Sample Submission Guidelines
What is APOE Genotyping?
APOE genotyping is a molecular technique used to identify the specific genetic variants, or alleles, of the Apolipoprotein E (APOE) gene. It is a fundamental tool for researchers investigating lipid metabolism and neuronal function. The APOE gene codes for a protein that is a primary cholesterol carrier, making it a central target for basic research.
The Biology of APOE Alleles: ε2, ε3, and ε4
The three major APOE alleles (ε2, ε3, and ε4) are defined by amino acid changes at two key positions (112 and 158). These differences are caused by two single nucleotide polymorphisms (SNPs): rs429358 and rs7412. This allelic variation is the primary driver for functional research into the protein's role.
| Allele | Key SNP (rs429358) | Key SNP (rs7412) | Amino Acid at 112 | Amino Acid at 158 |
|---|---|---|---|---|
| ε2 | T | T | Cys | Cys |
| ε3 | T | C | Cys | Arg |
| ε4 | C | C | Arg | Arg |
Why is APOE Genotyping Critical for Research?
The different APOE isoforms (E2, E3, and E4) specified by these alleles fundamentally alter the protein's structure. This structural change directly impacts its ability to bind lipids and interact with receptors (like the LDLR family).
Understanding this genotype-phenotype relationship is crucial for researchers investigating the basic mechanisms of:
- Neuronal lipid transport and maintenance
- Synaptic plasticity
- Amyloid-beta (Aβ) clearance pathways
- Overall cholesterol homeostasis
APOE genotyping allows researchers to confidently classify their in vitro and in vivo models (such as iPSCs or transgenic mice), ensuring their experimental data is robust, reproducible, and correctly interpreted.
APOE Genotyping Applications (For Research Use Only)
Our high-fidelity APOE genotyping service provides foundational data for a wide range of non-clinical research applications. All services are strictly for Research Use Only (RUO) and are not intended for clinical or diagnostic use.
Neurodegeneration Research
The APOE gene is the most significant genetic factor in studies of late-onset Alzheimer's disease (AD) mechanism. Our service enables researchers to:
- Elucidate Aβ Mechanisms: Investigate how different APOE isoforms (E2, E3, E4) modulate the clearance and aggregation of amyloid-beta (Aβ) peptides in vitro and in vivo.
- Study Tau Pathology: Explore the functional relationship between APOE genotype and the development of Tau phosphorylation and associated neuronal pathology.
- Model Synaptic Function: Characterize iPSC-derived neurons or astrocytes to understand how APOE alleles impact lipid transport, synaptic plasticity, and overall neuronal health.
Lipid Metabolism & Cardiovascular Research
APOE is a central node in lipid metabolism. Genotyping is essential for basic research aimed at:
- Understanding Cholesterol Homeostasis: Studying how APOE isoforms differentially bind to lipids and interact with receptors, such as the low-density lipoprotein receptor (LDLR).
- Characterizing Metabolic Models: Validating the genetic background of animal models used in atherosclerosis, dyslipidemia, and metabolic pathway research.
Pharmacogenomics (PGx) Research
APOE genotype can influence metabolic pathways. Our service supports foundational PGx research to:
- Investigate Differential Responses: Understand the genetic basis for varied responses to research compounds in preclinical models.
- Support Drug Discovery: Classify cell lines and in vivo models to screen for compounds that may modulate APOE-related pathways.
Characterizing Cell Lines & Animal Models
Confidence in your model system is paramount. Before beginning a costly or lengthy experiment, use our rapid service to:
- Verify iPSCs and Cell Lines: Confirm the APOE genotype of your human-derived cell lines (e.g., iPSCs, astrocytes, microglia).
- Validate Transgenic Models: Ensure the genetic integrity of your APOE knock-in or transgenic animal colonies.
Why Choose CD Genomics for Your APOE Genotyping?
We provide the definitive, publication-ready data you need to move your research forward with confidence. We focus on three key advantages: accuracy, speed, and value.
