QuantStudio™ 12K Flex pharmacogenomics extended to allele-specific copy number with digital PCR
The rapidly-growing field of pharmacogenomics (PGx) is the study of genetic variation as it relates to drug response, determined by variation in drug metabolism enzyme and transporter (DMET) genes. The significance of PGx will increase as personalized medicine becomes more widely adopted.
A flexible workflow from sample preparation through genotyping, genotype calling, copy number analysis and translation of sample genetic information to star allele haplotype nomenclature is readily available with a combination of the MagMAX™ DNA Isolation System, the QuantStudio™ 12K Flex Real-Time PCR System, and software analysis tools including TaqMan® Genotyper, CopyCaller™ and AlleleTyper™. Options for PGx SNP genotyping assay panels include a set of 158 DME assays derived from the PharmaADME consortium (the TaqMan® OpenArray PGx Panel), the TaqMan® PGx Express Panel (contains 60 popular PGx assays) or a custom panel, choosing from among 2,700 unique TaqMan® DME Assays, 6.2 million predesigned TaqMan® SNP Genotyping and Copy Number Assays. All genotyping assays are available in single tube format, or may be ordered in pre-plated format on OpenArray or TaqMan® Array plates to be run on QuantStudio™ 12K Flex Real-Time PCR System.
For more information about our pharmacogenomics solutions using TaqMan® assays, comprehensive page is available here with links to a PGx brochure, a workflow application note, and a list of commonly ordered PGx assays. In addition, the PGx Experiments User Guide) details about the AlleleTyper™ software for star allele reporting are available.
The important drug metabolism enzyme CYP2D6 is implicated in metabolizing roughly 20% of medications. Over 100 star allele haplotypes have been defined for the highly polymorphic CYP2D6 gene. For samples that carry CYP2D6 duplications and are heterozygous for star alleles associated with different functional categories, it may be important to identify the duplicated allele to accurately determine the metabolizer phenotype. By including the QuantStudio™ 3D Digital PCR System for allele-specific copy-number, an unambiguous CYP2D6 genotype and phenotype can be assigned.
For more information about this application, a recent presentation has been made available here. And of course if you have any questions feel free to leave them in the comments below.