Scalable Pharmacogenetic Screening of the Complex CYP2D6 Locus Using SMRT Long-read Amplicon Sequencing

The CYP2D6 enzyme metabolizes approximately 25% of commonly used pharmaceuticals and is of intense pharmacogenetic interest. Polymorphisms in CYP2D6 can alter an individual’s response to a wide range of commonly used medicines. Accurate allele typing of CYP2D6 has proved challenging due to frequent copy number variants (CNVs) and the paralogous CYP2D7 pseudogene. 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 Single Molecule Real Time (SMRT) sequencing platform has yielded promising results for CYP2D6 allele typing. Previous studies have been limited in scale and have employed nascent data processing pipelines. We have developed 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. PLASTER is implemented in Nextflow and is available at https://github.com/bahlolab/PLASTER.
 
Learning Objectives:

1. Explain how pharmacogenetic variation can alter responses to drug treatment, and how drug efficacy may vary from population to population.

2. Explain why CYP2D6 screening is useful for treatment of Plasmodium vivax Malaria.

3. Discuss the relative advantages and disadvantages of short and long read sequencing technologies for pharmacogenetic screening.