Pharmacogenetic Testing for DPD Deficiency

Four and a Half Years’ Experience in a Large German Laboratory

In April 2020, the European Medicines Agency (EMA) issued the recommendation that patients should undergo targeted testing for deficiency of the dihydropyrimidine dehydrogenase (DPD) enzyme, which is encoded by the DPYD gene, before receiving systemic treatment with 5-fluorouracil (5-FU) or its prodrugs capecitabine or tegafur.

DPD is the rate-limiting enzyme in the metabolism of the above-mentioned chemotherapeutic agents, with approximately 80% of the administered 5-FU dose being degraded by DPD (1).

Complete absence of DPD enzyme function (complete deficiency) is extremely rare in the European population (occurring in less than 0.1%), whereas reduced enzyme activity (partial deficiency) is seen in 2–8%. At a standard 5-FU dose, this reduced metabolism results in high levels of cytotoxic 5-FU metabolites and an increased risk for toxicity. This results in treatment delays and a 25.6-fold increase in treatment-related mortality (2.3% versus 0.1%) in individuals with partial DPD deficiency compared to individuals with normal DPD enzyme function (2).

The EMA recommendations were swiftly adopted by the relevant specialist societies, notably the German Society of Hematology and Medical Oncology (Deutsche Gesellschaft für Hämatologie und Medizinische Onkologie, DGHO) (3). The EMA announcement was preceded by years of discussion regarding the benefit of an official recommendation, with the primary focus being on cost–benefit considerations and questions about the medical profession’s acceptance of a diagnostic test of this kind.

Below, we report on our experience with DPYD testing at Labor Berlin–Charité Vivantes, a large diagnostic laboratory in Germany. As part of this, incidence figures for DPD deficiency were determined.

Methods

DPD deficiency testing was offered by Labor Berlin from June 2020 onwards. This included the four DPYD variants specified in the EMA and DGHO recommendations (3): *2A (rs3918290, c.1905+1G>A), *13 (rs55886062, c.1679T>G), c.2846A>T (rs67376798), and HapB3 (rs75017182, c.1129–5923C>G), and was initially performed using direct Sanger sequencing. From July 2020 onwards, a certified kit based on allele-specific polymerase chain reaction (PCR) amplification and capillary electrophoresis was used. Informed patient consent in accordance with the German Genetic Diagnostics Act (Gendiagnostikgesetz) was a prerequisite for testing.

The results issued included a dose recommendation based on international guidelines (4) (Figure). High-performance liquid chromatography (HPLC)-based measurement of plasma uracil levels, which are elevated in DPD deficiency, was also temporarily evaluated as an alternative to DPYD genotyping, since this option is likewise specified in the recommendations of the EMA/Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte, BfArM). Ultimately, this proved to be unfeasible since uracil levels are not stable in uncooled plasma, depend on food intake, and may be falsely elevated in (moderate to) severe renal impairment (Direct Healthcare Professional Communication 2024 [German: Rote-Hand-Brief]).

Figure

Frequencies of the tested genetic DPYD variants

In October 2020, testing for DPD deficiency became a standard service covered by German statutory health insurers with the introduction of fee schedule item (Gebührenordnungsposition, GOP) 32867 under the German Uniform Value Scale (Einheitlicher Bewertungsmaßstab, EBM).

Results

Between 06/2020 and 12/2024, a total of 6436 samples were tested at Labor Berlin. Samples were sent in primarily by hospitals, outpatient departments, and medical care centers in the Berlin/Brandenburg region (N = 4980), and less frequently from further away (N = 1456). The number of tests increased over time.

Clinical information relating to patients’ submitted samples was provided only sporadically. In all, 3697 individuals were male, 2722 were female, and 17 were unspecified. The median patient age was 66 years (16–94 years).

Of the 6436 patients tested, 334 (5.19%) had at least one of the DPYD variants responsible for reduced enzyme activity. Thus, the number needed to screen is 19.3, corresponding to current diagnostic costs of €2127 (based on the EBM) per positive case. The frequency of the four DPYD variants tested for is shown in the Figure. On average, results were reported between 3 and 4 working days after receipt of a sample.

