PGx Testing: First, Do No Harm

Interest in pharmacogenomics (PGx) is growing rapidly, especially for oncologic applications. The average response rate for an FDA-approved cancer drug is 41 percent, meaning that only two in every five patients see treatment success.¹ Not only that, but adverse drug reactions constitute up to one-sixth of all hospital admissions even without factoring in reactions not severe enough to require hospitalization.²

Many of these treatment failures and adverse events may be caused by unexpected differences in patients’ ability to safely and effectively metabolize the drugs they are given. Consequently, to minimize risk and maximize success, testing genes known to be involved in drug metabolism can form an important part of the treatment selection process.

New recommendations

“The evidence for many gene-drug relationships is growing and PGx testing is becoming more widely adopted,” says Victoria M. Pratt, who co-chairs the Association for Molecular Pathology’s (AMP’s) PGx Working Group.

In July 2024, AMP and several other organizations collaborated on recommendations for DPYD PGx testing.³ The DPYD gene encodes the enzyme dihydropyrimidine dehydrogenase (DPD), which metabolizes the fluoropyrimidine drugs used to treat a wide range of cancers.⁴ People who have DPYD mutations that compromise DPD activity are less able to break these drugs down into inactive metabolites, increasing their risk of treatment toxicity.

“DPYD is a great example of a PGx test that has probably not been as widely used as it could be,” says Pratt, who is also director of scientific affairs for pharmacogenetics at Agena Bioscience and an adjunct professor of clinical pharmacology at Indiana University School of Medicine. “It can be very helpful in identifying patients at risk for toxicity when treated with a standard dose of fluoropyrimidines, but has not been routinely used.”

The PGx Working Group has previously issued genotyping recommendations for CYP2C9,⁵ CYP2C19,⁶ CYP2D6,⁷ CYP3A4/CYP3A5,⁸ TPMT/NUDT15,⁹ and genes informing warfarin dosing.¹⁰

“The goal of PGx testing is to identify patients who may be at increased risk of toxicity when treated with a standard dose of an applicable chemotherapeutic (such as DPYD for fluoropyrimidines, TPMT and NUDT15 for thiopurines, or UGT1A1 for irinotecan),” Pratt explains. “If this testing is not performed, there is a risk of not recognizing someone who may benefit from a dose reduction. Laboratory professionals should become familiar with DPYD and the latest evidence supporting use of PGx testing.”

To learn more about PGx testing options, Pratt recommends that laboratorians turn to guidance from the Clinical Pharmacogenetics Implementation Consortium (CPIC), PharmGKB, or the U.S. Food and Drug Administration’s Table of Pharmacogenetic Associations.

Taking aim at alleles

The PGx Working Group has a six-step process for developing and testing new recommendations:

1. Identify variants to consider.
2. Establish the frequency of those variants.
3. Determine whether or not reference materials are available.
4. Evaluate whether or not the gene’s function is known.
5. Discuss any nuances as a group.
6. Determine whether labs are already testing the alleles—and, if not, make sure there isn’t a good technical reason they aren’t.

When choosing genes to investigate, the PGx Working Group considers variants that the CPIC associates with drug toxicity or that are included in other pharmacogene databases, such as PharmVar.

“We use a two-tier categorization of variants recommended for inclusion,” explains Pratt. The criteria for placing a variant on the Tier 1 list include:

• A well-characterized effect on gene expression or the protein’s functional activity
• An appreciable minor allele frequency (MAF) in a population or ancestral group; although the exact MAF varies based on the gene and prevalence of variants or alleles, genes associated with more significant drug-related toxicity are typically assigned a lower MAF threshold
• Reference materials available for assay validation
• Technically feasible for clinical laboratories to interrogate using standard molecular testing methods

Variants on the Tier 2 list meet at least one, but not all, of the Tier 1 criteria.

“These recommendations for clinical genotyping assays do not include variants with an unknown effect on protein function or gene expression,” says Pratt. “They are meant to be a reference guide and not a restrictive list. Members of the AMP PGx Working Group will continue to work together to prioritize genes for future guideline reports.”

