The Clinical Pharmacogenetics Implementation Consortium (CPIC) TPMT/NUDT15 Pharmacogene Curation Expert Panel (PCEP) conducted a comprehensive review of clinical, laboratory, and computational evidence to determine the clinical function assignments for TPMT and NUDT15 star alleles. These genes are critical for the metabolism of thiopurines, which are widely used in the treatment of cancer and autoimmune disorders. Standardized allele function assignment is essential for predicting metabolizer phenotypes and pharmacogenetics-guided thiopurine dosing. The work presented here includes the first designation of decreased function alleles for both TPMT and NUDT15, reflecting new clinical data that demonstrate partial loss of enzymatic activity and reduced dose tolerance. The panel also reclassified several alleles previously assigned uncertain or unknown function. The functional assignments were informed by a standardized framework incorporating clinical data, such as thiopurine tolerance and toxicity, as well as in vitro protein activity, ex vivo enzymatic measurements, and in silico variant effect prediction tools. These updates enhance the precision of genotype-to-phenotype mapping and support more personalized thiopurine therapy across diverse patient populations.

Importance Apolipoprotein L1 locus ( APOL1 ) high-risk alleles are associated with incidence of chronic kidney disease (CKD) among people with African ancestry. Few studies have examined the effect of genetic return of results on blood pressure (BP) management and control. Objective To determine whether providing APOL1 high-risk genotype results to people with hypertension and their clinicians would reduce systolic BP (SBP) and improve CKD screening and diagnosis. Design, Setting, and Participants From July 1, 2020, to September 30, 2023, adults aged 18 to 70 years with hypertension and self-reported African ancestry were enrolled at 14 institutions and 54 clinical sites across the US. Eligible patients either (1) lacked diagnoses of diabetes and CKD or (2) had a diagnosis of CKD with or without diabetes. Interventions Participants were randomized to receive APOL1 genotype results immediately (intervention) or 6 months after enrollment (control). Clinical decision support encouraged appropriate CKD screening, diagnosis, and antihypertensive therapy. Main Outcomes and Measures The primary outcome was change in SBP in individuals with APOL1 high-risk allelles at 3 months, assessed in a modified intention-to-treat analysis. Prespecified per-protocol subgroup analyses included those with uncontrolled BP (baseline SBP ≥140 mm Hg or diastolic blood pressure ≥90 mm Hg), uncontrolled BP while receiving antihypertensive therapy, and CKD at enrollment. Secondary outcomes included urine microalbumin screening and new CKD diagnoses. Results Of 6754 individuals recruited (mean [SD] age, 55.3 [10.3] years; 4310 women [63.8%]), 954 (14.1%; mean [SD] age, 54.9 [10.0] years; 600 women [62.9%]) had 2 APOL1 risk alleles. At 3 months, there was no difference in SBP between the intervention and control groups (between-group difference, −0.3 mm Hg [95% CI, −2.7 to 2.1 mm Hg]). Among 377 individuals with uncontrolled BP, the mean SBP change was −4.1 mm Hg (95% CI, −7.7 to −0.5 mm Hg) more in the intervention group than the control group ( P = .004). SBP improvement was also observed for the intervention in the subgroup of patients with uncontrolled BP receiving antihypertensive therapy (SPB difference, −4.3 mm Hg [95% CI −8.0 to −0.5 mm Hg]; P = .004), but not the CKD subgroup (SPB difference, 0.8 mm Hg [95% CI, −3.0 to 4.5 mm Hg]). Provision of APOL1 genotype led to increased urine microalbumin screening (between-group difference, 17.3% [95% CI, 9.6%-24.9%]; P < .001) and CKD diagnoses (between-group difference, 5.7% [95% CI, 2.2%-9.3%]; P = .002) at 6 months. Conclusions and Relevance Provision of APOL1 genotype high-risk results to participants and clinicians was not associated with SBP reduction overall. Among the subset of patients with uncontrolled BP, the intervention group had a significant SBP reduction. APOL1 disclosure also increased the rate of CKD screening and diagnosis. Effects of reporting APOL1 genotype merit further investigation among those with uncontrolled BP. Trial Registration ClinicalTrials.gov Identifier: NCT04191824

P2Y12 inhibitor selection involves numerous factors, including CYP2C19 genetics, since evidence demonstrates reduced clopidogrel efficacy in patients with decreased or no function CYP2C19 variants. In 2020, Indiana University health embedded interruptive clinical decision support (CDS) alerts in the electronic health record (EHR) to recommend alternative P2Y12 inhibitors for patients with decreased CYP2C19 function who had undergone percutaneous coronary intervention (PCI). The objective of this study was to evaluate prescriber response to these CDS alerts. Utilizing alert response data and P2Y12 inhibitor prescriptions from October 2020 to December 2023, we evaluated prescriber response for 362 patients who had a mean of 2.2 (SD: 1.7) CYP2C19-clopidogrel alerts fire post-PCI. Alert recommendations were accepted 24.5% ± 36.8% (mean ± SD) of the time. Alternative (i.e., non-clopidogrel) P2Y12 inhibitors were prescribed for 22.4% ± 36.8% of days during the year following PCI. Alerts were accepted more for CYP2C19 poor metabolizers than for intermediate metabolizers (P = 0.03). Each year after 2020 was associated with a 4.6% increase in the days prescribed alternative P2Y12 inhibitors. In contrast, increasing age was associated with decreased alert acceptance and decreased percentage of days prescribed alternatives, and concomitant oral anticoagulant use was associated with decreased percentage of days prescribed alternatives. Provider clinical judgment was the most common alert override reason, accounting for 68% of clinician responses. Our findings demonstrate that CYP2C19-clopidogrel CDS alerts promoted genotype-guided P2Y12 inhibitor prescribing in some cases (~22% of study days). Future research should better determine prescriber reasons for rejecting alert recommendations and establish best implementation practices to complement CDS alerts.

