ArticleThe pharmacogenomics journal2019
An optimized prediction framework to assess the functional impact of pharmacogenetic variants.
Article in The pharmacogenomics journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 2 of them syntheses that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
88 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The Clinical Pharmacogenetics Implementation Consortium's consensus-based framework for assigning allele function.American journal of human genetics · 2025Guideline
- DPYD genetic polymorphisms in non-European patients with severe fluoropyrimidine-related toxicity: a systematic review.British journal of cancer · 2024Pooled it
- Trial
- Homology-Based Variant-Effect Predictors Break Down on Cytochrome P450 Pharmacogenes.bioRxiv : the preprint server for biology · 2026Article
- Does Next Generation Sequencing (NGS)-Based CYP2D6 Sequencing Improve Genotype-Phenotype Concordance in Tamoxifen-Treated Patients?Clinical pharmacology and therapeutics · 2026Article
- Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3D.Nature communications · 2026Article
- Pharmacogenomic landscape of a Moroccan cohort: enhancing global diversity and addressing the North African gap.Scientific reports · 2026Article
- The potential of whole genome sequencing in pharmacogenetics: a retrospective health record study in rare disease patients.European journal of human genetics : EJHG · 2026Article
- Feed-Forward Deep Neural Networks Predict Substrate-Specific Effects of Transporter Variants to Explain Drug Response Variability.Clinical and translational science · 2026Article
- Genetic variants ofJournal of Taibah University Medical Sciences · 2026Article
- Computational variant predictors for pharmacogenomics: from evaluation of single alleles to assessment of adverse drug reactions to antidepressants.The pharmacogenomics journal · 2026Article
- The evolving landscape of pharmacogenomics: Current achievements and future directions.Pharmacological reviews · 2026Review
- Pharmacokinetic recall study of Estonian Biobank participants with novel genetic variants in CYP2C19 and CYP2D6.NPJ genomic medicine · 2026Article
- Allelic diversity of the pharmacogenes CYP2D6 and CYP2C19 in Māori from Te Tairāwhiti, Aotearoa New Zealand.Frontiers in genetics · 2026Article
- Genetic influences on antidepressant side effects: a CYP2C19 gene variation and polygenic risk study in the Estonian Biobank.European journal of human genetics : EJHG · 2025Article
- Proof of principle concept for the analysis and functional prediction of rare genetic variants in the CYP2C19 and CYP2D6 genes.Human genomics · 2025Article
- Implementation of pre-emptive testing of a pharmacogenomic panel in clinical practice: Where do we stand?British journal of clinical pharmacology · 2025Review
- Translating pharmacogenomic sequencing data into drug response predictions-How to interpret variants of unknown significance.British journal of clinical pharmacology · 2025Review
- Pharmacogenomic landscape of the Thai population from genome sequencing of 949 individuals.Scientific reports · 2024Article
- APF2: an improved ensemble method for pharmacogenomic variant effect prediction.The pharmacogenomics journal · 2024Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Prediction of phenotypic consequences of mutations constitutes an important aspect of precision medicine. Current computational tools mostly rely on evolutionary conservation and have been calibrated on variants associated with disease, which poses conceptual problems for assessment of variants in poorly conserved pharmacogenes. Here, we evaluated the performance of 18 current functionality prediction methods leveraging experimental high-quality activity data from 337 variants in genes involved in drug metabolism and transport and found that these models only achieved probabilities of 0.1-50.6% to make informed conclusions. We therefore developed a functionality prediction framework optimized for pharmacogenetic assessments that significantly outperformed current algorithms. Our model achieved 93% for both sensitivity and specificity for both loss-of-function and functionally neutral variants, and we confirmed its superior performance using cross validation analyses. This novel model holds promise to improve the translation of personal genetic information into biological conclusions and pharmacogenetic recommendations, thereby facilitating the implementation of Next-Generation Sequencing data into clinical diagnostics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.