{"title":"AARDVARK: an automated reversion detector for variants affecting resistance kinetics.","authors":"Thaidy Moreno, Joaquin Magana, David A Quigley","doi":"10.1093/bioinformatics/btad509","DOIUrl":null,"url":null,"abstract":"<p><strong>Summary: </strong>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.</p><p><strong>Availability and implementation: </strong>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.</p>","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"39 8","pages":""},"PeriodicalIF":4.4000,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457659/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btad509","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
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.
摘要美国 FDA 批准的针对 DNA 修复缺陷肿瘤的两类疗法的抗药性是由恢复肿瘤细胞 DNA 修复功能的突变引起的。目前，识别这些 "逆转 "突变需要对患者肿瘤序列数据进行人工标注。在此，我们介绍一款能从 DNA 序列数据中自动识别逆转突变的 R 软件包 AARDVARK：AARDVARK 由 R (≥3.5) 实现。它可在 GitHub 上获取：https://github.com/davidquigley/aardvark。它采用 MIT 许可。
期刊介绍：
The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.
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