PacBio long-read amplicon sequencing enables scalable high-resolution population allele typing of the complex CYP2D6 locus

The CYP2D6 enzyme is estimated to metabolize 25% of commonly used pharmaceuticals and is of intense pharmacogenetic interest due to the polymorphic nature of the CYP2D6 gene. Accurate allele typing of CYP2D6 has proved challenging due to frequent copy number variants (CNVs) and paralogous pseudogenes. SNP-arrays, qPCR and short-read sequencing have been employed to interrogate CYP2D6, however these technologies are unable to capture longer range information. Long-read sequencing using the PacBio Single Molecule Real Time (SMRT) sequencing platform has yielded promising results for CYP2D6 allele typing. However, previous studies have been limited in scale and have employed nascent data processing pipelines. We present a robust data processing pipeline PLASTER for accurate allele typing of SMRT sequenced amplicons. We demonstrate the pipeline by typing CYP2D6 alleles in a large cohort of 377 Solomon Islanders. This pharmacogenetic method will improve drug safety and efficacy through screening prior to drug administration.

Automated summary

The CYP2D6 enzyme is responsible for metabolizing 25% of commonly used pharmaceuticals and its gene typing is of great interest in pharmacogenetics due to its polymorphic nature. Accurate allele typing of the CYP2D6 gene has been challenging due to copy number variants and pseudogenes. This study presents a robust data processing pipeline called PLASTER for accurate allele typing using long-read sequencing. This pharmacogenetic method has the potential to improve drug safety and efficacy through screening prior to drug administration.