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Review
. 2019 Jan;105(1):29-32.
doi: 10.1002/cpt.1275. Epub 2018 Dec 7.

The Evolution of PharmVar

Andrea Gaedigk  1   2 , Katrin Sangkuhl  3 , Michelle Whirl-Carrillo  3 , Greyson P Twist  2   4 , Teri E Klein  3 , Neil A Miller  2   4 ; PharmVar Steering Committee
Affiliations
Review

The Evolution of PharmVar

Andrea Gaedigk et al. Clin Pharmacol Ther. 2019 Jan.
No abstract available

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Conflict of interest statement

The authors declared no competing interests for this work.

Figures

Figure 1
Figure 1
PharmVar gene page view for CYP2C19. The top portion of each gene page provides general information and links to important documents, including the READ ME and CHANGE LOG documents (some genes also have documentation for structural variation). In the middle section, the user can choose to visualize positions of sequence variations on the genomic or cDNA reference sequences (NG_008384.3 and NM_000769.1) or on the GRCh37 or GRCh38 genome build (information buttons link each to NCBI). The user also has the option between two count modes (start of the sequence or the ATG start codon). In the lower section, all defined alleles and suballeles are listed with their respective haplotype designation, legacy label, PharmVar ID, and sequence variations (those with rs IDs are highlighted in blue), followed by their impact (e.g., splicing defect or amino acid change) in parentheses, function (if available through the PharmGKB), evidence level, and selected reference(s). Download options include to download all gene data or individual haplotypes. On clicking a sequence variant of interest, the variant window (shown to the right) slides in “at a glance” information, including its rs ID and link to dbSNP.
See this image and copyright information in PMC

References

    1. Gaedigk, A. et al The Pharmacogene Variation (PharmVar) Consortium: incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature database. Clin. Pharm. Ther. 103, 399–401 (2018). - PMC - PubMed
    1. Nofziger, C. & Paulmichl, M. Accurately genotyping CYP2D6: not for the faint of heart. Pharmacogenomics 19, 999–1002 (2018). - PubMed
    1. Twist, G. et al Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole‐genome sequence. Genomic Med. (2016). http://www.nature.com/articles/npjgenmed20157. - PMC - PubMed
    1. Lee, S.B. et al Stargazer: a software tool for calling star alleles from next‐generation sequencing data using CYP2D6 as a model. Genet. Med. 10.1038/s41436-018-0054-0. [e‐pub ahead of print]. - DOI - PMC - PubMed
    1. Yang, J.J. et al Pharmacogene variation consortium gene introduction: NUDT15 . Clin. Pharm. Ther. 10.1002/cpt.1268. [e‐pub ahead of print]. - DOI - PMC - PubMed

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