Clinical Pharmacogenetics Implementation Consortium guideline for CYP2D6 and CYP2C19 genotypes and dosing of tricyclic antidepressants

Functional characterization of CYP2D6 enhancer polymorphisms

CYP2D6 metabolizes nearly 25% of clinically used drugs. Genetic polymorphisms cause large inter-individual variability in CYP2D6 enzyme activity and are currently used as biomarker to predict CYP2D6 metabolizer phenotype. Previously, we had identified a region 115 kb downstream of CYP2D6 as enhancer for CYP2D6, containing two completely linked single nucleotide polymorphisms (SNPs), rs133333 and rs5758550, associated with enhanced transcription. However, the enhancer effect on CYP2D6 expression, and the causative variant, remained to be ascertained. To characterize the CYP2D6 enhancer element, we applied chromatin conformation capture combined with the next-generation sequencing (4C assays) and chromatin immunoprecipitation with P300 antibody, in HepG2 and human primary culture hepatocytes. The results confirmed the role of the previously identified enhancer region in CYP2D6 expression, expanding the number of candidate variants to three highly linked SNPs (rs133333, rs5758550 and rs4822082). Among these, only rs5758550 demonstrated regulating enhancer activity in a reporter gene assay. Use of clustered regularly interspaced short palindromic repeats mediated genome editing in HepG2 cells targeting suspected enhancer regions decreased CYP2D6 mRNA expression by 70%, only upon deletion of the rs5758550 region. These results demonstrate robust effects of both the enhancer element and SNP rs5758550 on CYP2D6 expression, supporting consideration of rs5758550 for CYP2D6 genotyping panels to yield more accurate phenotype prediction.

Pharmacogenetics and analgesic effects of antidepressants in chronic pain management

Antidepressants are widely administered to chronic pain patients, but there is large interindividual variability in their efficacy and adverse effect rates that may be attributed to genetic factors. Studies have attempted to determine the impact of genetic polymorphisms in enzymes and transporters that are involved in antidepressant pharmacokinetics, for example, cytochrome P450 and P-gp. The impacts of genetic polymorphisms in the targets of antidepressants, such as the serotonin receptor or transporter, the noradrenaline transporter and the COMT and monoamine oxydase enzymes, have also been described. This manuscript discusses the current knowledge of the influence of genetic factors on the plasma concentrations, efficacy and adverse effects of the major antidepressants used in pain management.

Polymorphism in CYP2D6 and CYP2C19, members of the cytochrome P450 mixed-function oxidase system, in the metabolism of psychotropic drugs

Numerous studies in the field of psychopharmacological treatment have investigated the possible contribution of genetic variability between individuals to differences in drug efficacy and safety, motivated by the wide individual variation in treatment response. Genomewide analyses have been conducted in several large-scale studies on antidepressant drug response. However, no consistent findings have emerged from these studies. In a recent meta-analysis of genomewide data from the three studies capturing common variation for association with symptomatic improvement and remission revealed the absence of any strong genetic association and failed to replicate results of individual studies in the pooled data. However, there are good reasons to consider the possible importance of pharmacogenetic variants separately. These variants explain a large portion of the manifold variability in individual drug metabolism. More than 20 psychotropic drugs have now been relabelled by the FDA adding information on polymorphic drug metabolism and therapeutic recommendations. Furthermore, dose recommendations for polymorphisms in drug metabolizing enzymes, first and foremost CYP2D6 and CYP2C19, have been issued with the advice to reduce the dosage in poor metabolizers to 50% or less (in eight cases), or to choose an alternative treatment. Beside the well-described role in hepatic drug metabolism, these enzymes are also expressed in the brain and play a role in biotransformation of endogenous substrates. These polymorphisms may therefore modulate brain metabolism and affect the function of the neural substrates of cognition and emotion.

Effects and cost-effectiveness of pharmacogenetic screening for CYP2D6 among older adults starting therapy with nortriptyline or venlafaxine: study protocol for a pragmatic randomized controlled trial (CYSCEtrial)

Background

Nortriptyline and venlafaxine are commonly used antidepressants for treatment of depression in older patients. Both drugs are metabolized by the polymorphic cytochrome P450-2D6 (CYP2D6) enzyme and guidelines for dose adaptations based on the CYP2D6 genotype have been developed. The CYP2D6 Screening Among Elderly (CYSCE) trial is designed to address the potential health and economic value of genotyping for CYP2D6 in optimizing dose-finding of nortriptyline and venlafaxine.

Methods/Design

In a pragmatic randomized controlled trial, patients diagnosed with a major depressive disorder according to the DSM-IV and aged 60 years or older will be recruited from psychiatric centers across the Netherlands. After CYP2D6 genotyping determined in peripheral blood obtained by finger-prick, patients will be grouped into poor, intermediate, extensive, or ultrarapid metabolizers. Patients with deviant genotype (that is poor, intermediate or ultrarapid genotype) will be randomly allocated to an intervention group in which the genotype and dosing advice is communicated to the treating physician, or to a control group in which patients receive care as usual. Additionally, an external reference group of patients with the extensive metabolizer genotype is included. Primary outcome in all groups is time needed to obtain an adequate blood level of the antidepressant drug. Secondary outcomes include adverse drug reactions measured by a shortened Antidepressant Side-Effects Checklist (ASEC), and cost-effectiveness of the screening.

