TaqMan systems for genotyping of disease-related polymorphisms present in the gene encoding apolipoprotein E

Polymorphisms of the gene encoding apolipoprotein E have been implicated in the pathogenesis of peripheral and coronary artery disease and neurodegenerative disorders such as sporadic and late-onset familial forms of Alzheimer's disease. We have developed TaqMan assay systems for the single nucleotide polymorphisms -219G/T, located in the promoter of the apolipoprotein E gene, 113G/C, present in the transcriptional enhancer element of intron 1, 334T/C, determining Cys or Arg as amino acid residue 112 of mature apolipoprotein E, and 472C/T, determining Arg or Cys as residue 158. The accuracy of genotype determination with the TaqMan systems was demonstrated by analyses with restriction endonucleases. We determined the genotypes of the apolipoprotein E polymorphisms in 2349 study subjects. The genotypes were distributed as: -219GG=27.3%, -219GT=49.1%, and -219TT=23.6% (p=0.435); 113GG=41.3%, 113GC=45.2%, and 113CC=13.5% (p=0.343); 334TT=73.4%, 334TC=24.7%, and 334CC=1.9% (p=0.539); 472CC=86.3%, 472CT=12.8%, and 472TT=0.9% (p=0.004) (Hardy-Weinberg equilibrium estimates are given in parentheses). The allele combinations which define the three major isoforms of apolipoprotein E, namely apoE2, apoE3, and apoE4, had the following allele frequencies: 334T/472T (ε2, 112Cys/158Cys)=7.3%, 334T/472C (ε3, 112Cys/158Arg)=78.4%, and 334C/472C (ε4, 112Arg/158Arg)=14.2%, respectively. ApoE genotypes were distributed as: ε2ε2= 0.9%, ε2ε3= 11.2%, ε2ε4=1.6%, ε3ε3=61.3%, ε3ε4=23.1%, and ε4ε4= 1.9% (p=0.014). The TaqMan assays allow for fast and sensitive genotyping and are especially suitable for studies including large numbers of participants.