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

Area of Science:

• Pharmacogenomics
• Clinical Genetics
• Enzyme Deficiencies

Background:

• Dihydropyrimidine dehydrogenase (DPD) deficiency screening is recommended by EMA and FDA to prevent fluoropyrimidine toxicity.
• Current screening relies on phenotyping or genotyping, with varying national guidelines.
• The study investigated the utility of DPYD sequencing for identifying functional variants.

Purpose of the Study:

• To assess the benefit of DPYD sequencing in identifying unreported variants affecting enzyme function.
• To improve the genetic assessment of DPD deficiency.
• To enhance the prevention of fluoropyrimidine-induced toxicity.

Main Methods:

• Retrospective analysis of DPYD next-generation sequencing (NGS) data.
• Inclusion of 1145 individuals from Limoges University Hospital (Nov 2020 - Jul 2025).
• Identification and classification of DPYD variants, including rare and copy-number variations (CNVs).

Main Results:

• Fifty-one DPYD variants were identified, including rare and CNVs.
• 73 individuals (6.3%) carried decreased-function alleles; 28 (2.4%) had potentially damaging rare/structural variants (5 CNVs).
• Eight variants had CPIC scores indicating decreased/null activity; 31 had no CPIC annotation.

Conclusions:

• NGS analysis identifies DPYD rare/structural variants with potential functional impact.
• This improves the genetic assessment of DPD deficiency.
• Enhanced genetic assessment aids in preventing fluoropyrimidine toxicity.