StarTRAC-CYP2D6: a method for CYP2D6 allele-specific copy number determination using digital PCR

Area of Science:

• Pharmacogenomics
• Molecular Diagnostics
• Genetics

Background:

• Accurate CYP2D6 genotyping is crucial for personalized medicine.
• Existing methods struggle to differentiate duplicated alleles and diplotypes, impacting phenotype prediction.
• Novel methods are needed for precise copy number (CN) determination of specific CYP2D6 alleles.

Purpose of the Study:

• To develop and validate StarTRAC-CYP2D6, a novel method for determining the copy number (CN) of specific CYP2D6 star alleles.
• To assess the impact of DNA input and interfering variants on CN assay performance.
• To improve the accuracy of CYP2D6 diplotype and phenotype prediction.

Main Methods:

• Developed StarTRAC-CYP2D6 (Targeted Reporting of Allele-specific CNV) using digital PCR.
• Utilized seven multiplexed TaqMan genotyping assays targeting core variants in CYP2D6 duplications.
• Tested 17 Coriell samples with diverse CYP2D6 alleles and structural variants.

Main Results:

• StarTRAC-CYP2D6 reliably resolved allele-specific CN ranging from 0 to 4 copies.
• Accurately discriminated samples with duplications/multiplications and their expected star alleles.
• 200 ng DNA input maintained CN integrity for up to 6 copies; interfering variants showed variable effects.

Conclusions:

• StarTRAC-CYP2D6 is an effective method for determining specific CYP2D6 star allele CN.
• Consider DNA quantity and interfering variants for accurate interpretation and workflow optimization.
• Further development is underway for higher-plex CN testing and discrimination.