Discussion

Results of this trial will guide policy-making with regard to pharmacogenetic screening prior to treatment with nortriptyline or venlafaxine among older patients with depression.

Trial registration

ClinicalTrials.gov: NCT01778907; registration date: 22 January 2013.

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-015-0561-0) contains supplementary material, which is available to authorized users.

Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes

Haplotypes are often critical for the interpretation of genetic laboratory observations into medically actionable findings. Current massively parallel DNA sequencing technologies produce short sequence reads that are often unable to resolve haplotype information. Phasing short read data typically requires supplemental statistical phasing based on known haplotype structure in the population or parental genotypic data. Here we demonstrate that the MinION nanopore sequencer is capable of producing very long reads to resolve both variants and haplotypes of HLA-A, HLA-B and CYP2D6 genes important in determining patient drug response in sample NA12878 of CEPH/UTAH pedigree 1463, without the need for statistical phasing. Long read data from a single 24-hour nanopore sequencing run was used to reconstruct haplotypes, which were confirmed by HapMap data and statistically phased Complete Genomics and Sequenom genotypes. Our results demonstrate that nanopore sequencing is an emerging standalone technology with potential utility in a clinical environment to aid in medical decision-making.

Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes

Haplotypes are often critical for the interpretation of genetic laboratory observations into medically actionable findings. Current massively parallel DNA sequencing technologies produce short sequence reads that are often unable to resolve haplotype information. Phasing short read data typically requires supplemental statistical phasing based on known haplotype structure in the population or parental genotypic data. Here we demonstrate that the MinION nanopore sequencer is capable of producing very long reads to resolve both variants and haplotypes of HLA-A, HLA-B and CYP2D6 genes important in determining patient drug response in sample NA12878 of CEPH/UTAH pedigree 1463, without the need for statistical phasing. Long read data from a single 24-hour nanopore sequencing run was used to reconstruct haplotypes, which were confirmed by HapMap data and statistically phased Complete Genomics and Sequenom genotypes. Our results demonstrate that nanopore sequencing is an emerging standalone technology with potential utility in a clinical environment to aid in medical decision-making.

Pharmacogenomic testing for neuropsychiatric drugs: current status of drug labeling, guidelines for using genetic information, and test options

Advancements in pharmacogenomics have introduced an increasing number of opportunities to bring personalized medicine into clinical practice. Understanding how and when to use this technology to guide pharmacotherapy used to treat psychiatric and neurological (neuropsychiatric) conditions remains a challenge for many clinicians. Currently, guidelines exist to assist clinicians in the use of existing genetic information for drug selection and/or dosing for the tricyclic antidepressants, carbamazepine, and phenytoin. Additional language in the product labeling suggests that genetic information may also be useful for determining the starting and target doses, as well as drug interaction potential, for a number of other drugs. In this review, we outline the current status of pharmacogenomic testing for neuropsychiatric drugs as it pertains to information contained in drug labeling, consensus guidelines, and test panels, as well as considerations related to obtaining tests for patients.

Characterization of hepatic enzyme activity in older adults with dementia: potential impact on personalizing pharmacotherapy

Objective

To determine the frequency of pharmacogenomic variants and concurrent medications that may alter the efficacy and tolerability of acetylcholinesterase inhibitors (AChEIs).

Materials and methods

A multisite cross-sectional study was carried out across four memory care practices in the greater Indianapolis area. Participants were adults aged 65 years and older with a diagnosis of probable or possible Alzheimer’s disease (AD) (n=105). Blood samples and self-reported medication data were collected. Since two of the three AChEIs are metabolized by cytochrome P450 (CYP)-2D6, we determined the frequency of functional genetic variants in the CYP2D6 gene and calculated their predicted CYP2D6-activity scores. Concurrent medication data were collected from self-reported medication surveys, and their predicted effect on the pharmacokinetics of AChEIs was determined based on their known effects on CYP2D6 and CYP3A4/5 enzyme activities.

Results

Among the 105 subjects enrolled, 72% were female and 36% were African American. Subjects had a mean age of 79.6 years. The population used a mean of eight medications per day (prescription and nonprescription). The CYP2D6 activity score frequencies were 0 (3.8%), 0.5 (4.8%), 1.0 (36.2%), 1.5–2.0 (51.4%), and >2.0 (3.8%). Nineteen subjects (18.1%) used a medication considered a strong or moderate inhibitor of CYP2D6, and eight subjects (7.6%) used a medication considered a strong or moderate inhibitor of CYP3A4/5. In total, 28.6% of the study population was predicted to have reduced activity of the CYP2D6 or CYP3A4/5 enzymes due to either genetic variants or concomitant medications.

Conclusion

Both pharmacogenetic variants and concurrent drug therapies that are predicted to alter the pharmacokinetics of AChEIs should be evaluated in older adults with AD. Pharmacogenetic and drug-interaction data may help personalize AD therapy and increase adherence by improving tolerability.

