A long PCR assay to distinguish CYP2D6*5 and a novel CYP2D6 mutant allele associated with an 11-kb EcoRI haplotype.

BACKGROUND

We found a genomic DNA (N=1) associated with an unidentified 11-kb EcoRI haplotype of CYP2D6 and with amplification of the CYP2D65 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 CYP2D65 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.