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Pharmacogenomic testing interrogates germline sequence variants implicated in interindividual drug response variability to infer a drug response phenotype and to guide medication management for certain drugs. Specifically, discrete aspects of pharmacokinetics, such as drug metabolism, and pharmacodynamics, as well as drug sensitivity, can be predicted by genes that code for proteins involved in these pathways. Pharmacogenomics is unique and differs from inherited disease genetics because the drug response phenotype can be drug-dependent and is often unrecognized until an unexpected drug reaction occurs or a patient fails to respond to a medication. Genes and variants with sufficiently high levels of evidence and consensus may be included in a clinical pharmacogenomic test; however, result interpretation and phenotype prediction can be challenging for some genes and medications. This document provides a resource for laboratories to develop and implement clinical pharmacogenomic testing by summarizing publicly available resources and detailing best practices for pharmacogenomic nomenclature, testing, result interpretation, and reporting., Competing Interests: Conflict of Interest M.K.T., E.L., G.A.M., S.R., V.M.P., and S.A.S. serve as directors in clinical laboratories that perform a breadth of genetic and genomic analyses on a fee for service basis. The other authors declare no conflicts of interest., (Copyright © 2021 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.)

Background: Hydrocodone is the most prescribed opioid in the US. The objective was to evaluate associations between genetic, intrinsic, and extrinsic patient factors, plasma hydrocodone and metabolites, common side effects, and pain scores in a cohort of orthopedic surgery patients., Methods: Data for each patient was collected by review of the electronic hospital record (EHR), and patient interview. Patients were recruited from those with trauma or undergoing scheduled elective surgery for total knee replacement or total hip at the University of Louisville Hospital, Baptist East Hospital, and Jewish Hospital, Louisville, KY. Plasma opiate concentrations and a targeted genotyping panel was performed., Results: There were statistically significant correlations with daily (p < 0.001) and total dose (p = 0.002) of hydrocodone in hospital and duration of opioid therapy. The length of opioid administration was significantly shorter in CYP2D6 EM/UM versus CYP2D6 PM/IM patients (p = 0.018). Subjects with the OPRM1 c.118G variant were also on opioids longer (p = 0.022). The effect of co-administration of a CYP2D6 inhibitor had a significant effect on the length of opioid therapy (P < 0.001). And not surprisingly the effect of the inhibitor adjusted CYP2D6 phenotype was greater in both the hospital stay period and days of opioid use post hospital discharge (p < 0.001)., Conclusions: Based on this study, patients should be evaluated for the use of inhibitors of CYP2D6, during hydrocodone therapy can alter the phenotype of the patient (phenocopy) and increase the probability that the patient will be on opioids for longer periods of time., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Pharmacogenetic testing increasingly is available from clinical and research laboratories. However, only a limited number of quality control and other reference materials currently are available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories (Camden, NJ), has characterized 179 DNA samples derived from Coriell cell lines. Testing included the recharacterization of 137 genomic DNAs that were genotyped in previous Genetic Testing Reference Material Coordination Program studies and 42 additional samples that had not been characterized previously. DNA samples were distributed to volunteer testing laboratories for genotyping using a variety of commercially available and laboratory-developed tests. These publicly available samples will support the quality-assurance and quality-control programs of clinical laboratories performing CYP2D6 testing., (Copyright © 2019 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)

