Fluoropyrimidine-based (FU) chemotherapy can lead to severe toxicity, even life-threatening situations, for patients with dihydropyrimidine dehydrogenase (DPD) enzyme deficiency. It’s estimated that the mortality rate from FU is 0.5%-1%, which translates to 700-1,400 patients in the U.S. dying each year from FU toxicity.
The most widely used test for DPD deficiency is genotyping of DPYD gene variants, and it’s having an impact on personalized oncology and FU chemotherapy. Already reimbursed in Europe, this pharmacogenomics (PGx) testing became eligible for reimbursement in California over the summer.
DPYD testing advances a new standard of care
FU chemotherapy drugs can be used alone or combined with other medications to treat a variety of solid tumors, including colorectal, breast, head, and neck cancers. Patients who have a genetic variation in the DPYD gene causing reduced DPD activity have difficulty metabolizing FU, which increases the risk of severe toxicity.
Accurate DPYD genetic testing allows clinicians to create personalized treatments and therapies and proactively prevent toxicities. The incidence of DPD deficiency has been reported as 3%-5% for patients of European origin and 8% for those of African origin. Screening ahead of treatment is becoming the new standard of care. Pharmacology guidelines recommend avoiding or reducing doses of FU drugs for patients with DPYD genetic variants.
Global groups establish guidelines and recommendations
The Association for Molecular Pathology (AMP) Clinical Practice Committee's Pharmacogenomics (PGx) Working Group includes subject matter experts from the American College of Medical Genetics and Genomics, Centers for Disease Control, Clinical Pharmacogenetics Implementation Consortium (CPIC), College of American Pathologists, Dutch Pharmacogenetics Working Group (DPWG), European Society for Pharmacogenomics and Personalized Therapy (ESPT), Pharmacogenomics Knowledgebase (PharmGKB), PharmVar, and the PGx clinical testing and research communities.
The group’s work offers guidance to clinical laboratories and assay manufacturers who develop, validate, or provide DPYD pharmacogenomic testing by promoting standardization of testing. They have identified and recommended attributes of pharmacogenetic alleles for clinical testing and a minimum set of variants for clinical PGx genotyping assays. To develop their DYPD recommendations, they “considered the functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, and other technical considerations for PGx testing.”
Additional medical societies and regulatory agencies have offered guidance related to DPYD testing:
- Since 2020, the European Medicines Agency (EMA) recommends DPD testing by phenotyping or genotyping before treatment with FU drugs. This has supported the widespread implementation of testing in Europe.
- The U.S. Food and Drug Administration Table of Pharmacogenomics Biomarkers in Drug Labeling recognizes the connection between DPYD and FU toxicity.
- CPIC guidelines include 82 known DPYD variants: 21 are considered to have no DPD function and 6 to have diminished DPD function.
- The Spanish Pharmacogenetics and Pharmacogenomics Society, the Spanish Society of Medical Oncology, and the French National Network of Pharmacogenetics recommend making genotype-guided adjustments to dosages or using alternative drugs for those identified as poor or intermediate metabolizers.
- DPYD screening for four gene variants found more frequently in Europeans is mandated in the UK before treatment to reduce the risk of severe and potentially fatal FU toxicity. It is one of the first pharmacogenomic tests to apply nationally in the UK.
Next-generation sequencing holds key to detecting variants
Next-generation sequencing (NGS) technology’s cost-effectiveness and wider use allow screening of the entire DPYD full gene, detecting rare and novel variants and identifying a more significant number of DPD deficiencies. Identifying rare DPYD variants continues to strengthen NGS’ role as a powerful predictive tool for clinicians. Incorporating NGS-based pharmacogenomic analysis into the clinical setting can help reduce FU chemotherapy toxicity without impacting treatment efficacy.
