Added Value of Clinical Sequencing: WGS-Based Profiling of Pharmacogenes

Int J Mol Sci. 2020 Mar 26;21(7):2308. doi: 10.3390/ijms21072308.


Although several pharmacogenetic (PGx) predispositions affecting drug efficacy and safety are well established, drug selection and dosing as well as clinical trials are often performed in a non-pharmacogenetically-stratified manner, ultimately burdening healthcare systems. Pre-emptive PGx testing offers a solution which is often performed using microarrays or targeted gene panels, testing for common/known PGx variants. However, as an added value, whole-genome sequencing (WGS) could detect not only disease-causing but also pharmacogenetically-relevant variants in a single assay. Here, we present our WGS-based pipeline that extends the genetic testing of Mendelian diseases with PGx profiling, enabling the detection of rare/novel PGx variants as well. From our in-house WGS (PCR-free 60× PE150) data of 547 individuals we extracted PGx variants with drug-dosing recommendations of the Dutch Pharmacogenetics Working Group (DPWG). Furthermore, we explored the landscape of DPWG pharmacogenes in gnomAD and our in-house cohort as well as compared bioinformatic tools for WGS-based structural variant detection in CYP2D6. We show that although common/known PGx variants comprise the vast majority of detected DPWG pharmacogene alleles, for better precision medicine, PGx testing should move towards WGS-based approaches. Indeed, WGS-based PGx profiling is not only feasible and future-oriented but also the most comprehensive all-in-one approach without generating significant additional costs.

Keywords: CYP2D6; DPWG; PGx; gnomAD; next-generation sequencing; pharmacogenetics; precision medicine; whole-genome sequencing.

Publication types

  • Comparative Study
  • Validation Study

MeSH terms

  • Cytochrome P-450 CYP2D6 / genetics
  • Genetic Testing / methods*
  • Genetic Testing / standards
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Nucleotide Sequencing / standards
  • Humans
  • Pharmacogenomic Variants*
  • Whole Genome Sequencing / methods*
  • Whole Genome Sequencing / standards


  • Cytochrome P-450 CYP2D6