Barriers to incorporating pharmacogenetics into routine clinical practice in the United States are well documented. Initial surveys by the Clinical Pharmacogenetics Implementation Consortium (CPIC) in 2009 and 2010 identified barriers across four key domains that have hindered the widespread adoption of clinical pharmacogenetic testing. These are presented verbatim as: (i) absence of a definition of the processes required to interpret genotype information and to translate genetic information into clinical actions; (ii) need for recommended drug/gene pairs to implement clinically now; (iii) clinician resistance to consider pharmacogenetic information at the bedside; and (iv) concerns about test costs and reimbursement. Over time, many of these challenges have been overcome, and clinical pharmacogenetic testing has subsequently reached broader implementation. Despite this progress, several barriers remain that block further adoption. This narrative review used authors' expertise and experience to identify and describe current barriers to pharmacogenetic implementation across seven domains in the United States: equity and inclusion; guidelines and supporting evidence; regulatory agency oversight; payer coverage and insurance; availability of quality pharmacogenetic tests; electronic health records; and provider and patient education. Within each domain, it revisits past successes and challenges and explores remaining barriers. We also propose solutions to address ongoing challenges across these domains, including further expansion of recommendations beyond pharmacogenetic-specific guidelines, standards for designing clinical decision support tools, and broader pharmacogenetics education. Addressing these remaining obstacles directs work to enable broader adoption of clinical pharmacogenetic implementation to ultimately improve patient outcomes.

Regulations, accreditation standards, and professional guidance require laboratories to use reference materials for assay development, validation, quality control, and proficiency testing of clinical genetic tests. There are, however, few publicly available reference materials for most genetic tests. To address this issue, the CDC's Genetic Testing Reference Material Program (GeT-RM), the Coriell Institute for Medical Research, and the genetic testing community have conducted 19 studies, including nine for pharmacogenetic (PGx) and human leukocyte antigen (HLA) testing, to generate characterized, renewable, and publicly available DNA samples for use as reference materials. Because new PGx alleles are frequently identified, and allele designations change over time, many samples were reanalyzed for the same gene(s) in subsequent GeT-RM studies. These studies used more comprehensive and sensitive methods and panels that examined additional single-nucleotide variants and/or star alleles to expand and update the consensus genotypes. Up-to-date information is available in two newly established resources: the GeT-RM Consolidated PGx and HLA Table and the GeT-RM PGx Search Tool. These resources contain all available PGx and HLA genotypes for 363 publicly available samples characterized during nine GeT-RM PGx or HLA studies for 34 genes/loci in a consolidated and searchable format.

Pharmacogenetics is the study of the genetic determinants of drug response variability, and increasing enthusiasm for implementing clinical pharmacogenetic testing is evidenced by the growing number of personalized medicine programs and the recent availability of clinical practice guidelines to facilitate the interpretation of pharmacogenetic test results. Although not all cancer therapies have germline genetic variants associated with response variability, some treatments have been found to be significantly influenced by germline variants in genes that encode enzymes involved in drug absorption, distribution, metabolism, and/or excretion. Despite challenges to demonstrate clinical utility, clinical tests are currently available for selected genes where clinical validity has largely been established. This chapter describes pharmacogenetic applications for personalized cancer treatment, including DPYD, UGT1A1, G6PD, CYP2D6, and TPMT/NUDT15.

Pharmacogenomics (PGx), the study of inherited genomic variation and drug response or safety, is a vital tool in precision medicine. In oncology, testing to identify PGx variants offers patients the opportunity for customized treatments that can minimize adverse effects and maximize the therapeutic benefits of drugs used for cancer treatment and supportive care. Because individuals of shared ancestry share specific genetic variants, PGx factors may contribute to outcome disparities across racial and ethnic categories when genetic ancestry is not taken into account or mischaracterized in PGx research, discovery, and application. Here, we examine how the current scientific understanding of the role of PGx in differential oncology safety and outcomes may be biased toward a greater understanding and more complete clinical implementation of PGx for individuals of European descent compared with other genetic ancestry groups. We discuss the implications of this bias for PGx discovery, access to care, drug labeling, and patient and provider understanding and use of PGx approaches. Testing for somatic genetic variants is now the standard of care in treatment of many solid tumors, but the integration of PGx into oncology care is still lacking despite demonstrated actionable findings from PGx testing, reduction in avoidable toxicity and death, and return on investment from testing. As the field of oncology is poised to expand and integrate germline genetic variant testing, it is vital that PGx discovery and application are equitable for all populations. Recommendations are introduced to address barriers to facilitate effective and equitable PGx application in cancer care.

The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This article provides recommendations for a minimum panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories when designing assays for PGx testing. The Association for Molecular Pathology PGx Working Group considered the functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations. The ultimate goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This article focuses on clinical TPMT and NUDT15 PGx testing, which may be applied to all thiopurine S-methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15)-related medications. These recommendations are not to be interpreted as prescriptive, but to provide a reference guide.

In 2019, Indiana University launched the Precision Health Initiative to enhance the institutional adoption of precision medicine, including pharmacogenetics (PGx) implementation, at university-affiliated practice sites across Indiana. The overarching goal of this PGx implementation program was to facilitate the sustainable adoption of genotype-guided prescribing into routine clinical care. To accomplish this goal, we pursued the following specific objectives: (i) to integrate PGx testing into existing healthcare system processes; (ii) to implement drug-gene pairs with high-level evidence and educate providers and pharmacists on established clinical management recommendations; (iii) to engage key stakeholders, including patients to optimize the return of results for PGx testing; (iv) to reduce health disparities through the targeted inclusion of underrepresented populations; (v) and to track third-party reimbursement. This tutorial details our multifaceted PGx implementation program, including descriptions of our interventions, the critical challenges faced, and the major program successes. By describing our experience, we aim to assist other clinical teams in achieving sustainable PGx implementation in their health systems.

