Discrepancy in genotyping of Apolipoprotein e between allele-specific PCR and fluorescence resonance energy transfer or sequencing

The human apolipoprotein E (APOE) gene contains several single-nucleotide polymorphisms (SNPs) that are distributed across the gene. The genotype of the APOE gene has important implications as a risk factor for various diseases. We observed 2 cases in which the results of allele-specific PCR (AS-PCR) of the APOE gene were not consistent with those of fluorescence resonance energy transfer (FRET) or sequencing analysis. In these cases, genotyping by AS-PCR showed that patients were ε2 homozygotes, while sequencing analysis and FRET showed that they were ε2/ε3 heterozygotes. Herein, we describe the causes of the errors in genotyping and describe the significance of these errors.