Background: We found a genomic DNA (N=1) associated with an unidentified 11-kb EcoRI haplotype of CYP2D6 and with amplification of the CYP2D6*5 specific polymerase chain reaction (PCR) product without the 11.5-kb XbaI haplotype in a Japanese woman. We developed a long PCR assay to distinguish CYP2D6*5 and the novel mutant allele, and we evaluated the PCR method on 162 different genomic DNA samples.
Methods: Long PCR assays were performed to amplify a fragment specific for the novel mutant allele and to exclude coamplification of CYP2D6*5.
Results: A 1692-bp PCR product was amplified from the DNA sample with the novel mutant allele, while the PCR product was not amplified from any of the 162 DNA samples.
Conclusions: The long PCR assay enabled the detection of the novel mutant allele associated with an 11-kb EcoRI haplotype. Further population studies are required to confirm the frequency of the novel mutant allele in various populations, as it may be contained in samples reported as CYP2D6*5.