ArticlePLoS genetics2022
Cas9 targeted nanopore sequencing with enhanced variant calling improves CYP2D6-CYP2D7 hybrid allele genotyping.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 24 citations in OpenAlex.
- Amplicon-based long-read sequencing for accurate CYP2D6 gene deletion and duplication detection using CYP2D7 as a reference gene.The pharmacogenomics journal · 2026Article
- DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering.International journal of molecular sciences · 2026Review
- A de novo algorithm for allele reconstruction from Oxford nanopore amplicon reads, with application to CYP2D6.Bioinformatics (Oxford, England) · 2026Article
- Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.Cell reports methods · 2026Article
- MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.Cell reports methods · 2026Article
- Enhancing CYP2D6 genotyping with nanopore sequencing to address allele diversity P. vivax malaria elimination.Scientific reports · 2025Article
- Beyond the Cut: Long-read sequencing reveals complex genomic and transcriptomic changes in AAV-CRISPR therapy for Duchenne Muscular Dystrophy.bioRxiv : the preprint server for biology · 2025Article
- Long read sequencing reveals transgene concatemerization and vector sequences integration following AAV-driven electroporation of CRISPR RNP complexes in mouse zygotes.Frontiers in genome editing · 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
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Not Only Editing: A Cas-Cade of CRISPR/Cas-Based Tools for Functional Genomics in Plants and Animals.International journal of molecular sciences · 2024Review
- PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting.Clinical pharmacology and therapeutics · 2023Review
- Current status of the analytical validation of next generation sequencing applications for pharmacogenetic profiling.Molecular biology reports · 2023Review
- Beyond assembly: the increasing flexibility of single-molecule sequencing technology.Nature reviews. Genetics · 2023Review
- Long-Read Sequencing in Blood Group Genetics.Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie · 2023Review
- CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions.International journal of molecular sciences · 2023Article
- Targeted haplotyping in pharmacogenomics using Oxford Nanopore Technologies' adaptive sampling.Frontiers in pharmacology · 2023Article
- Haplotyping pharmacogenes using TLA combined with Illumina or Nanopore sequencing.Scientific reports · 2022Article
- Applications of advanced technologies for detecting genomic structural variation.Mutation research. Reviews in mutation researchReview
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CYP2D6 is a very important pharmacogene as it is responsible for the metabolization or bioactivation of 20 to 30% of the clinically used drugs. However, despite its relatively small length of only 4.4 kb, it is one of the most challenging pharmacogenes to genotype due to the high similarity with its neighboring pseudogenes and the frequent occurrence of CYP2D6-CYP2D7 hybrids. Unfortunately, most current genotyping methods are therefore not able to correctly determine the complete CYP2D6-CYP2D7 sequence. Therefore, we developed a genotyping assay to generate complete allele-specific consensus sequences of complex regions by optimizing the PCR-free nanopore Cas9-targeted sequencing (nCATS) method combined with adaptive sequencing, and developing a new comprehensive long read genotyping (CoLoRGen) pipeline. The CoLoRGen pipeline first generates consensus sequences of both alleles and subsequently determines both large structural and small variants to ultimately assign the correct star-alleles. In reference samples, our genotyping assay confirms the presence of CYP2D6-CYP2D7 large structural variants, single nucleotide variants (SNVs), and small insertions and deletions (INDELs) that go undetected by most current assays. Moreover, our results provide direct evidence that the CYP2D6 genotype of the NA12878 DNA should be updated to include the CYP2D6-CYP2D7 *68 hybrid and several additional single nucleotide variants compared to existing references. Ultimately, the nCATS-CoLoRGen genotyping assay additionally allows for more accurate gene function predictions by enabling the possibility to detect and phase de novo mutations in addition to known large structural and small variants.
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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.