Billing and reimbursement for medical services are codified by a code set, Current Procedural Terminology (CPT), that is maintained and administered by the American Medical Association. CPT codes are considered level 1 Healthcare Common Procedure Coding System, which is overseen by the Centers for Medicare & Medicaid Services (https://www.cms.gov/medicare/coding-billing/healthcare-common-procedure-system, last accessed January 3, 2024). CPT codes are assigned categories. Category I CPT codes are procedures that are consistent with contemporary medical practice, are widely performed, and demonstrate clinical validity (https://www.ama-assn.org/practice-management/cpt/cpt-overview-and-code-approval, last accessed January 3, 2024).

Abstract Chronic pain is a prevalent condition with enormous economic burden. Opioids such as tramadol, codeine, and hydrocodone are commonly used to treat chronic pain; these drugs are activated to more potent opioid receptor agonists by the hepatic CYP2D6 enzyme. Results from clinical studies and mechanistic understandings suggest that CYP2D6‐guided therapy will improve pain control and reduce adverse drug events. However, CYP2D6 is rarely used in clinical practice due in part to the demand for additional clinical trial evidence. Thus, we designed the ADOPT‐PGx (A Depression and Opioid Pragmatic Trial in Pharmacogenetics) chronic pain study, a multicenter, pragmatic, randomized controlled clinical trial, to assess the effect of CYP2D6 testing on pain management. The study enrolled 1048 participants who are taking or being considered for treatment with CYP2D6‐impacted opioids for their chronic pain. Participants were randomized to receive immediate or delayed (by 6 months) genotyping of CYP2D6 with clinical decision support (CDS). CDS encouraged the providers to follow the CYP2D6‐guided trial recommendations. The primary study outcome is the 3‐month absolute change in the composite pain intensity score assessed using Patient‐Reported Outcomes Measurement Information System (PROMIS) measures. Follow‐up will be completed in July 2024. Herein, we describe the design of this trial along with challenges encountered during enrollment.

The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations for a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clinical laboratories when designing assays for PGx testing. The Association for Molecular Pathology PGx Working Group considered functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, and other technical considerations for PGx testing when developing these recommendations. The goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This document will focus on clinical CYP3A4 and CYP3A5 PGx testing that may be applied to all CYP3A4- and CYP3A5-related medications. These recommendations are not to be interpreted as prescriptive but to provide a reference guide. The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations for a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clinical laboratories when designing assays for PGx testing. The Association for Molecular Pathology PGx Working Group considered functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, and other technical considerations for PGx testing when developing these recommendations. The goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This document will focus on clinical CYP3A4 and CYP3A5 PGx testing that may be applied to all CYP3A4- and CYP3A5-related medications. These recommendations are not to be interpreted as prescriptive but to provide a reference guide. Clinical providers can use pharmacogenomics (PGx) testing to facilitate medication selection and prescribe appropriate doses for their patients for certain drugs with sufficient evidence to support clinical implementation. There is a wide spectrum of variant alleles or variants that are interrogated by clinical PGx tests (https://www.ncbi.nlm.nih.gov/gtr, last accessed February 10, 2023).1CAP/ACMG Biochemical and Molecular Genetics CommitteePharmacogenetics, PGX-B, 2021 Proficiency Testing Program. College of American Pathologists, Northfield, IL2021Google Scholar,2Pratt V.M. Everts R.E. Aggarwal P. Beyer B.N. Broeckel U. Epstein-Baak R. Hujsak P. Kornreich R. Liao J. Lorier R. Scott S.A. Smith C.H. Toji L.H. Turner A. Kalman L.V. Characterization of 137 genomic DNA reference materials for 28 pharmacogenetic genes: a GeT-RM collaborative project.J Mol Diagn. 2016; 18: 109-123Abstract Full Text Full Text PDF PubMed Scopus (94) Google Scholar Some tests use comprehensive genotyping panels or sequencing to detect many variants in a pharmacogene, whereas others are designed to detect only a limited number of variants and may not identify variants that are most relevant to clinical care. This can lead to an individual's genotype being reported as a default ∗1 normal function allele or no variants detected, although clinically relevant variants that were not interrogated may be unknowingly present. Ultimately, these differences in test design may cause discrepancies in interpretation, complicate advancement and clinical implementation of PGx testing, and ultimately impact patient care. It is also common for clinical laboratories to design assays without including variants that are preferentially present in population(s) with certain ancestry backgrounds, which potentially leads to underuse and/or incorrect interpretation of PGx testing in such populations. Until recently, there has been little effort to standardize the specific variants that should be included in clinical PGx tests. The Association for Molecular Pathology (AMP) PGx Working Group has developed a series of documents that recommend a minimum set of variants and alleles to include in clinical PGx tests to facilitate standardization across laboratories and ensure that the most clinically relevant variants and alleles are included in clinical PGx tests. The previous documents covered CYP2C19,3Pratt V.M. del Tredici A.L. Hachad H. Ji Y. Kalman L.V. Scott S.A. Weck K.E. Recommendations for clinical CYP2C19 genotyping allele selection: a report of the Association for Molecular Pathology.J Mol Diagn. 