AARDVARK: an automated reversion detector for variants affecting resistance kinetics

SUMMARY: Resistance to two classes of FDA-approved therapies that target DNA repair-deficient tumors is caused by mutations that restore the tumor cell's DNA repair function. Identifying these “reversion” mutations currently requires manual annotation of patient tumor sequence data. Here we pre...

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Detalles Bibliográficos
Autores principales: Moreno, Thaidy, Magana, Joaquin, Quigley, David A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457659/
https://www.ncbi.nlm.nih.gov/pubmed/37584701
http://dx.doi.org/10.1093/bioinformatics/btad509
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author Moreno, Thaidy
Magana, Joaquin
Quigley, David A
author_facet Moreno, Thaidy
Magana, Joaquin
Quigley, David A
author_sort Moreno, Thaidy
collection PubMed
description SUMMARY: Resistance to two classes of FDA-approved therapies that target DNA repair-deficient tumors is caused by mutations that restore the tumor cell's DNA repair function. Identifying these “reversion” mutations currently requires manual annotation of patient tumor sequence data. Here we present AARDVARK, an R package that automatically identifies reversion mutations from DNA sequence data. AVAILABILITY AND IMPLEMENTATION: AARDVARK is implemented in R (≥3.5). It is available on GitHub at https://github.com/davidquigley/aardvark. It is licensed under the MIT license.
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spelling pubmed-104576592023-08-27 AARDVARK: an automated reversion detector for variants affecting resistance kinetics Moreno, Thaidy Magana, Joaquin Quigley, David A Bioinformatics Applications Note SUMMARY: Resistance to two classes of FDA-approved therapies that target DNA repair-deficient tumors is caused by mutations that restore the tumor cell's DNA repair function. Identifying these “reversion” mutations currently requires manual annotation of patient tumor sequence data. Here we present AARDVARK, an R package that automatically identifies reversion mutations from DNA sequence data. AVAILABILITY AND IMPLEMENTATION: AARDVARK is implemented in R (≥3.5). It is available on GitHub at https://github.com/davidquigley/aardvark. It is licensed under the MIT license. Oxford University Press 2023-08-16 /pmc/articles/PMC10457659/ /pubmed/37584701 http://dx.doi.org/10.1093/bioinformatics/btad509 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Moreno, Thaidy
Magana, Joaquin
Quigley, David A
AARDVARK: an automated reversion detector for variants affecting resistance kinetics
title AARDVARK: an automated reversion detector for variants affecting resistance kinetics
title_full AARDVARK: an automated reversion detector for variants affecting resistance kinetics
title_fullStr AARDVARK: an automated reversion detector for variants affecting resistance kinetics
title_full_unstemmed AARDVARK: an automated reversion detector for variants affecting resistance kinetics
title_short AARDVARK: an automated reversion detector for variants affecting resistance kinetics
title_sort aardvark: an automated reversion detector for variants affecting resistance kinetics
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457659/
https://www.ncbi.nlm.nih.gov/pubmed/37584701
http://dx.doi.org/10.1093/bioinformatics/btad509
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