Towards population-specific pharmacogenomics in the era of next-generation sequencing

Pharmacogenomics (PGx) has essential roles in identifying optimal drug responders, optimizing dosage regimens and avoiding adverse events. Population-specific therapeutic interventions that tackle the genetic root causes of clinical outcomes are an important precision medicine strategy. In this perspective, we discuss next-generation sequencing genotyping and its significance for population-specific PGx applications. We emphasize the potential of NGS for preemptive pharmacogenotyping, which is crucial to population-specific clinical studies and patient care. We also provide examples that use publicly available population-based genomics data for population-specific PGx studies. Last, we discuss the remaining challenges and regulatory efforts towards improvements in this field.     

Pharmacogenetics-based therapeutic recommendations--ready for clinical practice?

Although considerable progress has been made in basic pharmacogenetic research, less has been demonstrated in the application of pharmacogenetics (PGx)-based diagnostics to drug development and in clinical practice. There are drugs that are currently used in the clinic for which individualized therapy could be beneficial based on PGx data. However, specific, actionable recommendations on how to implement individualized therapy--particularly with respect to dosage--still have to be developed. Moreover, to apply PGx efficiently in clinical drug development, and later in drug therapy, study designs and the generation and handling of PGx data need to become more standardized. Here, we argue for the development of concise guidelines for implementation of PGx analyses in drug development and therapy.     

Learning from product labels and label changes: how to build pharmacogenomics into drug-development programs

The 2010 US FDA-Drug Industry Association (DIA) Pharmacogenomics (PGx) Workshop follows a series that began in 2002 bringing together multidisciplinary experts spanning regulatory authorities, medical research, healthcare and industry. This report summarizes the 'Building PGx into Labels' sessions from the workshop, which discussed the critical elements in developing PGx outcomes leading to product labels that inform efficacy and/or safety. Examples were drawn from US prescribing information, which integrated PGx knowledge into medical decisions (e.g., panitumumab, warfarin and clopidogrel). Attendees indicated the need for broader dialog and for guidelines on evidentiary considerations for PGx to be included into product labels. Also discussed was the understanding of appropriate PGx placement on labels; how to encourage adoption by medical communities of label recommendations on PGx tests; and, given the global nature of drug development, worldwide considerations including European Summary of Product Characteristics.     

临床药物基因组学在个体化用药中的应用

药物基因组学(PGx)作为实现个体化用药的一大助力,能指导临床更精准地调整用药方案.但我国PGx起步较迟,需要借鉴欧美国家的发展模式与现有平台,如利用其成熟的PharmGKB数据库、CPIC与DPWG指南等权威信息将PGx基础研究向有循证药学支撑的药物使用转化.本文针对PGx在临床的实施方案列举了临床可利用的数据库和指...     

Clinical implementation of pharmacogenetics: a nonrepresentative explorative survey to participants of WorldPharma 2010

Despite the fast-growing literature and the emerging support from regulatory drug agencies, the translation of pharmacogenetics (PGx) into the clinic is still rather limited; it seems that many existing challenges are yet to be overcome prior to an extensive adoption of PGx-based diagnostics. This article describes the results of an explorative nonrepresentative survey that attempted to evaluate the perceived status quo of, and the obstacles facing, PGx implementation in clinical practice in countries with emerging and developing economies versus countries with advanced economies. This study is a useful starting point to help gain better insight into the international, rather than merely the regional, barriers facing the lag in PGx implementation in the clinic. A more transparent picture about these priorities can be constructed through conducting a similar study on a more representative sample of respondents/participants.     

