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Targeted next generation sequencing as a tool for precision medicine.

Markus Gulilat1,2, Tyler Lamb2, Wendy A Teft1

  • 1Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.

BMC Medical Genomics
|June 5, 2019
PubMed
Summary

PGxSeq, a targeted sequencing panel, accurately identifies genetic variants in pharmacogenes, including copy number variations in CYP2D6 and UGT1A1*28. This enables personalized pharmacotherapy by detecting variants affecting drug response in most patients.

Keywords:
Copy number variationIn silico predictionNext generation sequencingPharmacogenesTargeted exome sequencing

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Area of Science:

  • Genomics
  • Pharmacogenomics
  • Molecular Biology

Background:

  • Targeted next-generation sequencing (NGS) is crucial for identifying genetic variations influencing drug response and adverse effects, essential for personalized pharmacotherapy.
  • Challenges exist in applying NGS to pharmacogenes with complex structures, high homology, and pseudogenes, particularly for detecting copy number variation (CNV) in CYP2D6 and specific polymorphisms like UGT1A1*28.
  • The PGxSeq panel was developed to address these challenges in pharmacogene analysis.

Purpose of the Study:

  • To develop and validate PGxSeq, a targeted exome sequencing panel for pharmacogenes.
  • To assess the panel's ability to detect single nucleotide variants (SNVs), copy number variations (CNVs), and specific polymorphisms in pharmacogenes.
  • To evaluate the clinical utility of PGxSeq for identifying individuals requiring altered pharmacotherapy.

Main Methods:

  • A capture probe panel was designed to target 422 kb of coding regions in 100 pharmacogenes.
  • Next-generation sequencing (NGS) was performed on 235 subjects.
  • Bioinformatics tools were used for variant calling, including CYP2D6 CNV detection, and in silico analysis of SNV frequency and functional impact.

Main Results:

  • The PGxSeq panel achieved a depth-of-coverage (DOC) ≥ 20× for over 94% of the target sequence.
  • Accurate detection of 39 clinically relevant gene variants was achieved with 99.9% concordance compared to standard genotyping, including CYP2D6 CNV and UGT1A1*28.
  • A significant proportion of subjects (78%) carried variants necessitating altered pharmacotherapy, with allele frequencies of novel variants aligning with large genomic datasets.

Conclusions:

  • PGxSeq provides a comprehensive, rapid, and reliable method for detecting common and novel SNVs in pharmacogenes.
  • The panel supports the advancement of precision medicine by facilitating individualized pharmacotherapy.
  • PGxSeq demonstrates high accuracy in identifying complex genetic variations relevant to drug response.