Uncompromising Accuracy (Publication-Ready Data)
We provide definitive, gold-standard results. Our allele-specific qPCR (AS-qPCR) platform avoids the ambiguity of melting curve (HRM) analysis, saving you from costly re-runs, false interpretations, and ensuring your published data is reliable.
Cost-Effective & Scalable (Maximize Your Budget)
Get the accuracy of sequencing at a fraction of the cost. Our validated AS-qPCR platform is highly efficient and scalable, offering competitive pricing for large-scale cohort studies, CRO partnerships, and core facilities.
Dedicated Scientific Support (Partners in Research)
You are not just an order number. From initial project design to data interpretation, our team of Ph.D-level experts is available to discuss your project and ensure its success.
Our APOE Genotyping Platform: Accuracy You Can Publish
Our platform's design is focused on one goal: delivering an unambiguous and accurate result. We achieve this by using a superior methodology.
The Gold Standard: Allele-Specific qPCR (AS-qPCR)
Our service employs a high-discrimination, probe-based AS-qPCR method. This technique uses specific primers that will only amplify a target if the correct allele (ε2, ε3, or ε4) is present, combined with a fluorescent probe for definitive confirmation. The result is a simple, binary "yes/no" answer for each allele, providing robust and easy-to-interpret data.
Why AS-qPCR is Superior to Melting Curve Analysis (HRM)
Many commercial assays use a less precise method called High-Resolution Melting (HRM).
- HRM Ambiguity: This method relies on detecting tiny shifts in a DNA melting curve to differentiate genotypes. This can be notoriously difficult to interpret and is highly sensitive to primer-dimers, non-specific amplification, or contaminants, leading to ambiguous or incorrect calls.
- Our AS-qPCR Advantage: Our probe-based system is not affected by these issues. It does not analyze a melt curve; it only produces a signal if the correct target is 100% present. This delivers confidence, not complexity.
Our APOE Genotyping Service Workflow
Our process is designed for speed and accuracy from start to finish.
- Consultation & Sample Submission: Contact our experts to discuss your project. Ship your gDNA, blood, or swab samples using our provided guidelines.
- Stringent Sample QC: All incoming samples undergo rigorous quality control (concentration, purity) to ensure they are suitable for analysis.
- AS-qPCR Genotyping: Samples are run on our validated AS-qPCR platform in triplicate, with all necessary positive and negative controls.
- Data Analysis & Report Delivery: Our informatics team analyzes the amplification data, makes the definitive genotype call, and delivers your secure, comprehensive report.
Case Study: 100% Concordance with Sequencing
Our methodology is based on validated, published, and peer-reviewed science. The AS-qPCR platform we employ has been rigorously tested against the gold standard of DNA sequencing.
Based on: Liu, G., et al. "A rapid and cost-effective method for genotyping apolipoprotein E gene polymorphism." Molecular Neurodegeneration 11, 6 (2016).
DOI: 10.1186/s13024-016-0069-4
Project Goal
To develop and validate a rapid, high-throughput, and cost-effective APOE genotyping method that matches the accuracy of DNA sequencing.
Methodology
An allele-specific real-time PCR (AS-qPCR) assay was developed to identify the ε2, ε3, and ε4 alleles. To validate the method, 1,158 human DNA samples were genotyped in parallel using both the new AS-qPCR method and traditional DNA sequencing.
Results
The AS-qPCR method achieved 100% concordance across all 1,158 samples when compared to the gold-standard DNA sequencing results. The method successfully and accurately identified all six possible APOE genotypes (e.g., ε2/ε3, ε3/ε4, ε4/ε4, etc.).
Conclusion
The study confirms that an AS-qPCR-based method is an extremely accurate, rapid, and robust platform for APOE genotyping. This validation provides high confidence that our service delivers data equivalent to sequencing, but with a significant improvement in speed and cost-effectiveness for researchers.
Figure Caption: Fig. 3 (Liu et al., 2016): Validation of the AS-qPCR method. The allele-specific PCR results (top) show 100% concordance with the gold-standard DNA sequencing results (bottom) for all six human APOE genotypes.