The promise of psychiatric pharmacogenomics

Clinicians already face "personalized" medicine every day while experiencing the great variation in toxicities and drug efficacy among individual patients. Pharmacogenetics studies are the platform for discovering the DNA determinants of variability in drug response and tolerability. Research now focuses on the genome after its beginning with analyses of single genes. Therapeutic outcomes from several psychotropic drugs have been weakly linked to specific genetic variants without independent replication. Drug side effects show stronger associations to genetic variants, including human leukocyte antigen loci with carbamazepine-induced dermatologic outcome and MC4R with atypical antipsychotic weight gain. Clinical implementation has proven challenging, with barriers including a lack of replicable prospective evidence for clinical utility required for altering medical care. More recent studies show promising approaches for reducing these barriers to routine incorporation of pharmacogenetics data into clinical care.

Pharmacological treatment of chronic non-cancer pain in pediatric patients

Chronic pain in children and young adults occurs frequently and contributes to early disability as well as personal and familial distress. A biopsychosocial approach to evaluation and treatment is recommended. Within this approach, there is a role for pharmacologic intervention. A variety of medications are used for chronic pain conditions in pediatric patients. Medication classes include anticonvulsants, muscle relaxants, antidepressants, opioids, local anesthetics, and anti-inflammatory drugs. Data is sparse, and most medications are used without condition-specific approval by national regulatory agencies such as the Food and Drug Administration in the US and the European Medicines Agency. In the absence of evidence on which to base practice, optimal drug therapy decisions rest on understanding proposed mechanisms of pain conditions, extrapolation from adult data-when such exists, and empirical and experiential knowledge. Drug delivery systems have evolved, and practitioners have to decide amongst not only medication classes, but also routes of delivery. Opioids are not recommended for use by non-pain specialists for the treatment of pediatric chronic pain, and even then the issues are more complex than can be addressed here. This article reviews the major medications used for pediatric chronic pain conditions.

Genomic architecture of pharmacological efficacy and adverse events

The pharmacokinetic and pharmacodynamic disciplines address pharmacological traits, including efficacy and adverse events. Pharmacogenomics studies have identified pervasive genetic effects on treatment outcomes, resulting in the development of genetic biomarkers for optimization of drug therapy. Pharmacogenomics-based tests are already being applied in clinical decision making. However, despite substantial progress in identifying the genetic etiology of pharmacological response, current biomarker panels still largely rely on single gene tests with a large portion of the genetic effects remaining to be discovered. Future research must account for the combined effects of multiple genetic variants, incorporate pathway-based approaches, explore gene-gene interactions and nonprotein coding functional genetic variants, extend studies across ancestral populations, and prioritize laboratory characterization of molecular mechanisms. Because genetic factors can play a key role in drug response, accurate biomarker tests capturing the main genetic factors determining treatment outcomes have substantial potential for improving individual clinical care.

Incorporation of pharmacogenomics into routine clinical practice: the Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline development process

The Clinical Pharmacogenetics Implementation Consortium (CPIC) publishes genotype-based drug guidelines to help clinicians understand how available genetic test results could be used to optimize drug therapy. CPIC has focused initially on well-known examples of pharmacogenomic associations that have been implemented in selected clinical settings, publishing nine to date. Each CPIC guideline adheres to a standardized format and includes a standard system for grading levels of evidence linking genotypes to phenotypes and assigning a level of strength to each prescribing recommendation. CPIC guidelines contain the necessary information to help clinicians translate patient-specific diplotypes for each gene into clinical phenotypes or drug dosing groups. This paper reviews the development process of the CPIC guidelines and compares this process to the Institute of Medicine’s Standards for Developing Trustworthy Clinical Practice Guidelines.

Genetic determinants of selective serotonin reuptake inhibitor related sexual dysfunction

Sexual dysfunction is a troubling obstacle for individuals being treated for depression and can be caused by both depressive symptoms as well as antidepressant drugs. Selective serotonin reuptake inhibitors (SSRIs) represent a class of antidepressants commonly associated with sexual dysfunction, even after symptomatic improvement. Candidate gene studies have identified associations between sexual dysfunction and altered SSRI pharmacokinetics or to the neurotransmitter systems affected by depression and SSRI treatment. The multifactorial nature of this phenotype and study heterogeneity are currently limitations to the translation of these findings to clinical use. Larger, prospective studies of genetic-guided antidepressant selection may help to clarify the clinical utility of pharmacogenetics in minimizing sexual side effects.

Pilot study: incorporation of pharmacogenetic testing in medication therapy management services

Aim: To describe the rationale and design of a pilot study evaluating the integration of pharmacogenetic (PGx) testing into pharmacist-delivered medication therapy management (MTM). Study rationale: Clinical delivery approaches of PGx testing involving pharmacists may overcome barriers of limited physician knowledge about and experience with testing. Study design: We will assess the addition of PGx testing to MTM services for cardiology patients taking three or more medications including simvastatin or clopidogrel. We will measure the impact of MTM plus PGx testing on drug/dose adjustment and clinical outcomes. Factors associated with delivery, such as time to prepare and conduct MTM and consult with physicians will be recorded. Additionally, patient interest and satisfaction will be measured. Anticipated results: We anticipate that PGx testing can be practically integrated into standard a MTM service, providing a viable delivery model for testing. Conclusion: Given the lack of evidence of an effective PGx delivery models, this study will provide preliminary evidence regarding a pharmacist-delivered approach.

Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease

The potential for personalized sequencing to individually optimize medical treatment in diseases such as cancer and for pharmacogenomic application is just beginning to be realized, and the utility of sequencing healthy individuals for managing health is also being explored. The data produced requires additional advancements in interpretation of variants of unknown significance to maximize clinical benefit. Nevertheless, personalized sequencing, only recently applied to clinical medicine, has already been broadly applied to the discovery and study of disease. It is poised to enable the earlier and more accurate diagnosis of disease risk and occurrence, guide prevention and individualized intervention as well as facilitate monitoring of healthy and treated patients, and play a role in the prevention and recurrence of future disease. This article documents the advancing capacity of personalized sequencing, reviews its impact on disease-oriented scientific discovery and anticipates its role in the future of medicine.

Distribution of CYP2D6 alleles and phenotypes in the Brazilian population

The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions.

Priority pharmacogenetics for the African continent: focus on CYP450

Countries in Africa have a high burden of communicable disease, and are experiencing an increase in noncommunicable diseases due to the effects of globalization, industrialization and urbanization. The costs incurred through adverse drug reactions and nonresponsiveness to therapy further aggravates the situation, and the application of pharmacogenetic principles is likely to provide some relief. Having undertaken an extensive evaluation of CYP450 reports in Africa, our objective was to map out areas of need based on regional disease burdens. The data confirms a paucity of CYP450 reports and illustrates large regions for which no population information exists. There is a dire need to address the health problems of Africa, and wide-scale pharmacogenetic profiling of these populations will add significantly to improving patient care on the continent. Priority pharmacogenetics for the African continent gives precedence to the profiling of clinically relevant pharmacogenetic biomarkers, and defines the immediate need in the context of disease burden.

Preemptive clinical pharmacogenetics implementation: current programs in five US medical centers

Although the field of pharmacogenetics has existed for decades, practioners have been slow to implement pharmacogenetic testing in clinical care. Numerous publications describe the barriers to clinical implementation of pharmacogenetics. Recently, several freely available resources have been developed to help address these barriers. In this review, we discuss current programs that use preemptive genotyping to optimize the pharmacotherapy of patients. Array-based preemptive testing includes a large number of relevant pharmacogenes that impact multiple high-risk drugs. Using a preemptive approach allows genotyping results to be available prior to any prescribing decision so that genomic variation may be considered as an inherent patient characteristic in the planning of therapy. This review describes the common elements among programs that have implemented preemptive genotyping and highlights key processes for implementation, including clinical decision support.

Striking a balance in communicating pharmacogenetic test results: promoting comprehension and minimizing adverse psychological and behavioral response

OBJECTIVE

Pharmacogenetic (PGx) testing can provide information about a patient's likelihood to respond to a medication or experience an adverse event, and be used to inform medication selection and/or dosing. Promoting patient comprehension of PGx test results will be important to improving engagement and understanding of treatment decisions.

METHODS

The discussion in this paper is based on our experiences and the literature on communication of genetic test results for disease risk and broad risk communication strategies.

RESULTS

Clinical laboratory reports often describe PGx test results using standard terminology such as 'poor metabolizer' or 'ultra-rapid metabolizer.' While this type of terminology may promote patient recall with its simple, yet descriptive nature, it may be difficult for some patients to comprehend and/or cause adverse psychological or behavioral responses.

CONCLUSION

The language used to communicate results and their significance to patients will be important to consider in order to minimize confusion and potential psychological consequences such as increased anxiety that can adversely impact medication-taking behaviors.

PRACTICE IMPLICATIONS

Due to patients' unfamiliarity with PGx testing and the potential for confusion, adverse psychological effects, and decreased medication adherence, health providers need to be cognizant of the language used in discussing PGx test results with patients.

Pharmacogenomic testing for treatment resistant depression

The percentage of patients who have failed to completely or partially respond to multiple trials of antidepressants at adequate doses and for an adequate duration of therapy has varied in the literature and is considered substantial. Numerous strategies exist to treat poor antidepressant response, but often medications are selected on a “trial and error” basis. Genetic factors may play a role in poor response or intolerance to treatment with antidepressants which lead to treatment failures. Currently, available genetic testing as well as genetic testing currently under research may help guide clinicians with proper medication and dose selection.

Implementation and utilization of genetic testing in personalized medicine

Clinical genetic testing began over 30 years ago with the availability of mutation detection for sickle cell disease diagnosis. Since then, the field has dramatically transformed to include gene sequencing, high-throughput targeted genotyping, prenatal mutation detection, preimplantation genetic diagnosis, population-based carrier screening, and now genome-wide analyses using microarrays and next-generation sequencing. Despite these significant advances in molecular technologies and testing capabilities, clinical genetics laboratories historically have been centered on mutation detection for Mendelian disorders. However, the ongoing identification of deoxyribonucleic acid (DNA) sequence variants associated with common diseases prompted the availability of testing for personal disease risk estimation, and created commercial opportunities for direct-to-consumer genetic testing companies that assay these variants. This germline genetic risk, in conjunction with other clinical, family, and demographic variables, are the key components of the personalized medicine paradigm, which aims to apply personal genomic and other relevant data into a patient’s clinical assessment to more precisely guide medical management. However, genetic testing for disease risk estimation is an ongoing topic of debate, largely due to inconsistencies in the results, concerns over clinical validity and utility, and the variable mode of delivery when returning genetic results to patients in the absence of traditional counseling. A related class of genetic testing with analogous issues of clinical utility and acceptance is pharmacogenetic testing, which interrogates sequence variants implicated in interindividual drug response variability. Although clinical pharmacogenetic testing has not previously been widely adopted, advances in rapid turnaround time genetic testing technology and the recent implementation of preemptive genotyping programs at selected medical centers suggest that personalized medicine through pharmacogenetics is now a reality. This review aims to summarize the current state of implementing genetic testing for personalized medicine, with an emphasis on clinical pharmacogenetic testing.

