DPYD Sequencing Identifies More Clinically Relevant Variants as Compared to Targeted Genotyping

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.