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Accurate DPYD gene variant testing is crucial for predicting dihydropyrimidine dehydrogenase (DPD) activity. Relying on the c.1236G>A variant as a proxy for the functional c.1129-5923C>G variant can lead to incorrect patient DPD metabolizer status and suboptimal cancer therapy.

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Area of Science:

  • Pharmacogenomics
  • Molecular Biology
  • Oncology

Background:

  • The DPYD gene encodes dihydropyrimidine dehydrogenase (DPD), essential for metabolizing fluoropyrimidine drugs like 5-fluorouracil and capecitabine.
  • Genetic variations in DPYD significantly impact DPD enzyme activity, influencing patient response and toxicity to fluoropyrimidine-based therapies.
  • Accurate DPD metabolizer status prediction is critical for personalized cancer treatment strategies.

Purpose of the Study:

  • To investigate the linkage disequilibrium (LD) between two single-nucleotide polymorphisms (SNPs) in the DPYD gene: c.1129-5923C>G (functional) and c.1236G>A (previously used proxy).
  • To determine if the c.1236G>A variant is a reliable surrogate for the functional c.1129-5923C>G variant in clinical DPYD genotyping.
  • To assess the clinical implications of relying solely on the c.1236G>A variant for predicting DPD activity.

Main Methods:

  • Retrospective analysis of clinical genotyping data for DPYD variants.
  • Inclusion of patient data from Children's Mercy Data Warehouse and the All of Us Research Program (version 7).
  • Comparative analysis of SNP linkage and correlation with DPD enzyme activity.

Main Results:

  • Identified individuals possessing the c.1236G>A variant without the functional c.1129-5923C>G variant, indicating incomplete linkage disequilibrium (LD).
  • Substantiated incomplete SNP linkage across multiple cohorts, challenging the assumption of perfect LD.
  • Demonstrated that testing only c.1236G>A can result in false-positive predictions of DPD metabolizer status.

Conclusions:

  • The previously assumed perfect linkage between DPYD SNPs c.1236G>A and c.1129-5923C>G is not consistently observed in patient populations.
  • Relying on the c.1236G>A variant as a proxy for the functional variant can lead to inaccurate DPD activity predictions and potentially harmful suboptimal dosing.
  • DPYD genotyping for predicting DPD activity must include the functional variant c.1129-5923C>G, not solely the c.1236G>A proxy, to ensure accurate patient stratification and optimize fluoropyrimidine therapy.