SNP genotyping using TaqMan® technology: The CYP2D6∗17 assay conundrum

Andrea Gaedigk, Natalie Freeman, Toinette Hartshorne, Amanda K. Riffel, David Irwin, Jeffrey R. Bishop, Mark A. Stein, Jeffrey H. Newcorn, Lazara Karelia Montané Jaime, Mariana Cherner, J. Steven Leeder

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CYP2D6 contributes to the metabolism of many clinically used drugs and is increasingly tested to individualize drug therapy. The CYP2D6 gene is challenging to genotype due to the highly complex nature of its gene locus. TaqMan® technology is widely used in the clinical and research settings for genotype analysis due to assay reliability, low cost, and the availability of commercially available assays. The assay identifying 1023C>T (rs28371706) defining a reduced function (CYP2D6∗17) and several nonfunctional alleles, produced a small number of unexpected diplotype calls in three independent sets of samples, i.e. calls suggested the presence of a CYP2D6∗4 subvariant containing 1023C>T. Gene resequencing did not reveal any unknown SNPs in the primer or probe binding sites in any of the samples, but all affected samples featured a trio of SNPs on their CYP2D6∗4 allele between one of the PCR primer and probe binding sites. While the phenomenon was ultimately overcome by an alternate assay utilizing a PCR primer excluding the SNP trio, the mechanism causing this phenomenon remains elusive. This rare and unexpected event underscores the importance of assay validation in samples representing a variety of genotypes, but also vigilance of assay performance in highly polymorphic genes such as CYP2D6.

Original languageEnglish (US)
Article number9257
JournalScientific reports
StatePublished - Mar 19 2015

Bibliographical note

Funding Information:
This project was supported in part by the National Institute of Child Health and Development R01 HD058556-05 (J.S.L. and A.G.), the National Institute for Drug Abuse R01 DA035736 (M.C., A.G. and A.K.R.), the National Institute of Mental Health R01 MH070935 (J.H.N.) and R01 MH70564 (M.A.S.), the CAMH Pharmacogenetics Program: Ministry of Research and Innovation, Mr. and Mrs. Larry Tanenbaum (N.F. and D.I.) and K08MH083888 (J.R.B.). We would also like to thank Mrs Shitalben Patel for technical support and laboratory assistance. Liver tissue specimen were obtained through the project entitled ‘‘Laboratory of Developmental Biology’’which is supported by grant 5R24HD0008836 of the National Institute of Health, Eunice Kennedy Shriver National Institute of Child Health & Human Development. The content does not necessarily represent the official views of the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the National Institutes of Health.

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© 2015, Nature Publishing Group. All rights reserved.


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