ArticleThe pharmacogenomics journal2026
Amplicon-based long-read sequencing for accurate CYP2D6 gene deletion and duplication detection using CYP2D7 as a reference gene.
Article in The pharmacogenomics journal, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
We developed an amplicon-based long-read sequencing approach that enables simultaneous detection of CYP2D6 single-nucleotide variants (SNVs) and copy-number variations (CNVs) in a single reaction. The SNVs of the two pseudogenes, CYP2D7 and CYP2D8, were also comprehensively characterized. CYP2D6 CNVs were inferred using CYP2D7 as a reference gene, integrating read-depth measurements with allele-frequency (AF) ratios. The entire CYP2D locus ( ~ 30.2Kb) and the three homologous genes separately (6.3-6.6Kb) were sequenced using Oxford Nanopore sequencing. Our analysis identified 21 CYP2D7 and 17 CYP2D8 unique haplotypes, and 57% of the SNVs detected in the pseudogenes had nucleotides corresponding to CYP2D6 reference nucleotides. A total of 36 variants found within the pseudogenes have also been annotated as functional variants in the CYP2D6 gene. The combined CYP2D6:CYP2D7 read-count ratio and reference-to-alternative alleles AF ratio accurately predicted CYP2D6 CNV status. This method is simple and rapid, making it potentially suitable for clinical implementation of pharmacogenomics.
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