Evaluation of a targeted next-generation sequencing-based CYP2D6 genotyping method compared with Sanger sequencing and multiplex ligation-dependent probe amplification.

Abstract

Introduction: CYP2D6 genotyping can guide the appropriate prescription of related drugs, but its complex genetic alterations make clinical implementation challenging. In this study, we evaluated the performance of a custom-made, targeted next-generation sequencing (NGS)-based CYP2D6 genotyping method by comparing it with Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) methods.

Methods: CYP2D6 was included in a customized NGS multigene panel. CYP2D6 genotypes were analyzed in 91 patients, including copy number variations (CNV) analysis based on read depth. For comparison, single-nucleotide variations (formerly single-nucleotide polymorphisms) and CNVs were assessed using Sanger sequencing and MLPA, and the genotype was determined. Differences in genotype and predicted phenotype according to these 2 approaches were evaluated.

Results: The NGS-based results were 100% concordant in single-nucleotide variations compared with Sanger sequencing, but 4 cases (4.4%) were discordant in CNVs with MLPA. Consequently, the NGS-based genotype was 95.6% concordant with the combined Sanger sequencing and MLPA approach. However, the classification of the predicted phenotype was unchanged in the 4 cases with differing assigned genotypes.

Discussion: The NGS-based CYP2D6 genotyping method showed good performance, suggesting its potential utility in clinical practice. Including CYP2D6 in an NGS panel for patients who may use drugs metabolized by CYP2D6 may provide additional useful information.