Dihydropyrimidine dehydrogenase testing: capturing what standard genotyping misses with next-generation sequencing

Screening for dihydropyrimidine dehydrogenase (DPD) deficiency has been recommended by both the European Medicines Agency (EMA) and the U.S. Food and Drug Administration (FDA) to prevent fluoropyrimidine toxicity. Depending on national guidelines, it relies on phenotyping or variants genotyping. We assessed the benefit of DPYD sequencing to identify unreported variants that may alter enzyme function.

We retrospectively analyzed DPYD next-generation sequencing results obtained from 1145 individuals at Limoges University Hospital between November 2020 and July 2025.

Fifty-one DPYD variants were identified including several rare variants and copy-number variation (CNV) that are not addressed in current guidelines. Four were common (MAF ≥ 5%), 6 rare (MAF ≥ 0.5% and < 5%) and 41 very rare (MAF < 0.5%). Eight showed a Clinical Pharmacogenetics Implementation Consortium (CPIC) score indicative of decreased or null activity; 12 were classified normal-function allele, and 31 had no CPIC annotation. In this cohort, 73 (6.3%) individuals carried at least one decreased-function allele, while 28 (2.4%) had potentially damaging rare or structural variants (including 5 CNVs).

NGS analysis enables the identification of DPYD rare or structural variants with potential functional impact, thereby improving the genetic assessment of DPD deficiency.