Introduction: The dihydropyrimidine dehydrogenase gene (DPYD)*9A (c.85T>C) genotype is relatively common. The correlation between DPYD*9A genotype and dihydropyrimidine dehydrogenase (DPD) deficiency phenotype is controversial. In a cohort of 28 patients, DPYD*9A was the most commonly diagnosed variant (13 patients [46%]) and there was a noticeable genotype-phenotype correlation. In this study we genotyped a larger cohort of a mixed racial background to explore the prevalence of DPYD*9A variant and to confirm the genotype-phenotype correlation., Patients and Methods: Between 2011 and 2018, in addition to genotyping for high-risk DPYD variants (DPYD*2A, DPYD*13 and DPYD*9B), genotyping for DPYD*9A variant was performed on 113 patients with gastrointestinal malignancies treated with fluoropyrimidines. Fluoropyrimidines-associated toxicity was graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events (version 5.0). Fisher exact test was used for statistical analysis., Results: Heterozygous and homozygous DPYD*9A genotypes were identified in 46 (41%) and 11 (10%) patients, respectively. Among patients with DPYD*9A genotypes (n = 57), men and women represented 30 (53%) and 27 (47%) patients, respectively. Caucasian, African American, and other ethnicities represented 29 (50.9%), 26 (45.6%), and 2 (3.5%) patients, respectively. Grade 3/4 toxicities were experienced in 26 patients with DPYD*9A genotype (3 patients had homozygous status) and in 20 patients with wild type DPYD*9A (P = .4405). In patients who received full-dose fluoropyrimidines (n = 85), Grade 3/4 toxicities were experienced in 22 patients with DPYD*9A genotype (2 patients had homozygous status), and in 17 patients with wild type DPYD (P = .8275)., Conclusion: In our updated analysis, the prevalence of heterozygous and homozygous DPYD*9A genotypes were 41% and 10%, respectively. The correlation between DPYD*9A genotype and DPD clinical phenotype was not reproduced. The noticeable correlation that we previously reported is likely because of small sample size and selection bias., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Understanding levels of in utero drug exposure is important to properly customize the immediate, as well as ongoing, medical and social management needs of affected newborns. Here, we present the development of a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the detection and quantification of 4 cannabinoid analytes in two neonatal matrices. The analytes targeted were Δ 9 -tetrahydrocannabinal (THC), 11-nor-9-carboxy-THC (THCA), 11-hydroxy-THC (11-OH-THC), and cannabinol (CBN). The matrices analyzed were umbilical cord tissue and meconium. A fifth analyte, cannabidiol (CBD), was also detected uniquely in meconium. Extracts were analyzed by LC-MS/MS in negative electrospray ionization mode. Paired meconium and umbilical cord samples (i.e., one specimen from each matrix collected from each single birth, n = 46 pairs) were tested to evaluate concentration and metabolite profiles. THCA was detected in all positive (containing one or more analytes) meconium samples (n = 32). CBN, THC, 11-OH-THC, and CBD were present in 57% (n = 26), 39% (n = 18), 24% (n = 11), and 20% (n = 9), respectively. Concentrations were lower in the umbilical cord samples for all analytes (i.e., 0.27-537 ng/g for meconium and 0.1-9 ng/g for umbilical cord). In umbilical cord THCA was also detected in all positive samples (n = 19) while THC, CBN, and 11-OH-THC were present in 24% (n = 11), 17% (n = 8), and 11% (n = 5), respectively. Testing neonatal matrices for cannabinoids could be used to support studies designed to detect newborns exposed to cannabis in utero , as well as provide data that could be examined for correlations with clinical and social outcomes., (© 2019 The Association for Mass Spectrometry: Applications to the Clinical Lab (MSACL). Published by Elsevier B.V. All rights reserved.)

