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PII‐28
Author(s) -
Lewis L. D.,
Lee H. K.,
Schurr B. C.,
Jannetto P. J.,
Wong S. H.,
Tsongalis G. J.,
Yeo K. J.
Publication year - 2006
Publication title -
clinical pharmacology and therapeutics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.941
H-Index - 188
eISSN - 1532-6535
pISSN - 0009-9236
DOI - 10.1016/j.clpt.2005.12.153
Subject(s) - genotyping , concordance , genotype , microarray , single nucleotide polymorphism , snp genotyping , snp , cyp2d6 , pyrosequencing , dna microarray , biology , snp array , genetics , computational biology , gene , gene expression
BACKGROUND The Phase I drug metabolizing enzyme, CYP2D6, is highly polymorphic and metabolizes approximately 20% of therapeutic drugs. The objective of this study was to validate a CYP2D6 genotyping assay using the Nanochip® Molecular Biology Workstation (Nanogen Inc., San Diego, CA). MATERIALS AND METHODS Following IRB approval, eighty DNA samples from anonymous patients were obtained. PCR primers, ratio‐references and reporters for SNP detection were provided by Nanogen Inc. For the Nanochip® microarray multipad addressing and duplicate runs were performed to test the intra‐ and inter‐pad, as well as within and between run precision and accuracy for the defined genotypes. RESULTS All 80 DNA samples were genotyped for CYP2D6 *3, *4, *5, *6, *7 and *8 using both Pyrosequencing (Biotage Inc., Uppsala, Sweden) and the Nanochip® microarray. There was 99.4% concordance in the genotype results for these SNPs between both methods. We found one discordant call each for the *5, *6 and *7 SNPs. DNA sequencing for the discordant *6 SNP confirmed the Nanochip® genotype and is pending for the discordant *5 and *7 SNPs. The intra‐ and inter‐pad studies and within run studies were 100% concordant for the Nanochip® microarray. CONCLUSIONS This validation study of the Nanochip® CYP2D6 microarray genotyping system suggested it was accurate and reproducible. Clinical Pharmacology & Therapeutics (2005) 79 , P43–P43; doi: 10.1016/j.clpt.2005.12.153