Pharmacogenomics Profiling to Identify Biomarkers of Drug Response

Pharmacogenomics (PGx) can enhance the accuracy of targeting patient therapy by enabling the use of an individual’s genome to assist predict drug response and guide optimal drug and dose selection. Ultimately, the goal is to provide safer, more impactful, and cost-effective treatment in patient therapy. Traditionally, pharmacogenomics is implemented reactively when there is a need to prescribe a high-risk drug. This is often expensive and suffers from a slow turnaround time. The field now recognizes the results and recommendations from pharmacogenomic profiling should be available preemptively in electronic health records and drug prescription systems.

Both pharmacogenomics research and clinical testing are converging from sequencing of the whole genome and testing of single targets, respectively, toward screening a panel of genes of pharmacological importance (pharmacogenes) and associating their variants to drug response. Amplicon-based targeted sequencing is an ideal approach for this screening because it is cost-effective and easy to implement in the laboratory. The workflow is fast and simple to carry out and allows researchers and assay developers to focus only on the pharmacogenes being investigated.

CleanPlex® NGS Panels – Simple, Affordable Solution for Pharmacogenomics Profiling

How Does NGS Amplicon Sequencing for Pharmacogenomics Work?

Next-Generation Sequencing technology for Pharmacogenomic genetic testing works by helping to identify potential new biomarkers and genetic variation in genes. When selecting targets, it’s critical to select genes that are clinically actionable and have strong evidence linking them to drug metabolism, efficacy, and toxicity. However, the gene list may vary depending on the population being tested and the drugs commonly prescribed in that population. PGx sample sources blood, extracted DNA (gDNA), buccal swabs, or saliva samples.

Product Highlight: Pre-Designed Pharmacogenomics Research Panel

Our Pre-designed Research Panel is suited to evaluate how an individual’s genetic variations impact drug efficacy and metabolism. The panel includes genes such as ADRA2A, CYP2C19, CYP2C9, DPYD, F2, HLA-B, VKORC1, SLCO1B1, but targets can be easily revised per application.

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Product Highlight: Pre-Designed Pharmacogenomics Research Panel

Our Pre-designed Research Panel is suited to evaluate how an individual’s genetic variations impact drug efficacy and metabolism. The panel includes genes such as ADRA2A, CYP2C19, CYP2C9, DPYD, F2, HLA-B, VKORC1, SLCO1B1, but targets can be easily revised per application.

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Obtain Accurate, Reproducible, and Highest-Quality Results to Predict Efficacy and Side Effects of Drugs

A third-party organization (an advanced molecular diagnostics company focused on precision medicine, non-invasive cancer testing, and digital health) developed CLIA-approved pharmacogenomics (PGx) NGS assay powered by Paragon Genomics’ CleanPlex technology. It was able to leverage CleanPlex technology’s ultra-high amplicon multiplexing capacity and extremely low PCR background to build a large 180-gene high-level evidence PGx panel that is both highly efficient and affordable. The NGS assay features a single-tube workflow that is easy to perform and minimizes the risk of handling errors.

CleanPlex Technology Highlights:

  • Scalable High-Throughput System. Target thousands of relevant markers in the same assay.
  • Fast Turnaround Time. Get custom assays delivered in 4 to 6 weeks. Our PhD-level expert scientists are here to provide speedy and comprehensive support throughout the design, ordering, and technology adoption process, including excellent after-sales technical support.
  • Cost-Effective Solution. Process thousands of samples at a time on the Illumina® platform.
  • Minimizes consumable consumption. This single-plate workflow reduces consumable costs and loss of material from the material transfer.
  • Streamlined, Automation-Friendly Workflow. Generate sequencing-ready libraries in just 3 hours using a simple, three-step protocol that can be easily automated.
  • High-Quality, Reproducible Results. Prepare high-quality NGS libraries with high marker call rates and efficient use of sequencing reads.

What do you need to get started with a custom panel design?

We only require the targeted bases you’re interested in and the reference genome for the genetic variants of interest. The bases can be provided as a BED file and submitted to our design portal:

How many samples can I sequence together?

Paragon Genomics NGS technology uses a multiplexed approach that allows users to interrogate large variants of interest across hundreds to thousands of samples. We support 2688 Illumina combinatorial indexes for high-throughput workflows. Our high uniformity of amplification, high mapping rates, and on-target rates enable efficient use of sequencing space. For example, for a 1000 amplicon panel, up to 150 samples can be fit on a Miseq and 1300 samples on a NextSeq with an average of 100X coverage.

What are the benefits of Pharmacogenomics?

  • Personalized medicine: Pharmacogenomics can enable personalized treatment plans tailored to an individual’s genetic makeup, improving the efficacy and safety of medications.
  • Improved drug efficacy: By identifying genetic variants that affect drug metabolism and efficacy, pharmacogenomics can help optimize drug selection and dosing, leading to better treatment outcomes.
  • Reduced adverse drug reactions: Pharmacogenomics can identify genetic variants that increase the risk of adverse drug reactions, allowing for proactive measures to minimize the risk or avoid the drug altogether.
  • Cost savings: By reducing the risk of adverse drug reactions and optimizing drug selection and dosing, pharmacogenomics can lead to cost savings by avoiding unnecessary treatments and hospitalizations.

What is Pharmacogenomics testing used for?

The primary goal of Pharmacogenomics testing is to identify medications that pose a risk to individuals and to therefore only select medications that will be the most effective and safest option for treatment.

What are the limitations of Pharmacogenomics?

  • Limited evidence: There may be limited evidence linking genetic variants to drug response variability or clinical outcomes, particularly for rare genetic variants.
  • Complex inheritance patterns: Many genetic variants associated with drug response are inherited in a complex manner, involving multiple genes and environmental factors, making it difficult to predict drug response with high accuracy.
  • Ethnic variability: Genetic variation can differ significantly among different ethnic groups, which can affect the applicability of pharmacogenomic testing in diverse populations.
  • Cost and accessibility: Pharmacogenomic testing can be expensive and may not be covered by insurance, making it less accessible to some patients.
  • Lack of standardization: There is currently a lack of standardization in pharmacogenomic testing, including variant selection, testing methodology, and interpretation of results, leading to variability in test accuracy and clinical utility.
  • Ethical and legal issues: Pharmacogenomic testing can raise ethical and legal issues related to privacy, informed consent, and discrimination based on genetic information.

High-Performance Targeted Sequencing Solution for Pharmacogenomics Profiling

CleanPlex Custom NGS Panels offer excellent performance and a high level of customization to help you build smarter NGS assays. To create a custom panel for pharmacogenomics profiling, schedule a free consultation below by entering your email address.

Free Consultation

Schedule a free consultation with our design team to learn how we can help you develop a NGS research solution to advance your genotyping projects.