PGRNseq: A targeted capture sequencing panel for pharmacogenetic research and implementation

Adam S. Gordon*, Robert S. Fulton, Xiang Qin, Elaine R. Mardis, Deborah A. Nickerson, Steve Scherer

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

46 Scopus citations

Abstract

Objectives Although the costs associated with whole-genome and whole-exome next-generation sequencing continue to decline, they remain prohibitively expensive for large-scale studies of genetic variation. As an alternative, custom-target sequencing has become a common methodology on the basis of its favorable balance between cost, throughput, and deep coverage. Methods We have developed PGRNseq, a custom-capture panel of 84 genes with associations to pharmacogenetic phenotypes, as a tool to explore the relationship between drug response and genetic variation, both common and rare. We utilized a set of 32 diverse HapMap trios and two clinical cohorts to assess platform performance, accuracy, and ability to discover novel variation. Results We found that PGRNseq generates ultra-deep coverage data (mean=496x) that are over 99.8% concordant with orthogonal datasets. In addition, in our testing sets, PGRNseq identified many novel, rare variants of interest, underscoring its value in both research and clinical settings. Conclusion PGRNseq is an ideal platform for carrying out sequencing-based analyses of pharmacogenetic variation in large cohorts. In addition, the high accuracy associated with genotypes from PGRNseq highlight its utility as a clinical test.

Original languageEnglish (US)
Pages (from-to)161-168
Number of pages8
JournalPharmacogenetics and genomics
Volume26
Issue number4
DOIs
StatePublished - 2016

Keywords

  • pharmacogenomics
  • rare variation
  • targeted sequencing

ASJC Scopus subject areas

  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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