Pharmacogenetic insights into migraine treatment in children

Pediatric migraine is a disabling condition that can affect the everyday activities and emotional states of children. Due to the multifactorial character of the pathology and the variety of the disease's phenotypes, establishment of an effective treatment is often challenging. Pharmacological treatment is often administered off-label and includes very different drugs, from analgesics to antidepressants. Since interindividual variability in therapy response commonly causes inefficacy and an exacerbation of symptoms, pharmacogenetics may help to decrease the prescription rate of useless or unsafe drugs. If there are many drugs used in migraine, then there are even more candidate or established pharmacogenetic markers that are implicated in clinical profiles. This article presents the current situation regarding the pharmacogenetics of drugs used in pediatric migraine.

Depression, antidepressants, and bone health in older adults: a systematic review

OBJECTIVES

To examine the association between depression, antidepressant use, and bone health in older adults and the implications for treatment.

DESIGN

Systematic review.

SETTING

All studies that measured depression or antidepressant exposure and bone mineral density (BMD).

PARTICIPANTS

Adults aged 60 and older.

MEASUREMENTS

Age, site of BMD measurement using dual-energy X-ray absorptiometry (DXA), measure of depression or depressive symptoms, association between BMD changes, and depression or antidepressant use.

RESULTS

Nineteen observational studies met the final inclusion criteria; no experimental studies were found. Several cross-sectional and longitudinal studies found that depression or depressive symptoms were associated with a decrease in BMD. Few studies and only two longitudinal studies addressed the association between serotonin reuptake inhibitor (SRI) antidepressant use and a decrease in BMD and they had conflicting results.

CONCLUSION

Depression and depressive symptoms are associated with low bone mass and accelerated bone loss in older adults; putative mechanisms underlying this relationship are discussed. There is insufficient evidence that SRI antidepressants adversely affect bone health. Thus, a change in current recommendations for the use of antidepressants in older adults is not justified at the present time. Given the high public health significance of this question, more studies are required to determine whether (and in whom) antidepressants may be deleterious for bone health.

Pharmacogenetics of antidepressant treatment in obsessive–compulsive disorder: an update and implications for clinicians

Obsessive–compulsive disorder (OCD) is a chronic neuropsychiatric disorder with high genetic influence. Antidepressants such as serotonin reuptake inhibitors, are widely accepted as the first-line medications for OCD; however, approximately 50% of OCD patients show poor response. Personalized medicine utilizing genetic testing has recently received much attention because the variability of antidepressant response and tolerability are partly due to an individual’s genetic variations. This has led to researchers investigating the role of specific genetic factors on antidepressant response and utility of testing in the clinical realm. Genetic test panels are showing promise for guiding antidepressant treatment to improve outcomes in depression. This article will review the most recent findings in the pharmacogenetics of OCD and its related disorders. Promising results have been reported for several serotonergic and glutamatergic system genes and the cytochrome CYP450 liver enzyme genes, which appear to play an important role in OCD and antidepressant response.

Pharmacogenetic biomarkers for predicting drug response

Drug response shows significant interpatient variability and evidence that genetics influences outcome of drug therapy has been known for more than five decades. However, the translation of this knowledge to clinical practice remains slow. Using examples from clinical practice six considerations about the implementation of pharmacogenetics (PGx) into routine care are discussed: the need for PGx biomarkers; the sources of genetic variability in drug response; the amount of variability explained by PGx; whether PGx test results are actionable; the level of evidence needed for implementation of PGx and the sources of information regarding interpretation of PGx data.

Jumping on the Train of Personalized Medicine: A Primer for Non- Geneticist Clinicians: Part 3. Clinical Applications in the Personalized Medicine Area

The rapid decline of sequencing costs brings hope that personal genome sequencing will become a common feature of medical practice. This series of three reviews aim to help non-geneticist clinicians to jump into the fast-moving field of personalized genetic medicine. In the first two articles, we covered the fundamental concepts of molecular genetics and the methodologies used in genetic epidemiology. In this third article, we discuss the evolution of personalized medicine and illustrate the most recent success in the fields of Mendelian and complex human diseases. We also address the challenges that currently limit the use of personalized medicine to its full potential.

Pharmacogenovigilance: a pharmacogenomics pharmacovigilance program

In this report, we review the importance of pharmacovigilance in detecting postmarketing adverse drug events and the potential for developing pharmacogenovigilance programs by integrating pharmacogenomics with pharmacovigilance. We propose to start developing such a program in primary healthcare systems that use basic features of electronic medical records and have access to large numbers of patients commonly prescribed drugs. Such programs, if carefully designed, may grow over time and hopefully enhance the collection and interpretation of useful data for the clinical applications of pharmacogenomics testing.

Pharmacogenetics in clinical practice: how far have we come and where are we going?

