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Validation of a Large Custom-Designed Pharmacogenomics Panel on an Array Genotyping Platform.

Nga Yeung Tang1, Xun Pei1, David George1

  • 1Department of Pathology, Advanced Technology Clinical Laboratory, The University of Chicago, Chicago, IL.

The Journal of Applied Laboratory Medicine
|July 15, 2021
PubMed
Summary

This study validated a custom pharmacogenomics panel, confirming its reliable interrogation of 437 single-nucleotide variants (SNVs) for predicting drug response and improving patient outcomes.

Keywords:
OpenArrayPGxSNV genotypingpharmacogenomicsvalidation

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Area of Science:

  • Genetics
  • Pharmacology
  • Biotechnology

Background:

  • Pharmacogenomics offers potential for personalized medicine by predicting individual drug responses.
  • Custom genotyping panels are crucial tools for advancing pharmacogenomic applications.
  • Evaluating the analytical performance of such panels is essential for clinical utility.

Purpose of the Study:

  • To design and assess the analytical performance of a custom OpenArray® pharmacogenomics panel.
  • The panel targets 478 single-nucleotide variants (SNVs) relevant to drug response.
  • To ensure the panel's reliability for clinical decision-making.

Main Methods:

  • Analytical validation using 40 Coriell Institute cell line (CCL) DNA samples and 28 whole-blood DNA samples.
  • Genotyping accuracy was compared against next-generation sequencing, Sequenom MassARRAY®, or Sanger sequencing.
  • Precision, reproducibility, and sensitivity were evaluated at varying DNA concentrations (10 ng/µL and 50 ng/µL).

Main Results:

  • The custom panel reliably interrogated 437 out of 478 targeted variants (91.4%) with concordant calls and reproducibility.
  • Six variants showed unsatisfactory performance, necessitating careful interpretation.
  • A DNA concentration of 50 ng/µL is recommended for optimal genotyping accuracy and call rates.

Conclusions:

  • The custom pharmacogenomics panel demonstrates reliable performance for interrogating a significant number of clinically relevant variants.
  • The panel's ability to provide clinically actionable results supports its use in pharmacogenomic studies for guiding treatment decisions.
  • Further application of this panel can enhance patient outcomes through personalized drug therapy.