2018; 20: 269-276Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar CYP2C9,4Pratt V.M. Cavallari L.H. del Tredici A.L. Hachad H. Ji Y. Moyer A.M. Scott S.A. Whirl-Carrillo M. Weck K.E. Recommendations for clinical CYP2C9 genotyping allele selection: a joint recommendation of the Association for Molecular Pathology and College of American Pathologists.J Mol Diagn. 2019; 21: 746-755Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar genes important for warfarin PGx testing,5Pratt V.M. Cavallari L.H. del Tredici A.L. Hachad H. Ji Y. Kalman L.V. Ly R.C. Moyer A.M. Scott S.A. Whirl-Carrillo M. Weck K.E. Recommendations for clinical warfarin genotyping allele selection: a report of the Association for Molecular Pathology and the College of American Pathologists.J Mol Diagn. 2020; 22: 847-859Abstract Full Text Full Text PDF PubMed Scopus (28) Google Scholar CYP2D6,6Pratt V.M. Cavallari L.H. del Tredici A.L. Gaedigk A. Hachad H. Ji Y. Kalman L.V. Ly R.C. Moyer A.M. Scott S.A. van Schaik R.H.N. Whirl-Carrillo M. Weck K.E. Recommendations for clinical CYP2D6 genotyping allele selection: a joint consensus recommendation of the Association for Molecular Pathology, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, and the European Society for Pharmacogenomics and Personalized Therapy.J Mol Diagn. 2021; 23: 1047-1064Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar and TPMT and NUDT15.7Pratt V.M. Cavallari L.H. Fulmer M.L. Gaedigk A. Hachad H. Ji Y. Kalman L.V. Ly R.C. Moyer A.M. Scott S.A. van Schaik R.H.N. Whirl-Carrillo M. Weck K.E. TPMT and NUDT15 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase.J Mol Diagn. 2022; 24: 1051-1063Abstract Full Text Full Text PDF PubMed Scopus (11) Google Scholar This document extends this series by focusing on two additional cytochrome P450 genes in the CYP3A subfamily of isoenzymes, CYP3A4 and CYP3A5. This document is intended to provide guidance to clinical laboratorians and manufacturers who develop, validate, and/or offer clinical CYP3A4 and CYP3A5 genotyping assays. This document should be implemented together with other relevant clinical guidelines, including those published by the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG), both of which focus primarily on the interpretation of PGx test results and therapeutic recommendations for specific drug-gene pairs (https://www.pharmgkb.org/guidelineAnnotations, last accessed February 10, 2023). The star (∗) allele definitions included in the AMP PGx Working Group recommendations are as defined by the Pharmacogene Variation Consortium.8Gaedigk A. Ingelman-Sundberg M. Miller N.A. Leeder J.S. Whirl-Carrillo M. Klein T.E. The Pharmacogene Variation (PharmVar) Consortium: incorporation of the human cytochrome P450 (CYP) allele nomenclature database.Clin Pharmacol Ther. 2018; 103: 399-401Crossref PubMed Scopus (264) Google Scholar,9Gaedigk A. Casey S.T. Whirl-Carrillo M. Miller N.A. Klein T.E. Pharmacogene Variation Consortium: a global resource and repository for pharmacogene variation.Clin Pharmacol Ther. 2021; 110: 542-545Crossref PubMed Scopus (31) Google Scholar The AMP PGx Working Group uses a two-tier strategy for selection criteria in recommending PGx variants for clinical testing.3Pratt V.M. del Tredici A.L. Hachad H. Ji Y. Kalman L.V. Scott S.A. Weck K.E. Recommendations for clinical CYP2C19 genotyping allele selection: a report of the Association for Molecular Pathology.J Mol Diagn. 2018; 20: 269-276Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar, 4Pratt V.M. Cavallari L.H. del Tredici A.L. Hachad H. Ji Y. Moyer A.M. Scott S.A. Whirl-Carrillo M. Weck K.E. Recommendations for clinical CYP2C9 genotyping allele selection: a joint recommendation of the Association for Molecular Pathology and College of American Pathologists.J Mol Diagn. 2019; 21: 746-755Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar, 5Pratt V.M. Cavallari L.H. del Tredici A.L. Hachad H. Ji Y. Kalman L.V. Ly R.C. Moyer A.M. Scott S.A. Whirl-Carrillo M. Weck K.E. Recommendations for clinical warfarin genotyping allele selection: a report of the Association for Molecular Pathology and the College of American Pathologists.J Mol Diagn. 2020; 22: 847-859Abstract Full Text Full Text PDF PubMed Scopus (28) Google Scholar, 6Pratt V.M. Cavallari L.H. del Tredici A.L. Gaedigk A. Hachad H. Ji Y. Kalman L.V. Ly R.C. Moyer A.M. Scott S.A. van Schaik R.H.N. Whirl-Carrillo M. Weck K.E. Recommendations for clinical CYP2D6 genotyping allele selection: a joint consensus recommendation of the Association for Molecular Pathology, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, and the European Society for Pharmacogenomics and Personalized Therapy.J Mol Diagn. 