Optimization of cytochrome P4502D6 (CYP2D6) phenotype assignment using a genotyping algorithm based on allele frequency data

Cytochrome P4502D6 (CYP2D6) is a highly polymorphic gene locus with > 50 va riant alleles which lead to a wide range in enzymatic activity. So called p oor metabolizers are carriers of any two non-functional alleles of the CYP2 D6 gene. CYP2D6 genotyping is cumbersome and the question of how much genot yping is necessary for an accurate phenotype prediction is still debated. T he goal of this study was to determine the optimum amount of genotyping req uired to accurately predict the phenotype at a reasonable cost in a white N orth American population, To address this issue, we designed a polymerase c hain reaction (PCR)/restriction fragment length polymorphism-based genotypi ng strategy to detect 'key' mutations linked to extensive metabolizer or po or metabolizer associated alleles in combination with extra-long PCR (XL-PC R). All mutations with the exception of gene deletions and duplications are detectable by simple restriction digestion analysis and agarose gel electr ophoresis. in addition, we utilized a genotyping algorithm based on our own and published allele frequency data and phenotype analysis to calculate th e probability of a correct genotype (and thus, phenotype) assignment. As li ttle as one XL-PCR reaction followed by a maximum of six reamplification re actions allows an accurate prediction of an individual's genotype to 99.15% . As few as four reamplification reactions identify 97.9% of poor metaboliz er individuals. We evaluated our model in 208 white North Americans by test ing for the presence of 'key' mutations linked to CYP2D6*2, *3, *4, *6, *7, *8, *9, *10, *11, *12, *15, *17 and *18 alleles and the *5, *13 and *16 ge ne deletions. For all individuals, the correct phenotype has been predicted . Discordant phenotype assignment occurred in only two individuals which su bsequently was attributed to CYP2D6 inhibition by concomitant drug therapy. Pharmacogenetics 9:669-682 (C) 1999 Lippincott Williams & Wilkins.