Exploring the 1000 Genomes Project haplotype reporting for the CYP2D6 pharmacogene
The Gaedigk et al. article “A perspective by PharmVar: Are the hundreds of CYP2D6 haplotypes predicted by Wendt and colleagues real?” describes shortcomings of the 2017 Wendt et al. article “Full-gene haplotypes refine CYP2D6 metabolizer phenotype inferences” . To summarize, they discuss (1) the lack of submission of novel variants to www.PharmVar.org; (2) inaccurate activity score reporting, namely for those haplotypes containing the 843T>G SNP; (3) use of 1000 Genomes Project (1kGP) data from the inaccessible regions of the database; and (4) lack of sequence and structural validation for any of the described haplotypes.
We thank Gaedigk and colleagues for their review of the Wendt et al. 2017 findings and in many ways share their concerns. In general, the authors’ letter raises valid concerns for the data presented in the original Wendt et al. study and many pharmacogenomics studies utilizing publically available data. However, the authors’ appear to overstate our reported...
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