Pharmacogenetics (PGx)

PHARMACOGENETIC TESTING

Targeting genes involved with drug metabolism and transport pathways

PGx testing (pharmacogenetic analysis) is performed to provide information for clinicians prescribing medication for patients. The University of Arizona Molecular Clinical Core (AZClinCore) pharmacogenetics panel targets 61 variable sites within 18 different genes involved with drug metabolism and transport pathways. DNA is isolated from a patient cheek swab and genomic regions containing the various polymorphic sites are amplified and subsequently tested using the Agena MassArray™ platform. The allelic status of each site is then recorded and results are converted into a patient haplotype profile. These haplotype profiles can be used to assess the metabolic status of known drug classes and specific medications for each individual patient

• The DNA is isolated from patient cheek swab samples.
• DNA is both amplified and extended in separate reactions via the Agena VeriDose® with CYP2D6 CNV panel for downstream analysis on the Agena MassArray™ platform to generate patient genotypes.
• The patient genotypes are converted to a haplotype profile for use in determining metabolic status of the patient.

Targeted Genes:

CYP3A5   CYP2C19   CYP2C9  CYP2D6  CYP3A4  DRD2 

FACTOR II   FACTOR V   MTHFR   OPRM1  SLCO1B1  SULT4A1 

ABCB1   VKORC1  APOE  COMT   CYP1A2   CYP2B6

CLINICAL UTILITY

Recent research has linked a number of genes, including CYP2C19, CYP2C9, CYP2D6, and VKORC1, with an individual’s drug response.^1-4 Single nucleotide polymorphisms (SNP) in these genes have been shown to influence the rate of drug metabolism.^5-7 An extended panel of genes may help to guide clinical research for therapeutic treatment and response.^8-9

The Arizona Molecular Clinical Core (AZClinCore) clinically validated Agena VeriDose® with CYP2D6 CNV Panel provides genotype and haplotype reports for clinical providers. The AZClinCore does not include interpretation of the results for clinical application. The information provided from this test may supplement decision making and should only be used in conjunction with routine monitoring by a physician. PGx testing is not intended for diagnosis, to detect response to therapy, or to help select the optimal therapy for patients without a physician’s input and guidance.

Note: Test results do not rule out the possibility that an individual could be a carrier of other mutations/variations not detected by this gene variation panel. Rare variants surrounding these alleles may also affect our detection of genetic variations. Other non-genetic and genetic factors that are not tested by this assay can affect the management and sensitivity of drugs. The interpretation is given as a probability. Therefore, this genetic information shall be interpreted in conjunction with other clinical findings and familial history for the administration of specific drugs.

Criteria for patient testing

Any patient deemed eligible by their physician is qualified for testing with this assay. The information provided from this test may supplement decision making and should only be used in conjunction with routine monitoring by a physician. The intended use of this assay is for use as a decision support tool for clinicians when making medication determinations for an individual patient.

Specimen requirements

Sample Type: Buccal swab (contact AZClinCore for validated product types); whole blood collected in a lavender EDTA tube (K2EDTA, K3EDTA)

*DNA samples may be received if they are the only samples available. DNA specimens are only accepted if the nucleic acid isolation occurred in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or the CMS. Such samples will be processed, however, a successful outcome may not be guaranteed.

Turnaround Time

Results delivered 10–15 working days from receipt of the tissue sample(s) by AZClinCore, based on business hours of the laboratory: Monday through Friday, 9am–5pm Arizona Time. Contact AZClinCore for expedited turn around.

Methodology and Additional Details

Agena Biosystems iPLEX® VeriDose Core Panel uses site-specific primers to amplify target regions of interest. Data is acquired using a MassARRAY MALDI-TOF mass spectrometer. Results analyzed using MassARRAY PGx Report software. AZClinCore reports on the following genes and loci: ABCB1-rs1045642; APOE-rs429358, rs7412; COMT-rs4680; CYP1A2-rs2069514, rs762551, rs12720461, rs56107638, rs72547513; CYP2B6-rs28399499, rs3745274; CYP2C19-rs4244285, rs4986893, rs28399504, rs56337013, rs72552267, rs72558186, rs41291556, rs12248560; CYP2C9-rs1799853, rs1057910, rs56165452, rs28371686, rs9332131, rs7900194, rs28371685, rs9332239, rs72558187, rs72558190, rs1304490498; CYP2D6-rs16947, rs1135840, rs35742686, rs3892097, rs1065852, rs5030655, rs5030867, rs5030865, rs5030656, rs5030862, rs774671100, rs28371706, dup4125_4133, rs72549353, rs72549354, rs59421388, rs28371725, rs201377835 ; CYP3A4-rs55785340, rs4987161, rs35599367; CYP3A5-rs28365083, rs776746, rs41303343, rs10264272; DRD2-rs1800497; F2-rs1799963; F5-rs6025; MTHFR-rs1801131, rs1801133; OPRM1-rs1799971; SLCO1B1-rs4149056; SULT4A1-rs763120; VKORC1-rs9923231.

Agena Biosystems iPLEX® CYP2D6 Panel uses site-specific primers to assay interrogate 22 loci in 7 regions of across the CYP2D6 gene. Data is acquired using a MassARRAY MALDI-TOF mass spectrometer. Results were analyzed using the MassARRAY PGx Report software. AZClinCore reports on CYP2D6 gene copy number (0N, 1N, 2N and 3N+) and detects common CYP2D6 hybrid alleles. CNV results are reported with qualification of ‘high’, ‘medium’ and ‘low’ confidence. CNV call confidence is determined using the coefficient of variation calculated as the difference between the CNV interpretation (0N, 1N, 2N or 3N+) and the average, quantified CNV call. A difference < 0.2 is a high confidence call, a difference >0.2 but < 0.4 is a medium confidence call, and a difference > 0.4 is a low confidence call.

References:

1. Jaja C., et al. “Progressing Preemptive Genotyping of CYP2C19 Allelic Variants for Sickle Cell Disease Patients” Genet Test Mol Biomarkers (2016) 20(10):609-615.
2. Hirose T., et al. “Association of Pharmacokinetics and Pharmacogenomics with Safety and Efficacy of Gefitinib in Patients with EGFR Mutation Positive Advanced Non-Small Cell Lung Cancer” Lung Cancer (2016) 93:69–76
3. Scott S. A., et al. “Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C19 Genotype and Clopidogrel Therapy: 2013 update” Clin Pharmacol Ther (2013) 94(3):317-323
4. Wang L., et al. “Genomics and Drug Response” N Engl J Med (2011) 364:1144-1153
5. Brauch H., et al. “Pharmacogenomics of Tamoxifen Therapy” Clin Chem (2009) 55(10):1770-82
6. Ingelman-Sundberg, Magnus, et al. “Influence of Cytochrome P450 Polymorphisms on Drug Therapies: Pharmacogenetic, Pharmacoepigenetic and Clinical Aspects” Pharmacology & Therapeutics (2007) 496-526
7. Evans W.E. and Relling M.V. “Moving Towards Individualized Medicine with Pharmacogenomics” Nature (2004) 429(6990):464-468
8. Goh L.L. et al., “Analysis of Genetic Variation in CYP450 Genes for Clinical Implementation” PLoS One (2017) 12(1): e0169233

9. Pratt V.M., et al. “Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes” J Mol Diagn (2016) 18(1):109-23