Comprehensive Genotype Report
You will receive a secure, publication-ready PDF report containing:
- A clear, definitive APOE genotype call (e.g., ε3/ε4)
- A full summary of the input sample QC (concentration, purity)
- Raw amplification data (Ct values) and assay quality metrics
Accepted Sample Types for Research
| Sample Type | Minimum Volume / Amount | Notes |
|---|---|---|
| Genomic DNA (gDNA) | ≥ 200 ng (at ≥ 10 ng/μL) | OD260/280 ratio: 1.8–2.0. No degradation. |
| Whole Blood | ≥ 500 μL | Collect in EDTA (purple-top) tubes. |
| Oral (Buccal) Swab | 2 swabs | Use recommended collection kit. |
| Cell Lines | ≥ 1 × 10⁶ cells | Submit as frozen pellet. |
Frequently Asked Questions (FAQ)
1. What is APOE genotyping?
APOE genotyping is a molecular technique used to identify the specific genetic variants, or alleles, of the Apolipoprotein E (APOE) gene. It specifically determines the combination of two key SNPs (rs429358 and rs7412), which result in the three main alleles: ε2, ε3, and ε4.
2. What is the role of the APOE gene in research?
The APOE gene is a central focus of research due to its critical role in lipid metabolism. The protein it codes for, Apolipoprotein E, is a primary cholesterol carrier in the brain and periphery, making it a key research target for understanding lipid transport, neuronal maintenance, and synaptic plasticity.
3. What are the APOE ε2, ε3, and ε4 alleles?
The ε2, ε3, and ε4 alleles are the three primary isoforms (versions) of the APOE gene. They differ by single amino acid changes at positions 112 and 158. These structural differences alter the protein's ability to bind to lipids and receptors, forming the basis for extensive research into their functional consequences.
4. What is the best method for APOE genotyping?
While several methods exist, allele-specific qPCR (AS-qPCR) and DNA sequencing are considered gold standards for accuracy. AS-qPCR provides a highly sensitive, rapid, and cost-effective solution that has been validated to have 100% concordance with sequencing, avoiding the interpretation challenges of older methods like melting curve analysis.
5. What is the difference between APOE genotyping and sequencing?
APOE genotyping is a targeted assay that specifically determines the known ε2/ε3/ε4 alleles. Whole genome or exome sequencing, in contrast, analyzes the entire gene (or genome) for all variations. For focused APOE studies, genotyping is significantly faster and more cost-effective.
6. What samples are suitable for APOE genotyping?
Our platform is validated for a flexible range of research inputs, including genomic DNA (gDNA), whole blood (preserved in EDTA), and buccal (oral) swabs.
What is the most accurate method for APOE genotyping?
7. Why choose allele-specific qPCR over melting curve analysis?
AS-qPCR eliminates the ambiguity of HRM analysis by detecting each allele with high discrimination and specificity.
Accelerate Your Research with Definitive APOE Genotyping
Stop relying on ambiguous assays. Partner with CD Genomics for high-confidence, publication-ready APOE genotyping. Contact our scientific team today to discuss your project and receive a no-obligation quote.
References:
- Validated according to: Liu, G. et al. "A rapid and cost-effective method for genotyping apolipoprotein E gene polymorphism." Molecular Neurodegeneration 11, 6 (2016)."
- Hixson, J. E., & Vernier, D. T. (1990). Restriction isotyping of human apolipoprotein E by gene amplification and cleavage with HhaI. Journal of Lipid Research, 31(3), 545–548.
- Corder, E. H., et al. (1993). Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late-onset families. Science, 261(5123), 921–923.
- Mahley, R. W., & Rall, S. C. Jr. (2000). Apolipoprotein E: far more than a lipid transport protein. Annual Review of Genomics and Human Genetics, 1, 507–537.
- Eichner, J. E., Dunn, S. T., Perveen, G., Thompson, D. M., Stewart, K. E., & Stroehla, B. C. (2002). Apolipoprotein E polymorphism and cardiovascular disease: a HuGE review. American Journal of Epidemiology, 155(6), 487–495.