2021; 23: 1047-1064Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar Briefly, tier 1 recommended alleles are those that meet all the following criteria: i) have a well-characterized effect on the function of the protein and/or gene expression; ii) have an appreciable minor allele frequency (MAF) in a population/genetic ancestry; iii) have publicly available reference materials (RMs); and iv) are technically feasible for clinical laboratories to interrogate using standard molecular testing methods. Tier 2 recommended variant alleles include those that were considered due to having a well-characterized function and/or appreciable MAF but did not meet all the tier 1 criteria. The tier 2 alleles may be upgraded to tier 1 alleles in the future if additional information, RM(s), or advances in testing technology become available. The human cytochrome P450 family 3 subfamily A (CYP3A) accounts for approximately 30% of the total CYP450 enzyme content in the human liver.10Shimada T. Yamazaki H. Mimura M. Inui Y. Guengerich F.P. Interindividual variations in human liver cytochrome P-450 enzymes involved in the oxidation of drugs, carcinogens and toxic chemicals: studies with liver microsomes of 30 Japanese and 30 Caucasians.J Pharmacol Exp Ther. 1994; 270: 414-423PubMed Google Scholar CYP3A serves an important role in the metabolic transformation of a wide variety of compounds, including drugs, corticosteroids, xenobiotics, and carcinogens. CYP3A enzymes are important for metabolizing approximately 50% of marketed drugs,10Shimada T. Yamazaki H. Mimura M. Inui Y. Guengerich F.P. Interindividual variations in human liver cytochrome P-450 enzymes involved in the oxidation of drugs, carcinogens and toxic chemicals: studies with liver microsomes of 30 Japanese and 30 Caucasians.J Pharmacol Exp Ther. 1994; 270: 414-423PubMed Google Scholar, 11Lamba J. Hebert J.M. Schuetz E.G. Klein T.E. Altman R.B. PharmGKB summary: very important pharmacogene information for CYP3A5.Pharmacogenetics Genom. 2012; 22: 555-558Crossref PubMed Scopus (115) Google Scholar, 12Saravanakumar A. Sadighi A. Ryu R. Akhlaghi F. Physicochemical properties, biotransformation, and transport pathways of established and newly approved medications: a systematic review of the top 200 most prescribed drugs vs. the FDA-approved drugs between 2005 and 2016.Clin Pharmacokinet. 2019; 58: 1281-1294Crossref PubMed Scopus (73) Google Scholar including fentanyl, midazolam, quetiapine, paclitaxel, statins, and immunosuppressants. CYP3A4 is the major isoform expressed in most individuals; however, CYP3A5 may contribute to total CYP3A activity because the two isoforms have overlapping substrate specificities (eg, cyclosporine and fentanyl).13Lamba J.K. Lin Y.S. Schuetz E.G. Thummel K.E. Genetic contribution to variable human CYP3A-mediated metabolism.Adv Drug Deliv Rev. 2002; 54: 1271-1294Crossref PubMed Scopus (834) Google Scholar CYP3A5 is the primary extrahepatic CYP3A isoform and thus may contribute also to tissue-specific CYP3A metabolism.13Lamba J.K. Lin Y.S. Schuetz E.G. Thummel K.E. Genetic contribution to variable human CYP3A-mediated metabolism.Adv Drug Deliv Rev. 2002; 54: 1271-1294Crossref PubMed Scopus (834) Google Scholar The CYP3A4 and CYP3A5 genes are located in a CYP3A gene locus on chromosome 7. The CYP3A4/5 genes are oriented on the negative strand of the chromosome, and therefore the coding DNA sequence is the reverse complement of the human reference genome sequence. Because of its abundant expression in both the liver and small intestine,14Paine M.F. Hart H.L. Ludington S.S. Haining R.L. Rettie A.E. Zeldin D.C. The human intestinal cytochrome P450 "pie.".Drug Metab Dispos. 2006; 34: 880-886Crossref PubMed Scopus (721) Google Scholar CYP3A4 contributes significantly to the first-pass and systemic metabolism of substrate drugs. Hence, CYP3A4 is an important determinant for oral bioavailability and systemic clearance and thereby systemic drug exposure. There is substantial interindividual variability in CYP3A4 enzyme activity because of genetic variability, environmental factors, disease state, and comedications (ie, induction and inhibition) (https://medicine.iu.edu/internal-medicine/specialties/clinical-pharmacology/drug-interaction-flockhart-table, last accessed February 10, 2023). Analyzing sequence variation in CYP genes to predict the phenotype or enzymatic activity and adjust dosing accordingly is applied clinically for several genes associated with altered drug response. Genetic variants in CYP3A4 were thought to have a limited contribution to the observed variability in activity because of the unimodal distribution of enzyme activity15Lin Y.S. Dowling A.L.S. Quigley S.D. Farin F.M. Zhang J. Lamba J. Schuetz E.G. Thummel K.E. Co-regulation of CYP3A4 and CYP3A5 and contribution to hepatic and intestinal midazolam metabolism.Mol Pharmacol. 2002; 62: 162-172Crossref PubMed Scopus (405) Google Scholar and wide range of hepatic protein expression.13Lamba J.K. Lin Y.S. Schuetz E.G. Thummel K.E. Genetic contribution to variable human CYP3A-mediated metabolism.Adv Drug Deliv Rev. 2002; 54: 1271-1294Crossref PubMed Scopus (834) Google Scholar In 2011, the CYP3A4∗22 intron 6 variant (NM_017460.6:c.522-191C>T; rs35599367) was characterized using an allelic expression imbalance approach,16Wang D. Guo Y. Wrighton S.A. Cooke G.E. Sadee W. Intronic polymorphism in CYP3A4 affects hepatic expression and response to statin drugs.Pharmacogenomics J. 2011; 11: 274-286Crossref PubMed Scopus (379) Google Scholar which explained 12% of the variability in CYP3A4 enzyme activity among individuals. The CYP3A4∗22 allele predominantly occurs in individuals of European (MAF, 5%) and admixed American (MAF, 2.6%) descent and is less common among individuals of African (MAF, <0.1%) and/or Asian (MAF, <0.6%) descent.17Mulder T.A.M. van Eerden R.A.G. de With M. Elens L. Hesselink D.A. Matic M. Bins S. Mathijssen R.H.J. van Schaik R.H.N. CYP3A4∗22 genotyping in clinical practice: ready for implementation?.Front Genet. 