title: Novel structure of the CYP2D6 gene that confuses genotyping for the CYP2D6*5 allele.
abstract: We encountered DNA samples which showed a positive product using a long PCR-based method for the detection of CYP2D6*5, indicating deletion of the entire CYP2D6 gene, but the samples did not show a band related to CYP2D6*5 in either XbaI- or EcoRI-RFLP analysis. To achieve genotyping with accuracy, we performed a further genetic analysis to clarify the discrepancy. An unknown 1.6-kb insert was identified in a region downstream from the CYP2D6 stop codon where a specific primer was designed for long-PCR analysis for CYP2D6*5 genotyping. This finding suggested that the CYP2D6 gene might not be deleted in the samples even if a positive product was detected by the long-PCR method. Furthermore, the allelic frequency of this type was found to be approximately 0.3% (4 heterozygous/771 samples) in a Japanese population. In conclusion, we found a novel structure of the CYP2D6 gene, which might lead to incorrect genotyping for CYP2D6*5. Although the long PCR-based strategy for the detection of CYP2D6*5 has been widely used due to its usefulness and convenience, we recommend caution when adopting this method and propose re-evaluating the method for detecting CYP2D6*5.
authors.affiliation: Clinical Evaluation of Medicines and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka, Osaka, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Fukuda
authors.forename: Hiromi
authors.initials: H
authors.lastname: Maune
authors.forename: Yuka
authors.initials: Y
authors.lastname: Ikenaga
authors.forename: Masakazu
authors.initials: M
authors.lastname: Naohara
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Fukuda
authors.forename: Junichi
authors.initials: J
authors.lastname: Azuma
mesh_terms: D000483:Alleles; D015139:Blotting, Southern; D019389:Cytochrome P-450 CYP2D6 / Q000235:genetics*; D017931:DNA Primers; D017353:Gene Deletion; D005787:Gene Frequency; D005838:Genotype; D006801:Humans; D007564:Japan; D008297:Male; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D019389:Cytochrome P-450 CYP2D6