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DPYD sequencing identifies more DPYD variants linked to fluoropyrimidine toxicity than targeted genotyping. A standardized classification system is needed for consistent variant interpretation and improved patient safety.

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Area of Science:

  • Pharmacogenomics
  • Clinical Chemistry
  • Molecular Diagnostics

Background:

  • DPYD testing is crucial for identifying patients at risk of severe toxicity from fluoropyrimidine chemotherapy.
  • Sequencing methods are effective in detecting rare DPYD variants, but these require accurate classification for clinical utility.

Purpose of the Study:

  • To evaluate the diagnostic yield of DPYD sequencing compared to targeted genotyping strategies.
  • To assess the concordance of variant classifications between laboratory protocols, ClinVar, and CPIC expert panel designations.
  • To highlight the need for standardized variant classification in pharmacogenomics.

Main Methods:

  • Analysis of DPYD sequencing results over a 9-year period (up to 2024).
  • Comparison of positive test rates between targeted genotyping (AMP Tiers 1 & 2) and comprehensive sequencing.
  • Evaluation of variant classification concordance with ClinVar and CPIC guidelines.

Main Results:

  • DPYD variants were identified in 12.79% of tested individuals, with 2.53% classified as variants of uncertain significance.
  • Targeted genotyping (AMP Tier 1 or Tiers 1 & 2) would have identified fewer at-risk patients compared to sequencing.
  • A significant proportion of non-AMP Tier 1/2 variants identified by sequencing were unclassified by CPIC or unreported in ClinVar, despite general concordance in classifications.

Conclusions:

  • DPYD sequencing offers a more comprehensive approach than targeted genotyping, detecting 26% more reportable variants.
  • The lack of standardized classification systems poses challenges for consistent interpretation of pharmacogenomic variants.
  • Implementing a standard framework for variant classification is essential for transitioning to sequencing and ensuring patient safety.