2021; 12711943Crossref PubMed Scopus (24) Google Scholar This variant was also shown to decrease the quantity of mRNA and protein expressed and was correlated with decreased enzymatic activity in vivo.17Mulder T.A.M. van Eerden R.A.G. de With M. Elens L. Hesselink D.A. Matic M. Bins S. Mathijssen R.H.J. van Schaik R.H.N. CYP3A4∗22 genotyping in clinical practice: ready for implementation?.Front Genet. 2021; 12711943Crossref PubMed Scopus (24) Google Scholar The data for association of CYP3A4 genetic variants with drug response are most consistent for quetiapine, an atypical antipsychotic indicated for the treatment of schizophrenia and bipolar disorder. Quetiapine's pharmacologic activity is primarily provided by the parent compound, which is extensively metabolized via CYP3A4. One of its metabolites, N-desalkyl quetiapine (also referred to as norquetiapine), is also active and believed to provide antidepressant effects.18López-Muñoz F. Alamo C. Active metabolites as antidepressant drugs: the role of norquetiapine in the mechanism of action of quetiapine in the treatment of mood disorders.Front Psychiatr. 2013; 4: 102Crossref PubMed Scopus (57) Google Scholar Studies using various established clinical CYP3A4 substrates, such as midazolam and erythromycin, have shown that CYP3A4∗22 results in a 40% reduction in erythromycin clearance and a 21% lower midazolam metabolic ratio.19Elens L. Nieuweboer A. Clarke S.J. Charles K.A. de Graan A.-J. Haufroid V. Mathijssen R.H.J. van Schaik R.H.N. CYP3A4 intron 6 C>T SNP (CYP3A4∗22) encodes lower CYP3A4 activity in cancer patients, as measured with probes midazolam and erythromycin.Pharmacogenomics. 2013; 14: 137-149Crossref PubMed Scopus (41) Google Scholar This CYP3A enzyme was found to be expressed in approximately 10% to 20% of individuals with European ancestry. The full-length coding DNA sequence of CYP3A5 was originally published in 1989.20Schuetz J.D. Molowa D.T. Guzelian P.S. Characterization of a cDNA encoding a new member of the glucocorticoid-responsive cytochromes P450 in human liver.Arch Biochem Biophys. 1989; 274: 355-365Crossref PubMed Scopus (79) Google Scholar CYP3A5∗3, defined by the intronic variant (NM_000777.5:c.219-237A>G; rs776746), is associated with poor metabolism (historically also known as the nonexpressor phenotype).21Hustert E. Haberl M. Burk O. Wolbold R. He Y.Q. Klein K. Nuessler A.C. Neuhaus P. Klattig J. Eiselt R. Koch I. Zibat A. Brockmöller J. Halpert J.R. Zanger U.M. Wojnowski L. The genetic determinants of the CYP3A5 polymorphism.Pharmacogenetics. 2001; 11: 773-779Crossref PubMed Scopus (595) Google Scholar,22Kuehl P. Zhang J. Lin Y. Lamba J. Assem M. Schuetz J. Watkins P.B. Daly A. Wrighton S.A. Hall S.D. Maurel P. Relling M. Brimer C. Yasuda K. Venkataramanan R. Strom S. Thummel K. Boguski M.S. Schuetz E. Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression.Nat Genet. 2001; 27: 383-391Crossref PubMed Scopus (1930) Google Scholar The gene sequence in genome reference consortium human build 37 (GRCh37) corresponds to the CYP3A5∗3 allele (C in the reference genome and G in the coding DNA sequence), whereas the genome reference consortium human build 38 (GRCh38) reference genome corresponds to the CYP3A5∗1 allele (T in the reference genome and A in the coding DNA sequence). Therefore, when using GRCh37 as reference, the CYP3A5∗3 allele is considered the reference sequence and is not reported as a variant. The CYP3A5∗3 no function allele has a frequency of approximately 90% in individuals with European ancestry23van Schaik R.H.N. van der Heiden I.P. van den Anker J.N. Lindemans J. CYP3A5 variant allele frequencies in Dutch Caucasians.Clin Chem. 2002; 48: 1668-1671Crossref PubMed Scopus (275) Google Scholar and ranges widely in other populations, with the lowest frequencies of 24% to 32% being observed in individuals with African ancestry. Frequencies range between 67% and 75% in populations with Asian ancestry. Two other no function alleles, CYP3A5∗6 and CYP3A5∗7, occur predominately in individuals of African ancestry, with reported frequencies of 11% to 19% and 9% to 12%, respectively. These alleles have frequencies of <0.5% in populations of European and Asian ancestry. Approximately 85% of individuals with European ancestry, 50% of individuals with Asian ancestry, and 30% of individuals with African ancestry are CYP3A5 poor metabolizers.23van Schaik R.H.N. van der Heiden I.P. van den Anker J.N. Lindemans J. CYP3A5 variant allele frequencies in Dutch Caucasians.Clin Chem. 2002; 48: 1668-1671Crossref PubMed Scopus (275) Google Scholar The Pharmacogene Variation Consortium CYP3A5 GeneFocus review24Francke M.I. Andrews L.M. Le H.L. van de Wetering J. Clahsen-van Groningen M.C. van Gelder T. van Schaik R.H.N. van der Holt B. de Winter B.C.M. Hesselink D.A. Avoiding tacrolimus underexposure and overexposure with a dosing algorithm for renal transplant recipients: a single arm prospective intervention trial.Clin Pharmacol Ther. 2021; 110: 169-178Crossref PubMed Scopus (19) Google Scholar provides an extensive overview of CYP3A5. For CYP3A5, a strong pharmacogenetic association exists for the metabolism of tacrolimus, which is a commonly prescribed immunosuppressant following solid organ transplant. The parent compound of tacrolimus is pharmacologically active and undergoes extensive metabolism by CYP3A enzymes. CYP3A5 normal and intermediate metabolizers (historically called expressors) have a higher rate of tacrolimus clearance, have lower dose-adjusted trough concentrations, and require higher tacrolimus doses to attain similar blood concentrations compared with poor metabolizers.25Birdwell K.A. Decker B. Barbarino J.M. Peterson J.F. Stein C.M. Sadee W. Wang D. Vinks A.A. He Y. Swen J.J. Leeder J.S. van Schaik R. Thummel K.E. Klein T.E. Caudle K.E. MacPhee I.A.M. Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for CYP3A5 genotype and tacrolimus dosing.Clin Pharmacol Ther. 2015; 98: 19-24Crossref PubMed Scopus (425) Google Scholar Given the narrow therapeutic index of tacrolimus, higher clearance rates have important implications for drug effectiveness as low systemic exposure correlates with increased risk for organ rejection,26Undre N.A. Stevenson P.J. European Tacrolimus Heart Study GroupPharmacokinetics of tacrolimus in heart transplantation.Transplant Proc. 2002; 34: 1836-1838Crossref PubMed Scopus (15) Google Scholar,27Undre N.A. van Hooff J. Christiaans M. Vanrenterghem Y. Donck J. Heeman U. Kohnle M. Zanker B. Land W. Morales J.M. Andrés A. Schäfer A. Stevenson P. Low systemic exposure to tacrolimus correlates with acute rejection.Transplant Proc. 1999; 31: 296-298Crossref PubMed Scopus (156) Google Scholar although the correlation of CYP3A5 genotype with biopsy-confirmed acute rejection has not been proven. Studies have demonstrated earlier attainment of therapeutic tacrolimus concentrations with genotype-guided dosing versus empirical dosing.28Pao C.C. Yao D.S. Lin M.Y. Lin C.Y. Hsieh T.T. Hepatitis B virus DNA in cervicovaginal cells.Arch Pathol Lab Med. 1991; 115: 607-609PubMed Google Scholar,29Min S. Papaz T. Lafreniere-Roula M. Nalli N. Grasemann H. Schwartz S.M. Kamath B.M. Ng V. Parekh R.S. Manlhiot C. Mital S. A randomized clinical trial of age and genotype-guided tacrolimus dosing after pediatric solid organ transplantation.Pediatr Transplant. 2018; 22e13285Crossref PubMed Scopus (31) Google Scholar On the basis of pharmacokinetic data, the DPWG has developed recommendations for CYP3A4 genotype-based dosing for quetiapine (https://www.g-standaard.nl/risicoanalyse/B0005991.PDF, last accessed February 10, 2023). Practice guideline for CYP3A5 genotype-based dosing for tacrolimus is provided by CPIC.25Birdwell K.A. Decker B. Barbarino J.M. Peterson J.F. Stein C.M. Sadee W. Wang D. Vinks A.A. He Y. Swen J.J. Leeder J.S. van Schaik R. Thummel K.E. Klein T.E. Caudle K.E. MacPhee I.A.M. Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for CYP3A5 genotype and tacrolimus dosing.Clin Pharmacol Ther. 2015; 98: 19-24Crossref PubMed Scopus (425) Google Scholar In addition, the US Food and Drug Administration lists the CYP3A5/tacrolimus gene-drug pair in their pharmacogenetic association table for which the available data support therapeutic management recommendations (https://www.fda.gov/medical-devices/precision-medicine/table-pharmacogenetic-associations, last accessed February 10, 2023). Selection of a molecular platform to use for testing PGx variants is based on many considerations that include but are not limited to technical feasibility of analysis of the genomic regions of interest, cost, laboratory workflow, test volume, and desired test turnaround time. Clinically relevant variants in the CYP3A4 and CYP3A5 genes are amenable to interrogation through molecular techniques commonly used in clinical laboratories, including targeted genotyping or sequencing (Sanger sequencing or next-generation sequencing) approaches. It is at the discretion of the specific laboratory to select a preferred testing platform. Unless long-read sequencing technology is used, almost all commonly used molecular testing platforms are unable to determine phasing information for detected variants. Therefore, as for other PGx genotyping assays, assigning diplotypes from genotyping or sequencing data is mostly empirical or inferred. The AMP PGx Working Group is composed of subject matter experts from the College of American Pathologists, CDC, CPIC, DPWG, European Society for Pharmacogenomics and Personalized Therapy, Pharmacogenomics Knowledgebase (PharmGKB), Pharmacogene Variation Consortium, and the PGx clinical testing and research communities. CYP3A4 and CYP3A5 variant alleles were reviewed and classified into tiers based on four criteria that received equal weight during deliberations.i)Functional characterization of the allele (ie, whether it is known to affect expression of the gene or function of the encoded protein).ii)Presence at an appreciable MAF in a population/genetic ancestry.30Huddart R. Fohner A.E. Whirl-Carrillo M. Wojcik G.L. Gignoux C.R. Popejoy A.B. Bustamante C.D. Altman R.B. Klein T.E. Standardized biogeographic grouping system for annotating populations in pharmacogenetic research.Clin Pharmacol Ther. 2019; 105: 1256-1262Crossref PubMed Scopus (63) Google Scholar In this CYP3A4 and CYP3A5 recommendation document, the Working Group used an MAF of ≥1% in at least one subpopulation as a criterion for tier 1 alleles, and ≥0.1% for tier 2 alleles based on currently available information from applicable resources (https://www.pharmgkb.org/page/cyp3a5RefMaterials, last accessed February 10, 2023).iii)Availability of RMs (Table 1).31Gaedigk A. Boone E.C. Turner A.J. van Schaik R.H.N. Chernova D. Wang W.Y. Broeckel U. Granfield C.A. Hodge J.C. Ly R.C. Lynnes T.C. Mitchell M.W. Moyer A.M. Oliva J. Kalman L.V. Characterization of reference materials for CYP3A4 and CYP3A5: a GeT-RM collaborative project.J Mol Diagn. 