PAnno: A pharmacogenomics annotation tool for clinical genomic testing Article Swipe
Yaqing Liu
,
Zipeng Lin
,
Qingwang Chen
,
Qiaochu Chen
,
Leqing Sang
,
Yunjin Wang
,
Leming Shi
,
Li Guo
,
Ying Yu
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.3389/fphar.2023.1008330
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.3389/fphar.2023.1008330
Introduction: Next-generation sequencing (NGS) technologies have been widely used in clinical genomic testing for drug response phenotypes. However, the inherent limitations of short reads make accurate inference of diplotypes still challenging, which may reduce the effectiveness of genotype-guided drug therapy. Methods: An automated Pharmacogenomics Annotation tool (PAnno) was implemented, which reports prescribing recommendations and phenotypes by parsing the germline variant call format (VCF) file from NGS and the population to which the individual belongs. Results: A ranking model dedicated to inferring diplotypes, developed based on the allele (haplotype) definition and population allele frequency, was introduced in PAnno. The predictive performance was validated in comparison with four similar tools using the consensus diplotype data of the Genetic Testing Reference Materials Coordination Program (GeT-RM) as ground truth. An annotation method was proposed to summarize prescribing recommendations and classify drugs into avoid use, use with caution, and routine use, following the recommendations of the Clinical Pharmacogenetics Implementation Consortium (CPIC), etc. It further predicts phenotypes of specific drugs in terms of toxicity, dosage, efficacy, and metabolism by integrating the high-confidence clinical annotations in the Pharmacogenomics Knowledgebase (PharmGKB). PAnno is available at https://github.com/PreMedKB/PAnno . Discussion: PAnno provides an end-to-end clinical pharmacogenomics decision support solution by resolving, annotating, and reporting germline variants.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fphar.2023.1008330
- OA Status
- gold
- Cited By
- 6
- References
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- OpenAlex ID
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https://openalex.org/W4318065592Canonical identifier for this work in OpenAlex
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https://doi.org/10.3389/fphar.2023.1008330Digital Object Identifier
- Title
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PAnno: A pharmacogenomics annotation tool for clinical genomic testingWork title
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articleOpenAlex work type
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enPrimary language
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2023Year of publication
- Publication date
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2023-01-26Full publication date if available
- Authors
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Yaqing Liu, Zipeng Lin, Qingwang Chen, Qiaochu Chen, Leqing Sang, Yunjin Wang, Leming Shi, Li Guo, Ying YuList of authors in order
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https://doi.org/10.3389/fphar.2023.1008330Publisher landing page
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.3389/fphar.2023.1008330Direct OA link when available
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Pharmacogenomics, Annotation, Computational biology, Medicine, Biology, BioinformaticsTop concepts (fields/topics) attached by OpenAlex
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6Total citation count in OpenAlex
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2025: 3, 2024: 1, 2023: 2Per-year citation counts (last 5 years)
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