Optimization and validation of the TaqMan SNP genotyping assay for the APOE gene
APOE (Apolipoprotein E) is the strongest genetic correlate to one’s risk of developing Alzheimer’s disease (AD) outside of the familial AD mutations in APP, PSEN1, and PSEN2. This gene generally exists in three variations - APOE2 (ε2), APOE3 (ε3), and APOE4 (ε4) – which result in protein structural differences that affect their ability to transport amyloid beta and important lipids, such as cholesterol, both important factors in assessing one’s risk of developing AD. The most common allele is ε3, which is considered “neutral” in its risk towards AD, but more than 50% of patients with AD carry the ε4 allele, making it a notable risk factor, while the ε2 allele is considered “protective” against the disease. The combination of the three APOE alleles allows for six possible genotypes as each patient carries two unique copies of the gene. The aim of this project is to create a clinical test that allows for fast and convenient genotyping of APOE by optimizing and validating a TaqMan SNP Genotyping Assay. DNA was extracted from 40 whole blood samples and genotyped with this assay. For each sample, the nucleotides present at SNPs rs429358 and rs7412 were identified and matched with their corresponding genotypes. The TaqMan genotyping results and the next generation sequencing data accompanying each sample were compared to calculate the sensitivity and specificity of each allele for this assay, both of which were 100% for all alleles. Upon completion of the validation process, we believe the patient population to benefit most from this test are patients with a family history of Alzheimer’s disease.