DPYD and UGT1A1 Pharmacogenetic Testing in Patients with Gastrointestinal Malignancies: An Overview of the Evidence and Considerations for Clinical Implementation

Gastrointestinal (GI) malignancies are among the most commonly diagnosed cancers worldwide. Despite the introduction of targeted and immunotherapy agents in the treatment landscape, cytotoxic agents, such as fluoropyrimidines and irinotecan, remain as the cornerstone of chemotherapy for many of these tumors. Pharmacogenetics (PGx) is a rapidly evolving field that accounts for interpatient variability in drug metabolism to predict therapeutic response and toxicity. Given the significant incidence of severe treatment-related adverse events associated with cytotoxic agents, utilizing PGx can allow clinicians to better anticipate drug tolerability while minimizing treatment interruptions or delays. In this review, the PGx profiles of drug-gene pairs with potential impact in GI malignancy therapy – DPYD-5-fluorouracil/capecitabine and UGT1A1-irinotecan – and the available clinical evidence of their roles in reducing severe adverse events are discussed. Considerations for clinical implementation, such as optimal laboratory workflows, electronic health record integration, and stakeholder engagement, as well as provider education, are addressed. Last, exploratory PGx markers in GI malignancy treatment are described. As the PGx knowledge base rapidly evolves, pharmacists will be vital in leveraging their pharmacology knowledge and clinical skills to implement PGx testing in the clinic.     

The current and future state of pharmacogenomics medical education in the USA

Healthcare professionals (e.g., physicians, physician assistants, pharmacists, nurses and genetic counselors) believe pharmacogenomics (PGx) is essential to personalized medicine; however, they still lack confidence prescribing, dosing, interacting with other healthcare professionals and counseling patients with regard to PGx. This is due to the inadequate incorporation of PGx content into professional curricula. Compared with other health professions, Doctor of Pharmacy programs have integrated more PGx content. Unlike other healthcare professionals, pharmacists have extensive training in pharmacology, drug selection, drug dosage, drug-drug interactions and are uniquely accessible to patients. We suggest pharmacists are the best poised to facilitate incorporating PGx into therapeutic decision-making. Based on our experience as undergraduate and pharmacy PGx educators, we further reflect on our experience educating future healthcare professionals on PGx.     

The impact of pharmacogenomics research on drug development

Over the last two decades, identification of polymorphisms that influence human diseases has begun to have an impact on the provision of medical care. The promise of genetics lies in its ability to provide insight into an individual's susceptibility to disease, the likely nature of the disease and the most appropriate therapy. For much of its history, pharmacogenomics (PGx) has been limited to relatively simple phenotypes such as plasma drug levels. Progress in genetic technologies has broadened the scope of exploratory PGx and its implementation into safety and efficacy studies, impacting a broad spectrum of drug discovery and development activities. Recent PGx data show the ability of this approach to generate information that can be applied to target selection, dose selection, efficacy determination and safety issues. This in turn will lead to significant opportunities to influence the approaches to drug discovery, clinical development and the probability of success. In particular, adverse drug reactions are critical issues for pharmaceutical companies and for the patients who will benefit from these new medicines. In this review, we outline current progress in PGx, using examples to highlight the influence of polymorphisms, and discuss contemporary challenges for both researchers and clinicians.     

Gap between the US and Japan in coverage of pharmacogenomic biomarkers by health insurance programs: More coverage is needed in Japan

In this study, we aimed to understand the gap in coverage of pharmacogenomic (PGx) biomarkers between Japan and the US. PGx biomarkers (1) in the Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines; (2) that are CPIC level A or B; or (3) have US Food and Drug Administration (FDA)-approved drug labels, were determined. Subsequently, their coverage by US health insurance companies and the National Health Insurance (NHI) in Japan was investigated. We identified the top six health insurance companies with the largest market shares in the US and investigated the coverage for the PGx biomarkers by these health insurers, Medicare, Medicaid, and the NHI in Japan. We found that 19.9% of these biomarkers are covered by the six companies (10.0%, the CPIC guidelines; 25.1%, the FDA-approved drug labels). The coverage of somatic and germline biomarkers was respectively 86.8% and 8.5% in the US and 56.3% and 0.6% in Japan. A few germline PGx biomarkers are covered both in Japan and the US, but the coverage of both somatic and germline biomarkers was lower in Japan. Therefore, more coverage should be considered to improve patient outcomes after prescribing medications in Japan.     