2023; 25: 655-664Abstract Full Text Full Text PDF Scopus (2) Google ScholarTable 1Reference MaterialsCYP3A4 allelesCoriell ID†Available at https://www.coriell.org.Diplotype‡According to Gaedigk et al.31CYP3A5 allelesCoriell ID†Available at https://www.coriell.org.Diplotype‡According to Gaedigk et al.31CYP3A4∗2HG00276∗1/∗2CYP3A5∗1NA07439∗1/∗1CYP3A4∗3NA12006∗1/∗3CYP3A5∗1NA18564∗1/∗1CYP3A4∗4HG00525∗1/∗4CYP3A5∗3HG00436∗3/∗3CYP3A4∗4HG01865∗1/∗4CYP3A5∗3NA10856∗1/∗3CYP3A4∗5HG01816∗1/∗5CYP3A5∗6NA18518∗1/∗6CYP3A4∗5NA18561∗1/∗5CYP3A5∗6NA19819∗3/∗6CYP3A4∗6NA18941∗1/∗6CYP3A5∗7NA19143∗6/∗7CYP3A4∗7HG00334∗1/∗7CYP3A5∗7NA19920∗7/∗7CYP3A4∗7NA20813∗1/∗7CYP3A5∗7NA18484∗1/∗7CYP3A4∗8HG00368∗1/∗8CYP3A5∗8NoneNoneCYP3A4∗9HG02146∗1/∗9CYP3A5∗9NoneNoneCYP3A4∗10HG00122∗1/∗10CYP3A4∗10HG00734∗10/∗22CYP3A4∗11HG00139∗3/∗11CYP3A4∗12HG03159∗1/∗12CYP3A4∗12NA19035∗1/∗12CYP3A4∗13NoneNoneCYP3A4∗14NoneNoneCYP3A4∗15NA19109∗1/∗15CYP3A4∗15NA19226∗1/∗15CYP3A4∗16NA18966∗1/∗16CYP3A4∗16NA18978∗1/∗16CYP3A4∗17NoneNoneCYP3A4∗18HG02134∗1/∗18CYP3A4∗18HG00704∗1/∗18CYP3A4∗19HG03885∗1/∗19CYP3A4∗19NA21095∗1/∗19CYP3A4∗20HG01275∗1/∗20CYP3A4∗21NA18603∗1/∗21CYP3A4∗22NA23313∗1/∗22CYP3A4∗22NA24008∗22/∗22CYP3A4∗23HG02054∗1/∗23CYP3A4∗24NA19160∗1/∗24CYP3A4∗26NoneNoneCYP3A4∗28HG02029∗1/∗28CYP3A4∗29NoneNoneCYP3A4∗30NoneNoneCYP3A4∗31NoneNoneCYP3A4∗32NoneNoneCYP3A4∗33NoneNoneCYP3A4∗34NoneNoneCYP3A4∗35NA12336∗1/∗35CYP3A4∗36NA07439∗1/∗1CYP3A4∗38NA18934∗1/38ID, identifier.† Available at https://www.coriell.org.‡ According to Gaedigk et al.31Gaedigk A. Boone E.C. Turner A.J. van Schaik R.H.N. Chernova D. Wang W.Y. Broeckel U. Granfield C.A. Hodge J.C. Ly R.C. Lynnes T.C. Mitchell M.W. Moyer A.M. Oliva J. Kalman L.V. Characterization of reference materials for CYP3A4 and CYP3A5: a GeT-RM collaborative project.J Mol Diagn. 2023; 25: 655-664Abstract Full Text Full Text PDF Scopus (2) Google Scholar Open table in a new tab iv)Technical feasibility for clinical laboratories to interrogate using standard molecular testing methods. This criterion was determined to not be relevant for these CYP3A4 and CYP3A5 recommendations, as none of the reviewed variant alleles was considered difficult to interrogate using standard methods. ID, identifier. In addition, commercially available genotyping platforms (Supplemental Table S1) were reviewed for assessing the ability of laboratories to implement the Working Group recommendations; however, these data were not used as a determinant of tier assignment. The AMP PGx Working Group used MAF and functional information from CPIC, PharmGKB, and the scientific literature. T

Adverse drug events (ADEs) account for a significant mortality, morbidity, and cost burden. Pharmacogenetic testing has the potential to reduce ADEs and inefficacy. The objective of this INGENIOUS trial (NCT02297126) analysis was to determine whether conducting and reporting pharmacogenetic panel testing impacts ADE frequency. The trial was a pragmatic, randomized controlled clinical trial, adapted as a propensity matched analysis in individuals ( N = 2612) receiving a new prescription for one or more of 26 pharmacogenetic-actionable drugs across a community safety-net and academic health system. The intervention was a pharmacogenetic testing panel for 26 drugs with dosage and selection recommendations returned to the health record. The primary outcome was occurrence of ADEs within 1 year, according to modified Common Terminology Criteria for Adverse Events (CTCAE). In the propensity-matched analysis, 16.1% of individuals experienced any ADE within 1-year. Serious ADEs (CTCAE level ≥ 3) occurred in 3.2% of individuals. When combining all 26 drugs, no significant difference was observed between the pharmacogenetic testing and control arms for any ADE (Odds ratio 0.96, 95% CI: 0.78–1.18), serious ADEs (OR: 0.91, 95% CI: 0.58–1.40), or mortality (OR: 0.60, 95% CI: 0.28–1.21). However, sub-group analyses revealed a reduction in serious ADEs and death in individuals who underwent pharmacogenotyping for aripiprazole and serotonin or serotonin-norepinephrine reuptake inhibitors (OR 0.34, 95% CI: 0.12–0.85). In conclusion, no change in overall ADEs was observed after pharmacogenetic testing. However, limitations incurred during INGENIOUS likely affected the results. Future studies may consider preemptive, rather than reactive, pharmacogenetic panel testing.

PURPOSE Precision medicine approaches, including germline pharmacogenetics (PGx) and management of drug-drug interactions (DDIs), are likely to benefit patients with advanced cancer who are frequently prescribed multiple concomitant medications to treat cancer and associated conditions. Our objective was to assess the potential opportunities for PGx and DDI management within a cohort of adults with advanced cancer. METHODS Medication data were collected from the electronic health records for 481 subjects since their first cancer diagnosis. All subjects were genotyped for variants with clinically actionable recommendations in Clinical Pharmacogenetics Implementation Consortium guidelines for 13 pharmacogenes. DDIs were defined as concomitant prescription of strong inhibitors or inducers with sensitive substrates of the same drug-metabolizing enzyme and were assessed for six major cytochrome P450 (CYP) enzymes. RESULTS Approximately 60% of subjects were prescribed at least one medication with Clinical Pharmacogenetics Implementation Consortium recommendations, and approximately 14% of subjects had an instance for actionable PGx, defined as a prescription for a drug in a subject with an actionable genotype. The overall subject-level prevalence of DDIs and serious DDIs were 50.3% and 34.8%, respectively. Serious DDIs were most common for CYP3A, CYP2D6, and CYP2C19, occurring in 24.9%, 16.8%, and 11.7% of subjects, respectively. When assessing PGx and DDIs together, approximately 40% of subjects had at least one opportunity for a precision medicine–based intervention and approximately 98% of subjects had an actionable phenotype for at least one CYP enzyme. CONCLUSION Our findings demonstrate numerous clinical opportunities for germline PGx and DDI management in adults with advanced cancer.