J. P.
author_sort Ren, Jingwen
collection PubMed
description Roughly 3% of the human genome is composed of variable-number tandem repeats (VNTRs): arrays of motifs at least six bases. These loci are highly polymorphic, yet current approaches that define and merge variants based on alignment breakpoints do not capture their full diversity. Here we present a method vamos: VNTR Annotation using efficient Motif Sets that instead annotates VNTR using repeat composition under different levels of motif diversity. Using vamos we estimate 7.4–16.7 alleles per locus when applied to 74 haplotype-resolved human assemblies, compared to breakpoint-based approaches that estimate 4.0–5.5 alleles per locus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03010-y.
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spelling pubmed-103733522023-07-28 vamos: variable-number tandem repeats annotation using efficient motif sets Ren, Jingwen Gu, Bida Chaisson, Mark J. P. Genome Biol Method Roughly 3% of the human genome is composed of variable-number tandem repeats (VNTRs): arrays of motifs at least six bases. These loci are highly polymorphic, yet current approaches that define and merge variants based on alignment breakpoints do not capture their full diversity. Here we present a method vamos: VNTR Annotation using efficient Motif Sets that instead annotates VNTR using repeat composition under different levels of motif diversity. Using vamos we estimate 7.4–16.7 alleles per locus when applied to 74 haplotype-resolved human assemblies, compared to breakpoint-based approaches that estimate 4.0–5.5 alleles per locus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03010-y. BioMed Central 2023-07-27 /pmc/articles/PMC10373352/ /pubmed/37501141 http://dx.doi.org/10.1186/s13059-023-03010-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Ren, Jingwen
Gu, Bida
Chaisson, Mark J. P.
vamos: variable-number tandem repeats annotation using efficient motif sets
title vamos: variable-number tandem repeats annotation using efficient motif sets
title_full vamos: variable-number tandem repeats annotation using efficient motif sets
title_fullStr vamos: variable-number tandem repeats annotation using efficient motif sets
title_full_unstemmed vamos: variable-number tandem repeats annotation using efficient motif sets
title_short vamos: variable-number tandem repeats annotation using efficient motif sets
title_sort vamos: variable-number tandem repeats annotation using efficient motif sets
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10373352/
https://www.ncbi.nlm.nih.gov/pubmed/37501141
http://dx.doi.org/10.1186/s13059-023-03010-y
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