Frequency of undetected CYP2D6 hybrid genes in clinical samples: impact on phenotype prediction.

Cytochrome P450 2D6 (CYP2D6) is highly polymorphic. CYP2D6-2D7 hybrid genes can be present in samples containing CYP2D64 and CYP2D610 alleles. CYP2D7-2D6 hybrid genes can be present in samples with duplication signals and in samples with homozygous genotyping results. The frequency of hybrid genes in clinical samples is unknown. We evaluated 1390 samples for undetected hybrid genes by polymerase chain reaction (PCR) amplification, PCR fragment analysis, TaqMan copy number assays, DNA sequencing, and allele-specific primer extension assay. Of 508 CYP2D64-containing samples, 109 (21.5%) harbored CYP2D668 + 4-like, whereas 9 (1.8%) harbored CYP2D64N + 4-like. Of 209 CYP2D610-containing samples, 44 (21.1%) were found to have CYP2D636 + 10. Of 332 homozygous samples, 4 (1.2%) harbored a single CYP2D7-2D6 hybrid, and of 341 samples with duplication signals, 25 (7.3%) harbored an undetected CYP2D7-2D6 hybrid. Phenotype before and after accurate genotyping was predicted using a method in clinical use. The presence of hybrid genes had no effect on the phenotype prediction of CYP2D64- and CYP2D610-containing samples. Four of four (100%) homozygous samples containing a CYP2D7-2D6 gene had a change in predicted phenotype, and 23 of 25 (92%) samples with a duplication signal and a CYP2D7-2D6 gene had a change in predicted phenotype. Four novel genes were identified (CYP2D613A1 variants 1 and 2, CYP2D613G1, and CYP2D613G2), and two novel hybrid tandem structures consisting of CYP2D613B + *68×2 + 4-like and CYP2D613A1 variant 2 + *1×N were observed.