In the past twenty-one years, 17 new antiepileptic drugs have been approved for use in the United States and/or Europe. These drugs are clobazam, ezogabine (retigabine), eslicarbazepine acetate, felbamate, gabapentin, lacosamide, lamotrigine, levetiracetam, oxcarbazepine, perampanel, pregabalin, rufinamide, stiripentol, tiagabine, topiramate, vigabatrin and zonisamide. Therapeutic drug monitoring is often used in the clinical dosing of the newer anti-epileptic drugs. The drugs with the best justifications for drug monitoring are lamotrigine, levetiracetam, oxcarbazepine, stiripentol, and zonisamide. Perampanel, stiripentol and tiagabine are strongly bound to serum proteins and are candidates for monitoring of the free drug fractions. Alternative specimens for therapeutic drug monitoring are saliva and dried blood spots. Therapeutic drug monitoring of the new antiepileptic drugs is discussed here for managing patients with epilepsy., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Background: Copper and zinc are essential trace elements and nutrients, which have important roles in physiology and disease and as cofactors in many metabolic pathways. We established age- and gender-specific reference intervals for serum copper and zinc, with a large healthy pediatric population., Methods: A total of 2115 clinically healthy children, 85.4% Caucasian, were enrolled: 1098 boys and 1017 girls 0.5-1 8y. Serum copper and zinc concentrations were measured by inductively coupled plasma-mass spectrometry (analytical measurement range: 10-400 μg/dl for each). Statistical analyses and related calculations were performed using the STATA Statistical software and R software., Results: There were no significant effects of gender or fasting status. For copper, but not zinc, there were significant differences in the reference intervals by age. Based on the central 95% and 95% confidence intervals, the resulting reference interval determined for serum zinc was 64-124 μg/dl. The age-dependent reference intervals for serum copper were 75-153 μg/dl for those <10.3 y, 64-132 μg/dl for those 10.3-12.5 y and 57-129 μg/dl for those >12.5 y., Conclusions: Our data defined reference intervals for serum copper and zinc in an American, clinically healthy, pediatric population., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Background: Lamotrigine is an anti-epileptic drug used as adjunct therapy for seizures. Lamotrigine is commonly used in pregnant women with epilepsy, a population in which therapeutic drug monitoring (TDM) is useful to optimize dose. Drug-drug interactions that can induce or inhibit metabolism or elimination and impaired hepatic function are also possible indications for lamotrigine TDM. Chromatographic techniques are currently used for performing most TDM of lamotrigine, but this may change, as automated immunoassays were recently introduced., Methods: Immunoassays available through Seradyn and ARK Diagnostics were validated using a Beckman AU400e automated chemistry analyzer. The intra-day precision was accessed with 5 replicates of three quality control materials, and inter-assay precision was estimated by assaying the same material over 4 days. Linearity was evaluated by serially diluting a spiked sample and measuring it in duplicate. The 2 methods were compared with ultra high performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) using 44 authentic patient specimens., Results: The intra-day (n=5) and inter-assay (n=20) coefficients of variation were ≤7.5% for the 3 levels tested. The analytical measurement ranges were confirmed as stated by the manufacturers (0 or 1-40 μg/ml). The percent recovery of the quality control materials and Deming regression for the 44 patient results showed good agreement of both immunoassays when compared to the UPLC-MS/MS assay., Conclusion: The lamotrigine assays studied here produced a slightly lower result than UPLC-MS/MS but were precise and easy to perform., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Background: CYP2C19 variants have been demonstrated to play an important role in determining response to clopidogrel and outcomes while on clopidogrel therapy. Predicting patient response through pre-therapeutic genotyping may therefore guide selection of antiplatelet therapy., Methods: CYP2C19 genotypes were determined for 111 samples with the eSensor and compared with the Autogenomics expanded CYP2C19 panel, Luminex reagents, and bi-directional sequencing. Samples were obtained from the University of Chicago, ARUP Laboratories, and the Coriell repositories. Reproducibility studies were performed with 5 DNA samples with known CYP2C19 genotypes., Results: Complete concordance was observed for all samples and all platforms. DNA concentrations as low as 0.05 ng/μl may be used on the eSensor platform. There was 100% reproducibility observed with 2.5% incidence of invalid tests., Conclusions: The eSensor CYP2C19 genotyping assay is accurate and compares well with 2 current commercial platforms. With a relatively rapid turn-around time of ~4 h and a high rate (97.5%) of valid tests, the eSensor can be translated into clinical use to identify slow and rapid metabolizers of clopidogrel who may benefit from alternate therapy or unconventional dosing of clopidogrel. An observed limitation of the eSensor is a maximum capacity of 24 tests/run., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Background: We describe a fully-automated turbulent-flow liquid chromatography-tandem mass spectrometry method for the detection of tricyclic antidepressant drugs (amitriptyline, desipramine, imipramine, and nortriptyline) in serum., Methods: Human serum and an internal standard were injected directly onto a Cyclone-P online solid-phase extraction (SPE) column (0.5 x 50 mm). Following removal of serum proteins and other components the analytes were transferred to a Hypersil Gold C-18 (50 x 3 mm) analytical column. Elution occurred with a gradient of water and acetonitrile each with 0.1% formic acid. Analytes were ionized and detected over a 3.5 min analysis time by electrospray-ionization mass spectrometry with selected reaction monitoring (SRM). Matrix effects were well-characterized and carryover, precision, linearity, recovery and limits of detection and quantitation were evaluated., Results: The simple and complex precision CVs for all compounds were < or = 16%. The limits of detection and quantitation for all drugs were < or = 3 ng/ml and <20 ng/ml, respectively. Recoveries were between 97 and 114%. Slopes for method comparison plots were all >0.96. Proficiency testing materials had values within 2 SDI of peer group means for all drugs., Conclusion: Based on validation data, this is a specific, sensitive fully-automated method for rapid quantitation of tricyclic antidepressants in serum., (Copyright 2010 Elsevier B.V. All rights reserved.)

Meconium has become the specimen of choice for determining fetal exposure to drugs of abuse, but its physical complexity can cause interferences from matrix effects. A new method to determine 9-carboxy-11-nor-Delta(9)-THC (9-THCA) and 11-hydroxy-Delta(9)-THC (11-OH-THC) using two-dimensional (2D) GC-MS was developed to reduce interferences and carryover. The method was validated using 70 spiked samples prepared in drug-free meconium and 46 residual patient specimens that were confirmed to contain cannabinoids. Ten patient specimens that failed to confirm due to interferences using the previous GC-MS method were analyzed using the new 2D method and 9-THCA was quantitated in all ten samples. The 2D GC-MS method improved chromatography which significantly reduced interferences and carryover when compared to the previous GC-MS method.

The development and characterization of a one-step homogeneous immunoassay-based multiwell ImmunoChip is reported for the simultaneous detection and quantitation of antiepileptic drugs (AEDs). The assay platform uses a cloned enzyme donor immunoassay (CEDIA) and a Beta-Glo assay system for generation of bioluminescent signal. Results of the one-step CEDIA for three AEDs (carbamazepine, phenytoin, and valproic acid), in the presence of serum, correlate well with the values determined by fluorescence polarization immunoassay. CEDIA intra- and interassay coefficients of variation are less than 10%. A microfabrication process, xurography, was used to produce the multiwell ImmunoChip. Assay reagents were dispensed and lyophilized in a three-layer pattern. The multiwell ImmunoChip prototype was used to detect and quantify AEDs in serum samples containing all three drugs. Luminescent signals generated from each well were recorded with a charge-coupled device (CCD) camera. The assays performed on an ImmunoChip were fast (5 min), requiring only small volumes of both the reagents (<1 microl/well) and the serum sample. The ImmunoChip assay platform described in this article may be well suited for therapeutic monitoring of drugs and metabolites at the point-of-care setting.