CYP2D6: novel genomic structures and alleles

Abstract

Objective CYP2D6 is a polymorphic gene. It has been observed to be deleted, to be duplicated and to undergo recombination events involving the CYP2D7 pseudogene and surrounding sequences. The objective of this study was to discover the genomic structure of CYP2D6 recombinants that interfere with clinical genotyping platforms that are available today. Methods Clinical samples containing rare homozygous CYP2D6 alleles, ambiguous readouts, and those with duplication signals and two different alleles were analyzed by long-range PCR amplification of individual genes, PCR fragment analysis, allele-specific primer extension assay, and DNA sequencing to characterize alleles and genomic structure. Results Novel alleles, genomic structures, and the DNA sequence of these structures are described. Interestingly, in 49 of 50 DNA samples that had CYP2D6 gene duplications or multiplications where two alleles were detected, the chromosome containing the duplication or multiplication had identical tandem alleles. Conclusion Several new CYP2D6 alleles and genomic structures are described which will be useful for CYP2D6 genotyping. The findings suggest that the recombination events responsible for CYP2D6 duplications and multiplications are because of mechanisms other than interchromosomal crossover during meiosis.

Frequency of Undetected CYP2D6 Hybrid Genes in Clinical Samples: Impact on Phenotype Prediction

“…For example, CYP2D6*4 is a subfamily with A to N members, and each has different SNPs associated with the defining SNP for CYP2D6*4: 1846GϾA. CYP2D6*4N has a gene conversion to CYP2D7 in exon 9, whereas CYP2D6*4-like, which is mentioned in this article, is different from CYP2D6*4N by the fact that it lacks a conversion to the CYP2D7 sequence in exon 9 (Kramer et al, 2009). Genotyping platforms are not designed to detect the exact allele present in the CYP2D6*4 subfamily so the suffix of A to N is often omitted in clinical genotyping results.…”

“…CYP2D6-2D7 and CYP2D7-2D6 genes were detected by PCR using primers specifically designed to allow them to be amplified as described in Kramer et al (2009) (Table 1; Figs. 1 and 2).…”

“…We recently described the CYP2D6*68 ϩ *4-like and CYP2D6*4N ϩ *4-like hybrid tandem arrangements (Kramer et al, 2009), and others described CYP2D6*36 ϩ *10 (Chida et al, 2002;Gaedigk et al, 2006). These three structures are of the CYP2D6-2D7 ϩ CYP2D6 hybrid tandem variety (Fig.…”

“…CYP2D6-2D7 and CYP2D7-2D6 genes will cause failure of A and/or B amplicon generation during the PCR step, depending upon the location of the switch from CYP2D6 to CYP2D7 sequence. Because there is a tendency for the CYP2D6 portions in the hybrid tandem gene to be identical to the CYP2D6 portion in the normal gene (Kramer et al, 2009), the kit will not detect partial failures in the ASPE step. In the case of a single CYP2D7-2D6 gene, total failure of PCR of the hybrid gene can occur, which can lead to a homozygous call on the basis of amplification of the nonhybrid allele.…”

“…2B), an example of which is CYP2D6*13A2 (EU530609) ϩ *2A (Kramer et al, 2009;Gaedigk et al, 2010a). The aim of this study was to determine the frequency of hybrid genes present in a large number of samples originally genotyped using the Luminex Tag-It Mutation Detection Kit for Cytochrome P450 2D6 (CYP2D6 ASPE kit) and to identify the impact of these variants on phenotype prediction.…”