Background: CYP2D6 is a highly polymorphic phase I enzyme that metabolizes 20%-25% of clinically used drugs. The objective of this study was to validate a CYP2D6 genotyping assay with the NanoChip Molecular Biology Workstation.
Methods: We genotyped 200 anonymized human DNA samples with the Pyrosequencing platform at the Medical College of Wisconsin and with the NanoChip platform at Dartmouth Medical School. We compared CYP2D6 genotypes and resolved samples with genotypic discrepancies with the Jurilab CYP2D6 duplication/deletion assay or with traditional DNA sequencing. The Jurilab assay is a long-range PCR assay used to evaluate sequence structures 3' of the CYP2D7 and CYP2D6 coding regions. For the NanoChip platform, we performed multipad addressing and duplicate runs to test the intra- and intercartridge precision, within- and between-run precision, and reproducibility of the defined genotypes.
Results: We used both platforms to genotype all 200 DNA samples for CYP2D6*3, *4, *5, *6, *7, *8, and gene duplication. The 2 methods showed 99.4% concordance in the genotyping results; we found only 8 discrepant genotypes among 1400 DNA analyses. Confirmatory molecular analysis of the discrepant genotypes revealed that the NanoChip assay showed better agreement. The imprecision of the NanoChip method (CV) was 8.9%-17.7%.
Conclusions: This validation study of the NanoChip electronic microarray-based CYP2D6 genotyping assay revealed a CV <20% and good concordance with the Pyrosequencing method and a confirmatory sequencing method.