Recent years have seen great advances in our understanding of genetic contributors to drug response. Drug discovery and development around targeted genetic (somatic) mutations has led to a number of new drugs with genetic indications, particularly for the treatment of cancers. Our knowledge of genetic contributors to variable drug response for existing drugs has also expanded dramatically, such that the evidence now supports clinical use of genetic data to guide treatment in some situations, and across a variety of therapeutic areas. Clinical implementation of pharmacogenetics has seen substantial growth in recent years and groups are working to identify the barriers and best practices for pharmacogenetic-guided treatment. The advances and challenges in these areas are described and predictions about future use of genetics in drug therapy are discussed.

Considerations for rare variants in drug metabolism genes and the clinical implications

INTRODUCTION

Large-scale whole genome and exome resequencing studies have revealed that humans have a high level of deleterious rare variation, which has important implications for the design of future pharmacogenetics studies.

AREAS COVERED

Current pharmacogenetic guidelines focus on the implementation of common variation into dosing guidelines. However, it is becoming apparent that rare variation may also play an important role in differential drug response. Current sequencing technologies offer the opportunity to examine rare variation, but there are many challenges associated with such analyses. Nonetheless, if a comprehensive picture of the role that genetic variants play in treatment outcomes is to be obtained, it will be necessary to include the entire spectrum of variation, including rare variants, into pharmacogenetic research.

EXPERT OPINION

In order to implement pharmacogenetics in the clinic, patients should be genotyped for clinically actionable pharmacogenetic variants and patients responding unfavourably to treatment after pharmacogenetics-based dosing should be identified and resequenced to identify additional functionally relevant variants, including rare variants. All derived information should be added to a central database to allow for the updating of existing dosing guidelines. By routinely implementing such strategies, pharmacogenetics-based treatment guidelines will continue to improve.

Obsessive-compulsive disorder

Obsessive-compulsive disorder (OCD) is a common heterogeneous psychiatric disorder manifesting with obsessions and compulsions. Obsessions are intrusive, recurrent, and persistent unwanted thoughts. Compulsions are repetitive behaviors or mental acts that an individual feels driven to perform in response to the obsessions. The heterogeneity of OCD includes themes of obsessions, types of rituals, presence or absence of tics, etiology, genetics, and response to pharmacotherapy. Complications of OCD include interpersonal difficulties, unemployment, substance abuse, criminal justice issues, and physical injuries. Areas of the brain involved in the pathophysiology include the orbitofrontal cortex, anterior cingulate gyrus, and basal ganglia. Overall, OCD may be due to a malfunction in the cortico-striato-thalamo-cortical circuit in the brain. Neurotransmitters implicated in OCD include serotonin, dopamine, and glutamate. Numerous drugs such as atypical antipsychotics and dopaminergic agents can cause or exacerbate OCD symptoms. The etiology includes genetics and neurological insults. Treatment of OCD includes psychotherapy, pharmacotherapy, electroconvulsive therapy, transcranial magnetic simulation, and in extreme cases surgery. Exposure and response prevention is the most effective form of psychotherapy. Selective serotonin reuptake inhibitors (SSRIs) are the preferred pharmacotherapy. Higher doses than listed in the package insert and a longer trial are often needed for SSRIs than compared to other psychiatric disorders. Alternatives to SSRIs include clomipramine and serotonin/norepinephrine reuptake inhibitors. Treatment of resistant cases includes augmentation with atypical antipsychotics, pindolol, buspirone, and glutamate-blocking agents.

Pharmacogenetics in American Indian populations: analysis of CYP2D6, CYP3A4, CYP3A5, and CYP2C9 in the Confederated Salish and Kootenai Tribes

OBJECTIVES

Cytochrome P450 enzymes play a dominant role in drug elimination and variation in these genes is a major source of interindividual differences in drug response. Little is known, however, about pharmacogenetic variation in American Indian and Alaska Native (AI/AN) populations. We have developed a partnership with the Confederated Salish and Kootenai Tribes (CSKT) in northwestern Montana to address this knowledge gap.

METHODS

We resequenced CYP2D6 in 187 CSKT individuals and CYP3A4, CYP3A5, and CYP2C9 in 94 CSKT individuals.

RESULTS

We identified 67 variants in CYP2D6, 15 in CYP3A4, 10 in CYP3A5, and 41 in CYP2C9. The most common CYP2D6 alleles were CYP2D6*4 and *41 (20.86 and 11.23%, respectively). CYP2D6*3, *5, *6, *9, *10, *17, *28, *33, *35, *49, *1xN, *2xN, and *4xN frequencies were less than 2%. CYP3A5*3, CYP3A4*1G, and *1B were detected with frequencies of 92.47, 26.81, and 2.20%, respectively. Allelic variation in CYP2C9 was low: CYP2C9*2 (5.17%) and *3 (2.69%). In general, allele frequencies in CYP2D6, CYP2C9, and CYP3A5 were similar to those observed in European Americans. There was, however, a marked divergence in CYP3A4 for the CYP3A4*1G allele. We also observed low levels of linkage between CYP3A4*1G and CYP3A5*1 in the CSKT. The combination of nonfunctional CYP3A5*3 and putative reduced function CYP3A4*1G alleles may predict diminished clearance of CYP3A substrates.

CONCLUSION

These results highlight the importance of carrying out pharmacogenomic research in AI/AN populations and show that extrapolation from other populations is not appropriate. This information could help optimize drug therapy for the CSKT population.

