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Rapid genotyping for relevant CYP1A2 alleles by pyrosequencing.

Skarke C, Kirchhof A, Geisslinger G, Lötsch J

pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany. skarke@em.uni-frankfurt.de

OBJECTIVE: To develop a rapid and reliable screening method for identifying the relevant cytochrome P450 (CYP) 1A2 alleles CYP1A2*1D (-2467Tdel), *1F (-163A>C), and *1K (-739T>G, -729C>T, -163A>C) that are in linkage disequilibrium with the functionally relevant CYP1A2 polymorphisms and therefore are considered to be predictive for the CYP1A2 phenotype. METHODS: CYP1A2 single nucleotide polymorphisms (SNPs) -2467Tdel, -739T>G, -729C>T, and -163A>C were screened for in 495 healthy Caucasian volunteers using newly developed pyrosequencing duplex and simplex assays. Conventional sequencing of randomly selected samples served as quality control. RESULTS: Frequencies were 7.9% for CYP1A2*1D, 31.8% for *1F, and 0.4% for *1K. The observed distribution of homozygous and heterozygous carriers of the alleles corresponded to the predicted one according to the Hardy-Weinberg law. It also corresponded to reported allelic frequencies from Caucasians but differed significantly from the distribution seen in other ethnicities. The most frequent haplotype was -2467T/-739T/-729C/-163A (allelic frequency 61.6%), followed by -2467T/-739T/-729C/-163C (30.5%), -2467Tdel/-739T/-729C/-163A (5.1%), -2467Tdel/-739G/-729C/-163A (1.2%), and -2467Tdel/-739T/-729C/-163C (1.1%). Complete linkage disequilibrium (value of D' nearly 1) existed between -2467Tdel, -739T>G, and -729C>T and between -729T>G and -163A>C. CONCLUSIONS: Pyrosequencing facilitates rapid and reliable detection of those CYP1A2 alleles that, based on current knowledge, can be considered predictive for the CYP1A2 phenotype.

Published 19 December 2005 in Eur J Clin Pharmacol, 61(12): 887-92.
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