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Stargazer: a software tool for calling star alleles from next-generation sequencing data using CYP2D6 as a model

Genetics in Medicinevolume 21pages361372 (2019) | Download Citation




Genotyping CYP2D6 is important for precision drug therapy because the enzyme it encodes metabolizes approximately 25% of drugs, and its activity varies considerably among individuals. Genotype analysis of CYP2D6 is challenging due to its highly polymorphic nature. Over 100 haplotypes (star alleles) have been defined for CYP2D6, some involving a gene conversion with its nearby nonfunctional but highly homologous paralog CYP2D7. We present Stargazer, a new bioinformatics tool that uses next-generation sequencing (NGS) data to call star alleles for CYP2D6 ( Stargazer is currently being extended for other pharmacogenes.


Stargazer identifies star alleles from NGS data by detecting single nucleotide variants, insertion-deletion variants, and structural variants. Stargazer detects structural variation, including gene deletions, duplications, and conversions, by calculating paralog-specific copy numbers from read depths.


We applied Stargazer to the NGS data of 32 ethnically diverse HapMap trios that were genotyped by TaqMan assays, long-range polymerase chain reaction, quantitative multiplex polymerase chain reaction, high-resolution melting analysis, and/or Sanger sequencing. CYP2D6 genotyping by Stargazer was 99.0% concordant with the data obtained by these methods, and showed that 28.1% of the samples had structural variation including CYP2D6/CYP2D7 hybrids.


Accurate genotyping of pharmacogenes with NGS and subsequent allele calling with Stargazer will aid the implementation of precision drug therapy.

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The authors acknowledge the Pharmacogenomics Research Network for supporting the development of PGRNseq. This work was supported by NIH grants HL069757, GM092676, GM116691, GM115318, GM115277, and S10OD021553, and the University of Washington’s Graduate School Fund for Excellence and Innovation.

Author information


  1. Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, USA

    • Seung-been Lee BS
    • , Marsha M. Wheeler PhD
    • , Karynne Patterson BS
    • , Sean McGee PhD
    •  & Deborah A. Nickerson PhD
  2. Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA

    • Rachel Dalton PharmD
    •  & Erica L. Woodahl PhD
  3. Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, Missouri, USA

    • Andrea Gaedigk PhD
  4. Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington, USA

    • Kenneth E. Thummel PhD
  5. Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA

    • Deborah A. Nickerson PhD


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The authors declare no conflicts of interest.

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Correspondence to Deborah A. Nickerson PhD.

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