Discussion

Following the EMA/BfArM recommendation, testing was quickly accepted by the referring centers. This is due in part to the early implementation of the recommendation by the management of referring hospitals.

The detailed recommendations on dose reduction likely also contributed to physicians’ acceptance of the testing procedure. It is not possible to say with accuracy the extent to which preemptive testing and subsequent DPYD genotype-based dose adjustment were implemented. For the Charité, which submitted a large proportion of the tested patient specimens, the authors directly involved in patient care (SS, LB, TB) assume an implementation rate close to 100%. It is not possible to comment in this regard on external referring centers.

When evaluating the genotype frequencies observed, it is important to note that the majority of patients tested were from the greater Berlin area. Frequencies in other regions of Germany may differ. One should also bear in mind that the distribution of DPYD variants is different in populations of non-European origin (2).

What is remarkable about DPYD testing is that, within a very short period of time, various specialist societies in Germany supported the need for this pharmacogenetic testing, health insurers quickly established reimbursement for the testing, and the testing process achieved a high level of acceptance, despite the requirement for written informed patient consent.

Thus, preemptive pharmacogenetic DPYD testing can be used as a blueprint for other drugs (for example, thiopurines, statins, clopidogrel), for which international guidelines (such as the Clinical Pharmacogenetics Implementation Consortium, CPIC, and the Dutch Pharmacogenetics Working Group, DPWG) make evidence-based recommendations on preemptive genetic testing as part of tailored drug therapy and support its implementation in clinical practice (5).

Thomas Pretzsch, Matthias Schwab, Olga Blau, Bernhard Wörmann, Sebastian Stintzing, Lars Bullinger, Thomas Burmeister

Conflict of interest statement
TP, OB, and LB either work at or are affiliated with Labor Berlin. TB worked there until 12/2024.

MS is Editor-in-Chief of Pharmacogenetics & Genomics and Drug Research, as well as Section Editor for Pharmacogenetics & Personalized Medicine in Genome Medicine.

SS received funding, fees for consultancy, lecture, and expert appraisal activities, as well as travel cost reimbursement from Amgen, AstraZeneca, Bayer, BMS, Daiichy-Sanyko, ESAI, Leo-Pharma, Lilly, Merck, MSD, Pierre-Fabre, Roche, Sanofi, Servier, Taiho, and Takeda. He is a member of the Advisory Boards of CV6 Therapeutics and Isofol Medical.

BW is Medical Director of the DGHO. In 2020, the DGHO coordinated a position paper by the scientific medical societies on the implementation of the EMA guidelines on DPD testing.

Manuscript submitted on 10 February 2025, revised version accepted on
15 May 2025.

Translated from the original German by Christine Rye.

Cite this as
Pretzsch T, Schwab M, Blau O, Wörmann B, Stintzing S, Bullinger L, Burmeister T: Pharmacogenetic testing for DPD deficiency: Four and a half years’ experience in a large German laboratory. Dtsch Arztebl Int 2025; 122: 445–6. DOI: 10.3238/arztebl.m2025.0092

References

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2. Sharma BB, Rai K, Blunt H, Zhao W, Tosteson TD, Brooks GA: ­Pathogenic DPYD variants and treatment-related mortality in patients ­receiving fluoropyrimidine chemotherapy: A systematic review and meta-analysis. Oncologist 2021; 26: 1008–16

3. Wörmann B, Bokemeyer C, Burmeister T, et al.: Dihydropyrimidine ­dehydrogenase testing prior to treatment with 5-fluorouracil, ­capecitabine, and tegafur: A consensus paper. Oncol Res Treat 2020; 43: 628–36

4. Pratt VM, Cavallari LH, Fulmer ML, 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; 26: 851–63

5. Tremmel R, Hübschmann D, Schaeffeler E, et al.: Innovation in cancer pharmacotherapy through integrative consideration of germline and tumor genomes. Pharmacol Rev 2025; 77: 100014