Common CYP2D6 polymorphisms affecting alternative splicing and transcription: long-range haplotypes with two regulatory variants modulate CYP2D6 activity

Cytochrome P450 2D6 (CYP2D6) is involved in the metabolism of 25% of clinically used drugs. Genetic polymorphisms cause substantial variation in CYP2D6 activity and serve as biomarkers guiding drug therapy. However, genotype-phenotype relationships remain ambiguous except for poor metabolizers carrying null alleles, suggesting the presence of yet unknown genetic variants. Searching for regulatory CYP2D6 polymorphisms, we find that a SNP defining the CYP2D6*2 allele, rs16947 [R296C, 17-60% minor allele frequency (MAF)], previously thought to convey normal activity, alters exon 6 splicing, thereby reducing CYP2D6 expression at least 2-fold. In addition, two completely linked SNPs (rs5758550/rs133333, MAF 13-42%) increase CYP2D6 transcription more than 2-fold, located in a distant downstream enhancer region (>100 kb) that interacts with the CYP2D6 promoter. In high linkage disequilibrium (LD) with each other, rs16947 and the enhancer SNPs form haplotypes that affect CYP2D6 enzyme activity in vivo. In a pediatric cohort of 164 individuals, rs16947 alone (minor haplotype frequency 28%) was associated with reduced CYP2D6 metabolic activity (measured as dextromethorphan/metabolite ratios), whereas rs5758550/rs133333 alone (frequency 3%) resulted in increased CYP2D6 activity, while haplotypes containing both rs16947 and rs5758550/rs133333 were similar to the wild-type. Other alleles used in biomarker panels carrying these variants such as CYP2D6*41 require re-evaluation of independent effects on CYP2D6 activity. The occurrence of two regulatory variants of high frequency and in high LD, residing on a long haplotype, highlights the importance of gene architecture, likely shaped by evolutionary selection pressures, in determining activity of encoded proteins.

Sources of interindividual variability

The efficacy, safety, and tolerability of drugs are dependent on numerous factors that influence their disposition. A dose that is efficacious and safe for one individual may result in sub-therapeutic or toxic blood concentrations in other individuals. A major source of this variability in drug response is drug metabolism, where differences in pre-systemic and systemic biotransformation efficiency result in variable degrees of systemic exposure (e.g., AUC, C max, and/or C min) following administration of a fixed dose.Interindividual differences in drug biotransformation have been studied extensively. It is well recognized that both intrinsic (such as genetics, age, sex, and disease states) and extrinsic (such as diet, chemical exposures from the environment, and even sunlight) factors play a significant role. For the family of cytochrome P450 enzymes, the most critical of the drug metabolizing enzymes, genetic variation can result in the complete absence or enhanced expression of a functional enzyme. In addition, up- and down-regulation of gene expression, in response to an altered cellular environment, can achieve the same range of metabolic function (phenotype), but often in a less reliably predictable and time-dependent manner. Understanding the mechanistic basis for drug disposition and response variability is essential if we are to move beyond the era of empirical, trial-and-error dose selection and into an age of personalized medicine that brings with it true improvements in health outcomes in the therapeutic treatment of disease.

Pharmacogenomic testing and personalized treatment of depression

BACKGROUND

There is wide variation in antidepressant efficacy and tolerability during the treatment of major depressive disorder, a brain disease associated with significant morbidity and mortality risk. The ability to rapidly identify optimal treatment, thereby shortening the time to symptomatic remission, could reduce these risks and associated costs.

CONTENT

Up to 42% of variance in antidepressant response is associated with common genetic variation, and there are over 10 psychotropic medications for which the US Food and Drug Administration-approved labeling reflects a genetic test. Most published studies have examined functional variations in genes of the cytochrome p450 system, relevant to metabolism of many antidepressants. However, there are few data supporting the clinical usefulness of specific pharmacogenetic tests. Randomized trials and cost-effectiveness studies are emerging, but larger-scale studies are needed. Specific challenges in translating genetic association results to clinical practice include need for replication to address risk of type I error, overestimation of effect sizes, absence of data from generalizable cohorts, and absence of comparative data that would suggest one specific intervention over another. Several opportunities to accelerate development and validation of new tools for stratification remain, including integration of these tests with clinical data or other biomarkers and application of electronic health records for test development and investigation.

SUMMARY

Although common genetic variation, particularly in genes of the cytochrome p450 system, has been associated with antidepressant response, evidence that this variation may be successfully applied to guide treatment selection is just emerging. Larger-scale studies facilitated by informatics tools will clarify the usefulness of such tests.

Clinically actionable genotypes among 10,000 patients with preemptive pharmacogenomic testing

Since September 2010, over 10,000 patients have undergone preemptive, panel-based pharmacogenomic testing through the Vanderbilt Pharmacogenomic Resource for Enhanced Decisions in Care and Treatment (PREDICT) program. Analysis of the genetic data from the first 9,589 individuals reveals the frequency of genetic variants is concordant with published allele frequencies. Based on five currently implemented drug-genome interactions, the multiplexed test identified one or more actionable variants in 91% of the genotyped patients and in 96% of African-American patients. Using medication exposure data from electronic medical records, we compared a theoretical “reactive,” prescription-triggered, serial single-gene testing strategy to our preemptive, multiplexed genotyping approach. Reactive genotyping would have generated 14,656 genetic tests. These data highlight three advantages of preemptive genotyping: 1)the vast majority of patients carry at least one pharmacogene variant; 2)data are available at the point of care; and 3)there is a substantial reduction in testing burden compared to a reactive strategy.

