Recommendations for Standardizing DPYD Pharmacogenomic Testing

Houda Hachad, PharmD, vice president, Aranscia, shares the Association for Molecular Pathology Working Group’s recommendations for standardizing dihydropyrimidine dehydrogenase (DPYD) pharmacogenomic testing, and why is it important for clinical PGx tests to include a comprehensive set of variants. The recommendations were published in the Journal of Molecular Diagnostics.

Hi, I'm Houda Hachad. I'm the vice president of clinical operations here at Aranscia. I'm trained as a pharmacist and a clinical pharmacologist. I spent 20 years in academia and in the industry building drug information technologies around drug interactions and pharmacogenomics. My goal has always been to advance the safe use of therapeutics for health care providers, but also to empower researchers in the industry to put safer medications on the market. I serve on multiple pharmacogenomic (PGx) working groups and committees, aiming to standardize and facilitate the adoption of PGx testing. Aranscia is an umbrella company with three entities that are synergistically fulfilling the precision medicine needs of various stakeholders. Our offerings span a wide range of genomic solutions, such as diagnostic testing, clinical decision support, workflow optimizations, and facilitating the incorporation of genomic insight in patient care.

What are the key goals of the Association for Molecular Pathology's current work on dihydropyrimidine dehydrogenase (DPYD) PGx testing?

This group has been developing, over the past 6 years, an extensive series of joint consensus guidelines to promote genotype concordance and test standardizations between the labs that are commonly used in clinical practice for these tests. The Association for Molecular Pathology (AMP) has added a guideline to facilitate the standardization of DPYD testing across all laboratories. The goal is to ensure that the appropriate and relevant variations are included in these tests offered by laboratories. This guideline also helps the implementer ensure that the testing partner is offering a test that is valid.

DPYD testing is for a specific gene that is important for proper and safe use of anticancer medications, namely fluorouracil and capecitabine. These are widely prescribed medications for a number of different types of cancers, and the toxicities with these medications can increase dramatically in patients who carry the DPYD variations. So, the focus of the AMP guideline is to complement the clinical guidelines from the Clinical Pharmacogenetics Implementation Consortium (CPIC) on what to do when a patient has these variations. So, they go hand-in-hand with the existing guidelines from CPIC and the US Food and Drug Administration (FDA) to promote the use of this type of testing.

Could you briefly summarize the recommendations set by the AMP PGx Working Group to determine which DPYD variants to include in comprehensive panel PGx tests?

Historically, laboratories offering these types of tests would include common variants that were mostly found in European populations, in which originally these toxicities were observed. But as new damaging variants were discovered in other ancestral groups or ethnic groups, we identified a need within the group to expand testing coverage and help labs discover the other types of variants that should be included for testing. The group uses the same approach for the other genes, which is a two-tier categorization or classification of variants that we recommend for inclusion. We followed previous clinical recommendations for other genes such as CYP2DC2, CYP2D6, etc.

The variants that are set up can be classified into two groups. We refer to the first group as the “must-test” or the “recommended variant for testing.” These are tier 1 variants. There are 7 of them as part of this guideline, and these are selected based on multiple criteria. The first important criterion is they have a well-studied, characterized, and documented effect on the functional activity of the DPD protein. In other words, we know that they are altering the enzyme function.

The second criterion is they need to have a specific cutoff or an appreciable minor allele frequency in the population and have at least one subpopulation where the frequency is found at 0.1%. The third criterion is that they need to have reference material that helps the laboratory when they do their validation. These reference materials are well-characterized materials that can be purchased by the laboratory to facilitate the validations of the tests. The final criterion is that the methodology to test for these variants needs to be easy and accessible to the majority of the laboratories. In other words, there are no complexities in terms of the technologies that are available for testing.

The second group, which is tier 2, is referred to as “optional variants”, and there are 6 of them. These tend to be variants that meet at least one criterion that I cited for tier 1, but they might be missing one or more criteria. However, it is important to remember that even for these tier 2 variants, they all have been well-characterized in terms of functional activity. In other words, we are not including variants with unknown effect on the protein because some variants have been discovered in populations, but we are unsure whether they are actually altering functions or not. For the second group within tier 2, the frequency cutoff that we have applied in at least one population is 0.01%; they can be found but they are rare. And finally, the second list is not restrictive and it is meant as a reference guide. Each laboratory can decide which variant within this list to include at its discretion, depending on the population they serve.

Why is it important for clinical PGx tests to include a comprehensive set of variants, and how does this impact clinical decision-making and medication management for patients?

The inclusion of key variants that are proposed by this guideline is important to ensure appropriate testing and appropriate testing by different laboratories in different settings, but also for a broader number of ethnically diverse patients. Given that the US is a multi-ethnic society, it is important to ensure equitable implementation of PGx-guided testing in oncology. So, the goal is that when appropriate, implementers now have confidence in offering this test to a broader set of patients. And by using these variations, this testing, the institutions will identify patients who are at risk.

The majority of the patients tested who carry these variants will probably carry one variant. There are extremely rare cases where patients might carry two damaging variants. These patients have an increased risk of toxicity and will require reductions in the doses that are provided to them during these chemotherapy cycles to treat their cancers. The decision we are trying to inform with these tests is proper dosing, but importantly, preemptively before the patient is provided these medications. This facilitates the medication management and the management of the expected toxicities in these patients. Like many chemotherapy medications, these medications have some toxicities that are extreme. We want to avoid forms of toxicities that will result in hospitalizations, and this testing will help us in this regard.