Clinical Application of PGx


A look into pharmacogenetics viewed from  a genome-wide approach to study the body’s response to drugs in a systemic and integrative manner

Vol. 24 • Issue 3 • Page 14

Cover Story

The goal of personalized medicine is to individualize healthcare by using knowledge of patients’ health history, behaviors, environments and, most importantly, genetic variation when making clinical decisions. Pharmacogenetics (PGx) is defined by the U.S. Food and Drug Administration (FDA) as “the study of variations in DNA sequence as related to drug response,” and it is one of the most important components of personalized medicine. A related term is “pharmacogenomics.” While pharmacogenetics can be viewed from the perspective of individual genes, pharmacogenomics implies more of a genome-wide approach to study the body’s response to drugs in a systemic and integrative manner.

The goal of PGx is to maximize drug efficacy and minimize adverse drug events (ADEs). For many therapeutic drugs, there is a small window between efficacy and ADEs. The application of pharmacogenetics is believed to be a strategy to reduce ADEs.

The human genome is composed of an estimated 3 ­billion base pairs of DNA. Only a small proportion, about 0.01 percent of the human genome, is variable between ­different individuals. However, this small difference in the genome is the key to determining an individual’s different reactions to external challenges, such as pathogens and drugs. Genetic variations that can affect human reaction to drugs include germline or somatic gene variants, functional status, expression changes and chromosomal abnormalities, such as deletions and amplifications.

PGx can be regarded as a combination of pharmacology and genetics. Pharmacology studies how drugs interact with the human body. There are four basic phases of a drug’s life in the body: absorption, distribution, metabolism and excretion (ADME). After entering the body, drugs are chemically modified or broken down by enzymes. The products of enzymatic breakdown can be either more active or inactive than the original drug. To understand the PGx for a specific drug, it is important to know the function of a specific gene product related to the drug, e.g. in which step of the ADMEs is the gene product involved. If the gene product is involved in metabolism, the question becomes what is the effect of the metabolism on the drug activity? It is then important to understand what functional changes are brought by the genetic variants, such as loss or gain of function.

Clinical Applications of PGx

PGx has been applied to preclinical, clinical and postmarket trials of drug development. Clinical application of PGx is also very broad and can be involved in any of the ADME steps. Most clinical applications of PGx focus on drug metabolism, addressing drug safety and efficacy. Genetic variations may themselves be the targets of drugs.

AL_022315_pg16_Table_lgAllelic variants of genes encoding enzymes involved in ADME can affect the function of gene products, thus affecting an individual’s metabolism and response to drugs. Drug metabolism is carried out in the liver, by enzymes of the cytochrome system, especially the cytochrome P450 (CYP) family. Cytochrome P450 enzymes account for 70-80 percent of enzymes involved in drug metabolism. There are 57 cytochrome P450 genes and many pseudogenes, grouped into 18 families (represented by a number) and 44 subfamilies (represented by a capitalized letter). Most prescription drugs are catalyzed by members of the CYP3, CYP2 and CYP1 families, such as CYP3A, CYP2D6 and CYP2C9.

The term “metabolizer phenotype” describes an individual’s ability to metabolize certain drugs. It is based on the number and type of functional alleles of genes the individual carries that are involved in metabolism. Variations of functional alleles will affect corresponding ­enzymatic activities. For example, for the CYP2D6 gene, the “poor metabolizer” and “intermediate metabolizer” have a lower-than-normal level of functional alleles and, thus, no or a low level of enzymatic activity. On the other hand, the “extensive metabolizer” has a normal number, and the “ultrarapid metabolizer” has a higher-than-normal number of functional alleles and greater enzymatic activity.

The ADME for any drug is regulated by many genes. For example, the widely prescribed anticoagulant warfarin’s anticoagulant activity is mediated by the enzyme VKORC1, and the drug itself is metabolized (inactivated) by the CYP2C9 enzyme. Genetic variations for both genes need to be considered to increase efficacy and prevent excessive bleeding.

