How to navigate through pharmacogenomics report on practitioner portal?

How to navigate through pharmacogenomics report on practitioner portal?

Written by: Nermin Đuzić, M.Sc. in Genetics, Content Specialist

Peer-reviewed by: Edin Hamzić, Ph.D. in Genetics, Chief Science Officer

Recently we have released our brand new product - pharmacogenomics report. In the previous article, we provided a brief introduction to pharmacogenomics as a young yet very popular scientific branch combining pharmacology and genomics. Pharmacogenomics explains how people respond differently to certain medications based on their unique genetic makeup.

To recall briefly, what we do in the pharmacogenomics report is to analyse individual genetic variants and their interactions with medications (i.e. gene-drug interactions) and the cumulative effect they have on specific phenotypes/diseases. 

We have a different way of representing pharmacogenomics results to users/customers and practitioners. The main difference is that our users visualize results via mobile app, and practitioners use the practitioners portal to access the results they should explain to their clients/customers. If you want to learn more about how to access and use portal, you can visit our library.

In this article, we aim to provide a guideline for navigating the pharmacogenomics report on the practitioners portal.  Below we provide stepwise instructions on how to navigate reports with all variables and terms explained. If you want to learn more about how to navigate through pharmacogenomics report from a user perspective using a mobile app, then please redirect here.

1. Personal and introductory information

Figure 1: Introductory view

Once you accept the session you are able to start exploring the pharmacogenomics report. Here we provide an example or demo for a BioCertica dummy user.

On the top of the report you will see introductory and personal information for your client, as well as any current therapy that the user is taking. It is important to take this information into account when considering other gene-drug and drug-drug interactions and their effect on user’s phenotype/disease, as it will probably affect the consultations and prescription you reccommend to your client. Once you finish exploring and analysing the report and results you can go to “Write a journal note” and close the session.

2. Quick & Custom view

Once you come to the main part of report, you have the option to view the results in two ways: 

  • Quick view
  • Custom view

2.1. What is Quick View and how to use it?

Figure 2: Quick view

Quick view (Figure 2) provides the all results paginated and adjusted for a brief look into results. You are able to see the drug names, class, category, phenotype category, user genetic information, and annotation text. On the other hand, the custom view (Figure 3) enables you to filter results according to relevant variables.

2.2. What is Custom View and how to use it?

Figure 3: Custom view’s main screen

The advantage of custom view is that it allows you to choose exactly what you want to visualize in your report. For example, if your client is suffering from high blood pressure, you may only want to check drugs that would help treat that condition. To enable custom view, you have to activate at least 3 out of 4 available filter options:

  • Phenotype category
  • Specialty population
  • Level of evidence
  • Disease

To filter for disease, one must first filter for the previous three variables. After you finish filtering, you will end up with a similar results representation as you get on quick view. Below is a visual representation of the custom view with filters applied for hypertension (Figure 4).

Figure 4: Custom view with applied filters for hypertension
3. Explanation of variables and terms within the report

Whether you look at the quick or custom view, or you filter results according to what you find the most relevant and useful, there are several technical terms you have to be familiar with in order to get the most out of this report. We will briefly explain each of them, starting with variables used in filtering.

1. Phenotype category

Phenotype category describes the effect that a drug has on the body, its nature in gene-drug interactions, or the category of gene-drug annotation according to what effect the drug has. Therefore, it can have one or more of the following effects:

  • Toxicity - if the drug is toxic to the body and causes side effects or increases the risk for certain disorders or complications when associated with a specific genetic variant.
  • Efficacy - mainly refers to the increased or decreased effect of a drug in alleviating symptoms of a specific disease
  • Dosage - claims whether to increase or decrease the dosage of a specific drug given the specific gene variants
  • Metabolism/PK - Pharmacokinetics describes the fate of drug administered to a body, or in other words, what the body does to the drug or how it circulates through the metabolism of the body.
  • Other - this category comprises of gene-drug interactions that are not encompassed by any of the above-mentioned categories. 

2. Specialty population

This variable has two possible options: pediatric and non-pediatric. The pediatric tag refers to any gene-drug interaction or annotation with at least one variant associated with children or infants, or the literature supporting that evidence is “pediatric”. Otherwise, the gene-drug interaction is considered to be non-pediatric and applies to adults only.

3. Level of evidence

Figure 5: Different levels of evidence. Learn more here.

Each gene-drug association described by annotation text (example given below) is supported and proven by a study and reported by curators at the PharmGKB website. All these gene-drug interactions have their level of evidence, which depicts the strength, reliability and certainty behind the annotation text. The evidence level goes from 1A to 4, where 1A represents the highest level of evidence, and 4 represents unsupported findings (Figure 5).

4. Disease

This represents a specific disease that is affected by particular gene-drug interaction.

5. Drug names

The first column in results section includes drugs with their generic name. Moreover, we also provide trade names as they are in the United States(US name) or South Africa (SA name).

6. Drug class & category

Although sometimes used interchangeably and causing confusion, these two terms have different meanings. Drug category refers to a type of drug from a medical perspective, according to organic systems and conditions they are used to treat. Drug class represents the categorization from a pharmacological perspective, mechanism of action and the biological target. 

We rely on the Anatomical Therapeutical Chemical (ATC) classification system, according to which drugs and their active substances are divided into different groups based on organs or systems they affect and their therapeutic, chemical and pharmacological properties.

7. Genetic information

Finally, an equally important segment of the report is the client’s genetic information. Here we include the following:

  • Gene(s) name(s) that interact with a drug
  • Genetic variants (SNPs) - variations specific to a particular person and located withing the given gene
  • Genotype - set of alleles of one gene that represent genetic information for a particular trait
8. Annotation text

Figure 6: Example of annotation text

Finally, there is annotation text for each gene-drug interaction describing how it affects the overall drug metabolism and the body’s response of how it handles the certain phenotype. The annotation text explains the relationship or interaction between a given drug and gene.  Above you see an example of a genetic variant of the YEATS gene and its association with hypertension.

In future releases and upgrades, we plan to significantly improve and personalize these annotation texts and make them more readable and interactive.

*Disclaimer: The term “drug” in the above article refers to a chemical substance used to treat, cure, diagnose or prevent a disease or condition. Alternatives for this term include medication, pharmaceutical or therapeutic agents. In this context, “drug” does not refer to any type of illegal stimulant or recreational drug.

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