In a study published early this year in The Pharmacogenomics Journal, the authors, using NGS, “comprehensively assessed the relationship between DPYD genotype and DPD phenotype in a series of 2,972 patients and identified new rare clinically relevant variants associated with DPD deficiency. Our results also show that rare DPYD genetic variants account for a significant part of the interindividual variability of DPD activity. Therefore, comprehensive NGS-based genotyping instead of candidate SNP interrogation should be considered for the guidance of personalized fluoropyrimidine therapy.”
Considerations for implementing DPYD testing
Assays to use for testing PGx variants can be based on many factors that include, but are not limited to, the spectrum of sequence variants, the technical feasibility of analysis of the genomic region of interest, cost, laboratory workflow, and test turnaround time required. As the DPYD gene resides on a genomic region that is amenable to interrogation using standard molecular techniques, clinical molecular laboratories may use targeted genotyping or sequencing (Sanger sequencing or next-generation sequencing) approaches, determined at the discretion of the testing laboratory.
The testing platform chosen, approach for variant classification, result interpretation, post-test recommendations, and clinical implementation can differ for DPYD testing for PGx and diagnostic indications. This may impact clinical test selection as some laboratories only perform testing and interpretation for one, and others offer an interpretation for both.
The American College of Medical Genetics and Genomics requires laboratories to determine the clinical and analytic validity of the technique chosen to analyze each gene using well-characterized samples. Performance should be compared with an existing gold standard assay, if available. Laboratories must document clinical validity through their own or other published studies and validate the technique for each sequence to be analyzed with known variants and normal samples.
ISO 15189 guidelines, the global standard for quality management in clinical laboratories, state that third-party controls should be used for quality monitoring test systems: use of independent third-party control materials should be considered, either instead of, or in addition to, any control materials supplied by the reagent or instrument manufacturer.
The independence of third-party controls is paramount since manufacturer controls are often
formulated from the same raw material as the assay calibrators and will not challenge the assay at lower detection limits, which is where the medical decision point lies. They are optimized for use with the manufacturer’s test system and are less likely to identify assay performance issues.
We’re excited to announce Seraseq® DPYD DNA Mutation Mix
LGC Clinical Diagnostic's SeraCare has launched a reference material for DPYD genetic testing compatible with a wide array of technology (NGS, PCR, mass-array). This 3rd party reference material is highly multiplexed, with over 39 DPYD variants believed to indicate no or diminished DPD function.
LGC Clinical Diagnostics is a trusted third-party control vendor with decades of experience designing and manufacturing effective quality control monitoring tools. Our high-quality products are traceable from sourcing through processing to delivery, offering a high level of confidence, quality, and safety. Our facilities are ISO 13485-certified and comply with cGMP regulations.
Sources
All You Need to Know About DPYD Genetic Testing for Patients Treated With Fluorouracil and Capecitabine: A Practitioner-Friendly Guide https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8462561/
DPYD genetic polymorphisms in non-European patients with severe fluoropyrimidine-related toxicity: a systematic review https://www.nature.com/articles/s41416-024-02754-z
DPYD Genotyping Recommendations https://www.jmdjournal.org/article/S1525-1578(24)00154-5/fulltext
Integrating rare genetic variants into DPYD pharmacogenetic testing may help prevent fluoropyrimidine-induced toxicity https://www.nature.com/articles/s41397-023-00322-x
Predicting Dihydropyrimidine Dehydrogenase Deficiency and Related 5-Fluorouracil Toxicity: Opportunities and Challenges of DPYD Exon Sequencing and the Role of Phenotyping Assays https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9694733/
Ten-year experience with pharmacogenetic testing for DPYD in a national cancer center in Italy: Lessons learned on the path to implementation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225682/
Technical Standards for Clinical Genetics Laboratories, American College of Medical Genetics and Genomics (ACMG) https://www.acmg.net/PDFLibrary/ACMG%20Technical%20Lab%20Standards%20Section%20G.pdf
International Organization for Standardization (ISO) 15189 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500734/