In cancer PGx, genetic variations may be somatic or germline. Germline abnormalities are present in all cells and mainly affect drug metabolism in chemotherapy, thus affecting drug safety. One example is dihydropyrimidine dehydrogenase (DPD) deficiency in patients treated with 5-fluorouracil (5-FU). Somatic mutations are present in tumor cells, and many have been confirmed to be “driver” mutations that play a key role in tumorgenesis. These driver mutations provide specific targets for therapy. For example, in lung cancer, there is EGFR-targeted tyrosine kinase inhibitor (TKI) therapy for patients whose tumor has a specific EGFRmutation in exon 19 or 21. In addition, lung cancer patients with KRAS mutations are usually resistant to thisEGFR TKI therapy. The table provides some examples of pharmacogenetic applications in oncology.

Laboratory Testing in PGx

PGx applications require corresponding tests that can detect genetic variations of interest. Pharmacogenetic testing is advancing rapidly alongside molecular diagnostics. These tests can be performed in both anatomic and clinical pathology laboratories. For example, breast cancer patients responsive to trastuzumab treatment have HER2/neu overexpression. The presence or absence of which can be determined either by immunohistochemical detection of the protein performed in an anatomic pathology lab or by fluorescence in situ hybridization (FISH) detection of gene amplification in a cytogenetics lab. Commonly used testing methods include sequencing, allele-specific PCR and real-time PCR or RT-PCR. Microarray and next-generation sequencing enable the examination of many genetic alterations at the same time. The AmpliChip CYP450 Test (Roche, NJ) can perform genotyping for multiple alleles in the CYP2D6 and CYP2C19 genes using microarray technology (Affymetrix, CA).

Wider Application of PGx

There are many issues that can affect the application of PGx. PGx enables more precise drug therapy based on a patient’s genetic profile instead of the conventional trial and error approach. However, many genes are involved in the body’s interaction with any given drug, and gene-drug interactions are very complex. Identification of small variants in genes may be difficult and time consuming. In addition, there are many other factors that can affect body-drug interactions, such as diet, the environment and drug-drug interactions.

Pharmacogenetic markers need to be validated and evaluated in clinical practice through an evidence-based approach.1 Clinical guidelines need to be established. Physician education is needed to help or prepare them to deal with the challenges of applying pharmacogenetic data. Many other social, economic and political barriers are not easily broken at the exponential rate by which technology progresses.

Personalized medicine will likely be very expensive, and this may interfere with efforts toward healthcare equity and access to drugs. Cost effectiveness also needs to be taken into consideration. Drugs developed using personalized medicine and PGx would be targeted to specific populations or ethnic groups in whom the drug will be effective. This may lead to a perception of stigma based on ethnicity. The assumption that an individual’s race can predict their genetic profile for drug response is itself problematic, since not all people who belong to a particular ethnic group will have the same genetic variations.

Nevertheless, despite the many issues and challenges ahead, PGx is a promising field, and it continues to evolve toward pharmacogenomics. Regulatory authorities, such as the FDA, have already implemented pharmacogenetic principles into drug labeling. The FDA stated that (21 CFR 201.57 ) “if evidence is available to support the safety and ­effectiveness of the drug only in selected subgroups of the larger population with a disease, the labeling shall describe the evidence and identify specific tests needed for selection or monitoring of patients who need the drug.” A list of pharmacogenomics labeling can be found on the FDA website.2


  1. Evaluation of Genomic Applications in Practice and Prevention (EGAPP™):
  2. Table of Pharmacogenomic Biomarkers in Drug Labeling (FDA):

About Author

Mai He, MD, PhD

Dr. He is medical director of the Hematology Lab, staff pathologist, Department of Pathology & Laboratory Medicine, Women & Infants Hospital of Rhode Island; and assistant professor, Alpert Medical School of Brown University.

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