Best Methods for Testing CYP2D6 Polymorphisms
The best way to test for CYP2D6 polymorphisms is through targeted next-generation sequencing (NGS) combined with specific copy number variant (CNV) detection assays, as this approach provides comprehensive detection of both single nucleotide polymorphisms and structural variations that affect CYP2D6 function. 1
Testing Methodology Options
Recommended Approach: Comprehensive Targeted Testing
- Targeted next-generation sequencing panels that cover:
- All coding regions of CYP2D6
- Exon-intron junctions that may affect splicing
- Known intronic variants that affect function
- Combined with specific CNV detection methods (e.g., quantitative PCR)
This approach provides the most complete assessment of CYP2D6 function by detecting both sequence variations and structural changes.
Alternative Testing Methods
Targeted genotyping assays:
- Advantages: Rapid results, lower cost, suitable when quick clinical decisions are needed
- Limitations: Only detect selected variants, may miss rare variants 1
- Best used when specific variants are of interest or rapid results are needed
Exome sequencing:
- Advantages: Detects variants in coding regions and exon-intron junctions
- Limitations: May miss deep intronic variants and structural variations unless specifically modified 1
Genome sequencing:
- Advantages: Most comprehensive coverage including intronic and regulatory regions
- Limitations: Higher cost, longer analysis time, may require specialized bioinformatic tools for CNV detection 1
Critical Considerations for CYP2D6 Testing
Copy Number Variations
- CYP2D6 is significantly affected by CNVs (deletions, duplications, multiplications)
- CNV detection is essential for accurate phenotype prediction
- Standard notation for CNVs: CYP2D6*1/*2×2 indicates two copies of *2 allele on same chromosome 1
Phasing Determination
- When heterozygous variants are detected, determining whether they are on the same chromosome (in cis) or opposite chromosomes (in trans) is important
- Most routine testing does not include phasing
- When phasing is ambiguous, population data should guide interpretation with appropriate disclaimers 1
Allele Assignment Challenges
- Default assignment of *1 (wild-type) allele when no tested variants are detected carries residual risk
- Comprehensive testing reduces but doesn't eliminate this risk
- Some variants appear in multiple alleles (e.g., p.Arg296Cys and p.Ser486Thr in CYP2D6*2 also occur in *8, *11, *12, *17, *29) 1
Clinical Impact of Testing
CYP2D6 metabolizer status significantly affects drug metabolism for approximately 25% of clinically used medications, including:
- Antidepressants: Poor metabolizers have higher risk of toxicity with fluoxetine and paroxetine 1
- Tamoxifen: Reduced efficacy in poor metabolizers due to decreased conversion to active metabolites 2
- Opioid analgesics: Poor conversion of prodrugs like codeine and tramadol to active forms 2
Phenotype Classification
The American College of Medical Genetics and Genomics (ACMG) recommends classifying CYP2D6 phenotypes as:
- Ultrarapid metabolizer (UM)
- Extensive metabolizer (EM)
- Intermediate metabolizer (IM)
- Poor metabolizer (PM)
Based on combinations of allele functionality and copy number 1
Common Pitfalls to Avoid
- Incomplete variant coverage: Testing only common variants may miss rare functional variants
- Overlooking CNVs: Failure to detect gene deletions/duplications leads to incorrect phenotype assignment
- Misinterpreting heterozygous variants: Without phasing information, incorrect diplotype assignment may occur
- Using only rs identifiers: These may be ambiguous; specific nomenclature is required 1
- Assuming all testing methods are equivalent: Different platforms vary in comprehensiveness and accuracy
By selecting appropriate testing methods that address these challenges, clinicians can obtain accurate CYP2D6 genotype information to guide medication selection and dosing decisions.