Performance of exome sequencing for pharmacogenomics

Eric R. Londin, Peter Clark, Marialuisa Sponziello, Larry J. Kricka, Paolo Fortina, Jason Y. Park

Research output: Contribution to journalArticle

12 Scopus citations

Abstract

Aim: We present the potential false-negative rate of exome sequencing for the detection of pharmacogenomic variants. Materials & Methods: Depth of coverage of 1928 pharmacogenomically relevant variant positions was ascertained from 62 exome-sequenced samples. Results: Approximately 14% of the 1928 variant locations examined had inadequate depth of coverage (<20×). The variants with inadequate coverage were predominantly located outside of protein-coding portions and included some clinically relevant variant positions, such as the warfarin VKORC1 variant. Conclusion: While the use of exome sequencing is becoming more prevalent in fundamental research, clinical trials and clinical use; there is a possibility of false-negative results. The possible quality issues such as false-negative rate should be considered with the use of exome sequencing.

Original languageEnglish (US)
Pages (from-to)109-115
Number of pages7
JournalPersonalized Medicine
Volume12
Issue number2
DOIs
StatePublished - Mar 1 2015

Keywords

  • exome sequencing
  • pharmacogenomics
  • warfarin

ASJC Scopus subject areas

  • Molecular Medicine
  • Pharmacology

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    Londin, E. R., Clark, P., Sponziello, M., Kricka, L. J., Fortina, P., & Park, J. Y. (2015). Performance of exome sequencing for pharmacogenomics. Personalized Medicine, 12(2), 109-115. https://doi.org/10.2217/pme.14.77