, Volume 61, Issue 12, pp 887-892
Date: 24 Nov 2005

Rapid genotyping for relevant CYP1A2 alleles by pyrosequencing

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Abstract

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.