Opening Pandora’s box in the UK: a hypothetical pharmacogenetic test for clozapine

Clozapine is a uniquely efficacious antipsychotic drug in treatment-resistant schizophrenia. Its use is restricted due to adverse effects including a rare but dangerous reduction in neutrophils (agranulocytosis) and the mandatory hematological monitoring this entails in many countries. We review the statistical, ethical and legal issues arising from a hypothetical pharmacogenetic test for clozapine, using the UK as an exemplary case for consideration. Our key findings include: a consideration of the probabilistic results that a pharmacogenetic test may return; the impact on drug licensing; and the potential for pharmacogenetic tests for clozapine being used without consent under the UK’s legal framework. We make recommendations regarding regulatory changes applicable to the special case of pharmacogenetic testing in clozapine treatment.

Complexities of CYP2D6 gene analysis and interpretation

Cytochrome P450 2D6 (CYP2D6) plays an important role in the metabolism and bioactivation of about 25% of clinically used drugs including many antidepressants, antipsychotics and opioids. CYP2D6 activity is highly variably ranging from no activity in so-called poor metabolizers to ultrarapid metabolism at the other end of the extreme of the activity distribution. A large portion of this variability can be explained by the highly polymorphic nature of the CYP2D6 gene locus for which > 100 variants and subvariants identified to date. Allele frequencies vary markedly between ethnic groups; some have exclusively or predominantly only been observed in certain populations. Pharmacogenetic testing holds the promise of individualizing drug therapy by identifying patients with CYP2D6 diplotypes that puts them at an increased risk of experiencing dose-related adverse events or therapeutic failure. Inferring a patient's CYP2D6 metabolic capacity, or phenotype, however, is a challenging task due to the complexity of the CYP2D6 gene locus. Allelic variation includes SNPs, small insertions and deletions, gene copy number variation and rearrangements with CYP2D7, a highly related non-functional gene. This review provides a summary of the intricacies of CYP2D6 variation and genotype analysis, knowledge that is invaluable for the translation of genotype into clinically useful information.

Towards the implementation of CYP2D6 and CYP2C19 genotypes in clinical practice: update and report from a pharmacogenetic service clinic

Genetic testing may help to improve treatment outcomes in order to avoid non-response or severe side effects to psychotropic medication. Most robust data have been obtained for gene variants in CYP2D6 and CYP2C19 enzymes for antipsychotics and antidepressant treatment. We reviewed original articles indexed in PubMed from 2008-2013 on CYP2D6 and CYP2C19 gene variants and treatment outcome to antidepressant or antipsychotic medication. We have started providing CYP2D6 and CYP2C19 genotype information to physicians and conducted a survey where preliminary results are reported. Studies provided mixed results regarding the impact of CYP2D6 and CYP2C19 gene variation on treatment response. Plasma levels were mostly found associated with CYP metabolizer status. Higher occurrence/severity of side effects were reported in non-extensive CYP2D6 or CYP2C19 metabolizers. Results showed that providing genotypic information is feasible and generally well accepted by both patients and physicians. Although currently available studies are limited by small sample sizes and infrequent plasma drug level assessment, research to date indicates that CYP2D6 and CYP2C19 testing may be beneficial particularly for non-extensive metabolizing patients. In summary, clinical assessment of CYP2D6 and CYP2C19 metabolizer status is feasible, well accepted and optimizes drug treatment in psychiatry.

Development and use of active clinical decision support for preemptive pharmacogenomics

Background

Active clinical decision support (CDS) delivered through an electronic health record (EHR) facilitates gene-based drug prescribing and other applications of genomics to patient care.

Objective

We describe the development, implementation, and evaluation of active CDS for multiple pharmacogenetic test results reported preemptively.

Materials and methods

Clinical pharmacogenetic test results accompanied by clinical interpretations are placed into the patient's EHR, typically before a relevant drug is prescribed. Problem list entries created for high-risk phenotypes provide an unambiguous trigger for delivery of post-test alerts to clinicians when high-risk drugs are prescribed. In addition, pre-test alerts are issued if a very-high risk medication is prescribed (eg, a thiopurine), prior to the appropriate pharmacogenetic test result being entered into the EHR. Our CDS can be readily modified to incorporate new genes or high-risk drugs as they emerge.

Results

Through November 2012, 35 customized pharmacogenetic rules have been implemented, including rules for TPMT with azathioprine, thioguanine, and mercaptopurine, and for CYP2D6 with codeine, tramadol, amitriptyline, fluoxetine, and paroxetine. Between May 2011 and November 2012, the pre-test alerts were electronically issued 1106 times (76 for thiopurines and 1030 for drugs metabolized by CYP2D6), and the post-test alerts were issued 1552 times (1521 for TPMT and 31 for CYP2D6). Analysis of alert outcomes revealed that the interruptive CDS appropriately guided prescribing in 95% of patients for whom they were issued.

Conclusions

Our experience illustrates the feasibility of developing computational systems that provide clinicians with actionable alerts for gene-based drug prescribing at the point of care.