ArticleGenome research2023
An efficient genotyper and star-allele caller for pharmacogenomics.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Does Next Generation Sequencing (NGS)-Based CYP2D6 Sequencing Improve Genotype-Phenotype Concordance in Tamoxifen-Treated Patients?Clinical pharmacology and therapeutics · 2026Article
- Characterization of NAT2 Using Long-Read Sequencing: Allele, Diplotype, and Phenotype Call Accuracy Compared to Other Testing Strategies.Clinical pharmacology and therapeutics · 2026Article
- A de novo algorithm for allele reconstruction from Oxford nanopore amplicon reads, with application to CYP2D6.Bioinformatics (Oxford, England) · 2026Article
- Benchmark of Open-Access Star-Allele Callers to Accurately Assess Haplotypes and Phenotypes in Pharmacogenetic Studies.Clinical pharmacology and therapeutics · 2026Article
- PharmVar GeneFocus: CYP1A2-Clinical Impact, Genetic Variation, and Updated Nomenclature.Clinical pharmacology and therapeutics · 2026Review
- Genome Sequencing Enhances Precision and Clinical Utility of Pharmacogenetic Data Compared to Arrays.Journal of clinical pharmacology · 2026Article
- Pharmacogenomic landscape of a Moroccan cohort: enhancing global diversity and addressing the North African gap.Scientific reports · 2026Article
- Analytical Validation of an Annotation Tool for WGS-Based Pharmacogenomics: Preparing for Clinical Implementation in Pediatric Oncology.Clinical and translational science · 2026Article
- PharmVar GeneFocus: NAT2-Genetic Variation and Updated Nomenclature.Clinical pharmacology and therapeutics · 2026Review
- Pharmacogenomics-guided personalized medicine in a clinical setting: real-world data.Pharmacogenetics and genomics · 2026Article
- Pharmacokinetic recall study of Estonian Biobank participants with novel genetic variants in CYP2C19 and CYP2D6.NPJ genomic medicine · 2026Article
- Pharmacogenomic Calling From Whole-Exome Sequencing in the Taiwanese Population-A Real-World Experience.Molecular genetics & genomic medicine · 2026Article
- Further Personalizing Medicine in Immune Disorders: Genomic Findings and Hematopoietic Cell Transplantation Survival.Transplantation · 2026Article
- Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping.Scientific reports · 2025Article
- Locityper enables targeted genotyping of complex polymorphic genes.Nature genetics · 2025Article
- Population-scale Long-read Sequencing in themedRxiv : the preprint server for health sciences · 2025Article
- Genotyping of selected germline adaptive immune system loci using short-read sequencing data.Genome research · 2025Article
- CYP2D6 Phenotypes and Emergency Department Visits Among Patients Receiving Opioid Treatment.JAMA network open · 2025Article
- New Resources to Identify Characterized DNA Reference Materials for Pharmacogenetic (PGx) and Human Leukocyte Antigen (HLA) Testing: The Genetic Testing Reference Material (GeT-RM) Program PGx Search Tool and GeT-RM Consolidated PGx and HLA Table.The Journal of molecular diagnostics : JMD · 2025Article
- Frequency and Implications of High-Risk Pharmacogenomic Phenotypes Identified in a Diverse Australian Pediatric Oncology Cohort.Clinical and translational science · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
High-throughput sequencing provides sufficient means for determining genotypes of clinically important pharmacogenes that can be used to tailor medical decisions to individual patients. However, pharmacogene genotyping, also known as star-allele calling, is a challenging problem that requires accurate copy number calling, structural variation identification, variant calling, and phasing within each pharmacogene copy present in the sample. Here we introduce Aldy 4, a fast and efficient tool for genotyping pharmacogenes that uses combinatorial optimization for accurate star-allele calling across different sequencing technologies. Aldy 4 adds support for long reads and uses a novel phasing model and improved copy number and variant calling models. We compare Aldy 4 against the current state-of-the-art star-allele callers on a large and diverse set of samples and genes sequenced by various sequencing technologies, such as whole-genome and targeted Illumina sequencing, barcoded 10x Genomics, and Pacific Biosciences (PacBio) HiFi. We show that Aldy 4 is the most accurate star-allele caller with near-perfect accuracy in all evaluated contexts, and hope that Aldy remains an invaluable tool in the clinical toolbox even with the advent of long-read sequencing technologies.
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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.