ArticleFrontiers in pharmacology2023
Targeted haplotyping in pharmacogenomics using Oxford Nanopore Technologies' adaptive sampling.
Article in Frontiers in pharmacology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 13 citations in OpenAlex.
- A de novo algorithm for allele reconstruction from Oxford nanopore amplicon reads, with application to CYP2D6.Bioinformatics (Oxford, England) · 2026Article
- Flexible and rapid validation of structural variation using adaptive sampling.European journal of human genetics : EJHG · 2026Article
- MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.Cell reports methods · 2026Article
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping.Scientific reports · 2025Article
- Haplotype Inference Using Long-Read Nanopore Sequencing: Application to GSTA1 Promoter.Molecular biotechnology · 2025Article
- Leveraging long-read sequencing technologies for pharmacogenomic testing: applications, analytical strategies, challenges, and future perspectives.Frontiers in genetics · 2025Review
- Comparative evaluation of Oxford Nanopore Technologies' adaptive sampling and the Twist long-read PGx panel for pharmacogenomic profiling.Frontiers in pharmacology · 2025Article
- ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.Briefings in bioinformatics · 2024Article
- Cas9-targeted-based long-read sequencing for genetic screening ofFrontiers in genetics · 2024Article
- Machine learning models for pharmacogenomic variant effect predictions - recent developments and future frontiers.PharmacogenomicsReview
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pharmacogenomics (PGx) studies the impact of interindividual genomic variation on drug response, allowing the opportunity to tailor the dosing regimen for each patient. Current targeted PGx testing platforms are mainly based on microarray, polymerase chain reaction, or short-read sequencing. Despite demonstrating great value for the identification of single nucleotide variants (SNVs) and insertion/deletions (INDELs), these assays do not permit identification of large structural variants, nor do they allow unambiguous haplotype phasing for star-allele assignment. Here, we used Oxford Nanopore Technologies' adaptive sampling to enrich a panel of 1,036 genes with well-documented PGx relevance extracted from the Pharmacogenomics Knowledge Base (PharmGKB). By evaluating concordance with existing truth sets, we demonstrate accurate variant and star-allele calling for five Genome in a Bottle reference samples. We show that up to three samples can be multiplexed on one PromethION flow cell without a significant drop in variant calling performance, resulting in 99.35% and 99.84% recall and precision for the targeted variants, respectively. This work advances the use of nanopore sequencing in clinical PGx settings.
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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.