What labs should know

Not every patient needs PGx testing—but care providers should be educated about the types of testing available and the scenarios in which it may be important.

In general, labs can choose which genes to include in their test menus based on what is most useful for the patients they serve. For labs with limited resources, it can make sense to offer the genes or panels most commonly requested by the physicians they work with and refer more esoteric requests to reference laboratories that offer a wider range of tests. “Our overall goal is to ensure that laboratories are testing for clinically important variants or alleles and that diverse and multiethnic genetic ancestries are represented,” says Pratt. “We want labs to not only be aware of PGx testing, but also be able to help providers find an appropriate test if they do not offer it themselves.”

Which patients are candidates for PGx testing? “The ideal patient scenario is someone who may be prescribed a medication with a robust PGx association,” Pratt says. “If a patient is going to be prescribed a medication for which there is no PGx association, testing would not be useful to guide that treatment. However, if a PGx panel is performed and the patient will need other medications in the future, the results may be useful at a later point.”

Pratt refers labs to the PGx Working Group’s recommendations to help determine which alleles or variants to include in their tests and to ensure that the test chosen for each patient is sufficiently complete. She acknowledges, however, that it can take time to adopt new recommendations as they come out. Methods are also changing, with genetic testing increasingly moving from genotyping to sequencing as the latter becomes faster and more affordable.¹¹ Even in an ideal scenario, though, PGx testing provides information—not guarantees. Pratt cautions, “It is important for patients and providers to have realistic expectations for what PGx can and can’t do when testing is pursued.”

With these considerations in mind, PGx testing can form an increasingly effective—and evidence-based—part of the precision oncology toolbox for the clinical lab.

References:

1. Chen EY et al. An overview of cancer drugs approved by the US Food and Drug Administration based on the surrogate end point of response rate. JAMA Intern Med. 2019;179(7):915–921. doi:10.1001/jamainternmed.2019.0583.
2. Osanlou R et al. Adverse drug reactions, multimorbidity and polypharmacy: a prospective analysis of 1 month of medical admissions. BMJ Open. 2022;12(7):e055551. doi:10.1136/bmjopen-2021-055551.
3. Pratt VM et al. DPYD genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, American College of Medical Genetics and Genomics, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, Pharmacogenomics Knowledgebase, and Pharmacogene Variation Consortium. J Mol Diagn. 2024;S1525-1578(24)00154-5. doi:10.1016/j.jmoldx.2024.05.015.
4. Thorn CF et al. PharmGKB summary: fluoropyrimidine pathways. Pharmacogenet Genomics. 2011;21(4):237–242. doi:10.1097/FPC.0b013e32833c6107.
5. Pratt VM et al. Recommendations for clinical CYP2C9 genotyping allele selection: a joint recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn. 2019;21(5):746–755. doi:10.1016/j.jmoldx.2019.04.003.
6. Pratt VM et al. Recommendations for clinical CYP2C19 genotyping allele selection: a report of the Association for Molecular Pathology. J Mol Diagn. 2018;20(3):269–276. doi:10.1016/j.jmoldx.2018.01.011.
7. Pratt VM et al. Recommendations for clinical CYP2D6 genotyping allele selection: a joint consensus recommendation of the Association for Molecular Pathology, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, and the European Society for Pharmacogenomics and Personalized Therapy. J Mol Diagn. 2021;23(9):1047–1064. doi:10.1016/j.jmoldx.2021.05.013.
8. VM Pratt et al. CYP3A4 and CYP3A5 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. 2023;25(9):619–629. doi:10.1016/j.jmoldx.2023.06.008.
9. VM Pratt et al. TPMT and NUDT15 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. 2022;24(10):1051–1063. doi:10.1016/j.jmoldx.2022.06.007.
10. VM Pratt et al. Recommendations for clinical warfarin genotyping allele selection: a report of the Association for Molecular Pathology and the College of American Pathologists. J Mol Diagn. 2020;22(7):847–859. doi:10.1016/j.jmoldx.2020.04.204.
11. Kockum I et al. Overview of genotyping technologies and methods. Curr Protoc. 2023;3(4):e727. doi:10.1002/cpz1.727.