TaqMan SNP Analysis For APOE Genotyping And SNP Assay

Challenge

Single Nucleotide Polymorphism (SNP) analysis plays a pivotal role in understanding human health and disease. SNPs are the most common type of genetic variation among people, occurring once in every 1,000 nucleotides on average. These tiny variations involve a single DNA building block (nucleotide) substitution. While most SNPs have no direct impact on health, some are crucial in predicting drug response, environmental susceptibility, and disease risk assessment.
Apolipoprotein E (Apo-E) is a protein crucial for lipid metabolism and APOE SNP analysis is crucial because of it’s central role in Alzheimer’s disease (AD) risk. The APOE ε4 allele is the most common genetic risk factor for AD and cognitive decline. However, not all carriers of APOE ε4 develop AD, and understanding why remains challenging. Ethnic variabilities in the APOE locus contribute to AD risk, and haplotype analysis helps unravel this complexity. By assessing SNP frequency profiles, researchers can identify population-specific haplotypes associated with AD. Because of this APOE genotyping are Based on these considerations, SNP analysis of APOE is of interest for pharmacogenomics and as inclusion criteria in various clinical trials. This necessitates coming up with a sensitive and robust assay to identify the APOE SNP.

Solution

A TaqMan assay with distinct fluorescent probes for each of the single nucleotide variations allows discriminate identification of the homozygous or heterozygous of each genotype. For APOE two SNPs rs429358 and rs7412 required two assays to identify the 6 possible SNP genotype variations. Assay was optimized to identify the minimum amount of genomic DNA required for distinct identification of 6 SNP genotypes. Positive controls reflecting the 6 possible genotypes were also identified and used in every assay. A robust assay was developed for use in the screening for inclusion and exclusion of subjects for clinical trial.

Outcome

A sensitive assay for discriminate identification of the APOE genotype was reliably used for screening of recruited subjects to assess if they meet the genotype of interest to be part of the study. A TaqMan assay allowed quick and reproducible identification of the genotype so study team could recruit the subjects for the clinical trial. These assessments make pharmacogenomics an integral part of drug development and discovery. Variations in genetic makeup accounts for differences in medication effectiveness and the occurrence of adverse drug reactions. Pharmacogenomics, although is still in its early stages, holds immense promise to enable the development of personalized therapeutics for widespread health issues such as neurodegenerative diseases, cardiovascular disorders, HIV, cancer, and asthma. By identifying susceptibility polymorphisms and adjusting dosage regimens, pharmacogenomics contributes to drug safety and efficacy during discovery and development.