Identification of Subtypes of CYP2D Gene Rearrangements among Carriers of CYP2D6 Gene Deletion and Duplication

Abstract

Background: Cytochrome P450 2D6 (CYP2D6) is one of the best-known polymorphic drug-metabolizing enzymes. Rapidly evolving genotyping techniques permit the identification of single-nucleotide polymorphisms (SNPs) and thereby a prediction of individual metabolic capacities for CYP2D6 substrates. A considerable part of interindividual variability in CYP2D6 enzyme activity, however, is not related to SNPs but to gene deletions and duplications. Currently used genotyping methods assume that these gene rearrangements are homogeneous. Methods: We analyzed the interindividual variability in CYP2D6 gene arrangements in genomic DNA from 740 Caucasian individuals by allele-specific PCR to identify common SNPs of the CYP2D6 gene that correspond to the variant alleles CYP2D6*3, *4, and *9. We investigated the presence and variability of CYP2D6*5 (gene deletion), CYP2D6x2 (gene duplication), and CYP2D6xn (gene amplification) by EcoRI and XbaI restriction fragment length polymorphism analyses and by long PCR plus KpnI and BamHI digestion. The presence of new mutations at the CYP2D locus was analyzed by sequencing. Results: CYP2D6 gene rearrangements were present in >12% of individuals. Variability in the rearrangements regarding both gene deletion and gene duplication existed, and one of the unusual arrangements led to incorrect phenotype prediction. The frequency for carriers of unusual gene rearrangements was <0.3% (95% confidence interval, 0%-0.6%) in the population studied. Conclusions: Heterogeneity in CYP2D6 gene rearrangement exists, but the allele frequency indicates that the risk for an erroneous phenotype prediction related to

Allelic distributions of CYP2D6 gene copy number variation in the Eastern Han Chinese population

“…Because individuals homozygous for CYP2D6*5 are very rare, with a frequency of less than 0.5% [10,26] , the 4.8 kb fragment also functions as a positive control for the amplification. In order to increase the efficiency of amplification, we used primer DuplF instead of DPKup, since the former does not form a hairpin structure and yields a shorter PCR product when combined with primer DPKlow [24] .…”

“…It is a semiquantitative method for the detection of the CYP2D6 gene copy number. Unusual CYP2D6 gene rearrangement may confuse the determination of the CYP2D6 gene copy number, but it occurs very rarely [26,34,35] . Long PCR are specific, costless and convenient for detecting CYP2D6 gene rearrangements.…”

The genomic architecture of segmental duplications and associated copy number variants in dogs

“…The set of copy number variable genes possess a wide spectrum of PANTHER molecular functions (Supplemental Tables 2,5), and provides a rich resource for testing hypotheses on the genetic basis of phenotypic variation within and among breeds. For example, in humans, copy number variation of cytochrome P450 genes, such as CYP2D6, contributes to interindividual variation in drug metabolism phenotypes (Daly 2004;Ledesma and Agundez 2005;Ouahchi et al 2006). Similar to humans, adverse drug responses have been described in dogs, which often show marked variation in prevalence between breeds (Hickford et al 2001;Mealey et al 2001Mealey et al , 2003Nelson et al 2003;Neff et al 2004;Trepanier 2004).…”

Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

“…In human, CYP2D6, one of the best-known polymorphic drug-metabolizing enzymes [57], is flanked by a 2.8 kb repeat sequence (CYP-REP element) containing an Alu element and a tandem 10-bp direct repeat in the wild type allele [61]. The remarkable degree of interindividual variability at the CYP2D6 locus is largely due to gene deletion and amplification of CYP2D6 generated through homologous unequal recombination of no-allelic CYP-REP elements [61,62].…”