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Sequencing identifies more pharmacogenomic variants than targeted genotyping, revealing clinically relevant alleles in 28% of patients. This highlights the need for sequencing to detect rare variants impacting patient care.

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Area of Science:

  • Pharmacogenomics
  • Genetics
  • Clinical Diagnostics

Background:

  • Clinical pharmacogenomic testing commonly uses targeted genotyping.
  • Targeted genotyping panels may miss clinically relevant variants.
  • Sequencing offers comprehensive detection of common and rare variants.

Purpose of the Study:

  • To compare the diagnostic yield of in silico targeted genotyping with comprehensive sequencing.
  • To evaluate the patient impact of variants missed by targeted genotyping.
  • To assess the utility of sequencing for pharmacogenomic variant detection.

Main Methods:

  • An in silico targeted genotyping panel was designed based on common clinical variants.
  • The panel was applied to 10,030 participants with existing sequencing data.
  • Results were compared between in silico genotyping and reported sequencing findings for genes including CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4, CYP3A5, DPYD, SLCO1B1, TPMT, UGT1A1, and VKORC1.

Main Results:

  • Sequencing identified potentially clinically relevant variants in 28% (2780/10,030) of participants missed by targeted genotyping.
  • SLCO1B1 (13%), DPYD (6.3%), and CYP2D6 (3.5%) had the highest proportion of variants uniquely detected by sequencing.
  • DPYD and CYP2D6 exhibited the largest number of unique variants exclusively identified through sequencing.

Conclusions:

  • Targeted genotyping captures most significant pharmacogenomic variants but misses rare alleles.
  • Sequencing-based approaches are crucial for comprehensive pharmacogenomic profiling, detecting variants that collectively impact many patients.
  • Standardization of variant classification and nomenclature is needed for widespread adoption of sequencing in pharmacogenomics.