ArticleFrontiers in pharmacology2016
Cross-Comparison of Exome Analysis, Next-Generation Sequencing of Amplicons, and the iPLEX(®) ADME PGx Panel for Pharmacogenomic Profiling.
Article in Frontiers in pharmacology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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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
12 citing papers in PubMed, 371 citations in OpenAlex.
- Analytical and Clinical Validation of Action PharmaKitDx: A Comprehensive NGS Panel for the Identification of Pharmacogenetic Variants in Diverse Populations.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Current status of the analytical validation of next generation sequencing applications for pharmacogenetic profiling.Molecular biology reports · 2023Review
- Cas9 targeted nanopore sequencing with enhanced variant calling improves CYP2D6-CYP2D7 hybrid allele genotyping.PLoS genetics · 2022Article
- Identification of pharmacogenetic variants from large scale next generation sequencing data in the Saudi population.PloS one · 2022Article
- Applying Next-Generation Sequencing Platforms for Pharmacogenomic Testing in Clinical Practice.Frontiers in pharmacology · 2021Review
- Technologies for Pharmacogenomics: A Review.Genes · 2020Review
- Review
- Pharmacogenomic Testing: Clinical Evidence and Implementation Challenges.Journal of personalized medicine · 2019Review
- Detection of brain specific cardiolipins in plasma after experimental pediatric head injury.Experimental neurology · 2019Article
- Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening.Genetics in medicine : official journal of the American College of Medical Genetics · 2017Article
- Genome sequencing as a platform for pharmacogenetic genotyping: a pediatric cohort study.NPJ genomic medicine · 2017Article
- Advantages of Array-Based Technologies for Pre-Emptive Pharmacogenomics Testing.Microarrays (Basel, Switzerland) · 2016Review
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-exome sequencing (WES) has been widely used for analysis of human genetic diseases, but its value for the pharmacogenomic profiling of individuals is not well studied. Initially, we performed an in-depth evaluation of the accuracy of WES variant calling in the pharmacogenes CYP2D6 and CYP2C19 by comparison with MiSeq(®) amplicon sequencing data (n = 36). This analysis revealed that the concordance rate between WES and MiSeq(®) was high, achieving 99.60% for variants that were called without exceeding the truth-sensitivity threshold (99%), defined during variant quality score recalibration (VQSR). Beyond this threshold, the proportion of discordant calls increased markedly. Subsequently, we expanded our findings beyond CYP2D6 and CYP2C19 to include more genes genotyped by the iPLEX(®) ADME PGx Panel in the subset of twelve samples. WES performed well, agreeing with the genotyping panel in approximately 99% of the selected pass-filter variant calls. Overall, our results have demonstrated WES to be a promising approach for pharmacogenomic profiling, with an estimated error rate of lower than 1%. Quality filters, particularly VQSR, are important for reducing the number of false variants. Future studies may benefit from examining the role of WES in the clinical setting for guiding drug therapy.
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