Routine pharmacogenetic testing in clinical practice: dream or reality?

Pharmacogenetics (PGx) has become progressively popular in recent years, thanks to growing anticipation among scientists, healthcare providers and the general public for the incorporation of genetic tests into the diagnostic arsenal at the physician's disposal. Indeed, much research has been dedicated to elucidation of genetic determinants underlying interindividual variability in pharmacokinetic parameters, as well as drug safety and efficacy. However, few PGx applications have thus far been realized in healthcare management. This review uses examples from PGx research of psychiatric drugs to illustrate why the current published findings are inadequate and insufficient for utilization as routine clinical predictors of treatment safety, efficacy or dosing. I therefore suggest the necessary steps to demonstrate the validity, utility and cost-effectiveness of PGx. These recommendations include a whole range of aspects, starting from standardization of criteria and assessment of the technical quality of genotyping assays, up to design of prospective PGx studies, providing the basis for reimbursement programs to be recognized in routine clinical practice.     

Functional significance of genetic polymorphisms in P-glycoprotein (MDR1, ABCB1) and breast cancer resistance protein (BCRP, ABCG2)

Recent pharmacogenomic/pharmacogenetic (PGx) studies have disclosed important roles for drug transporters in the human body. Changes in the functions of drug transporters due to drug/food interactions or genetic polymorphisms, for example, are associated with large changes in pharmacokinetic (PK) profiles of substrate drugs, leading to changes in drug response and side effects. This information is extremely useful not only for drug development but also for individualized treatment. Among drug transporters, the ATP-binding cassette (ABC) transporters are expressed in most tissues in humans, and play protective roles; reducing drug absorption from the gastrointestinal tract, enhancing drug elimination into bile and urine, and impeding the entry of drugs into the central nervous system and placenta. In addition to PK/pharmacodynamic (PD) issues, ABC transporters are reported as etiologic and prognostic factors (or biomarkers) for genetic disorders. Although a consensus has not yet been reached, clinical studies have demonstrated that the PGx of ABC transporters influences the overall outcome of pharmacotherapy and contributes to the pathogenesis and progression of certain disorders. This review explains the impact of PGx in ABC transporters in terms of PK/PD, focusing on P-glycoprotein and breast cancer resistance protein (BCRP).     

PhRMA white paper on ADME pharmacogenomics

Pharmacogenomic (PGx) research on the absorption, distribution, metabolism, and excretion (ADME) properties of drugs has begun to have impact for both drug development and utilization. To provide a cross-industry perspective on the utility of ADME PGx, the Pharmaceutical Research and Manufacturers of America (PhRMA) conducted a survey of major pharmaceutical companies on their PGx practices and applications during 2003-2005. This white paper summarizes and interprets the results of the survey, highlights the contributions and applications of PGx by industrial scientists as reflected by original research publications, and discusses changes in drug labels that improve drug utilization by inclusion of PGx information. In addition, the paper includes a brief review on the clinically relevant genetic variants of drug-metabolizing enzymes and transporters most relevant to the pharmaceutical industry.     

Consumers' views of pharmacogenetics—A qualitative study

BackgroundAdverse drug reactions are recognized as a significant public health issue. Pharmacogenetics (PGx) provides a potential means of preventing some adverse drug reactions by predicting the optimal medication dose for an individual; however, PGx is rarely used in clinical practice. Thus far, there have been few studies investigating consumers' perceptions of the barriers to the implementation of PGx in clinical practice.ObjectivesThis study explored the views of the general public regarding their current use of medications, and their experiences of side effects and opinions on PGx.MethodsMembers of the general public who suffered a chronic medical condition and/or had an immediate family member with a chronic medical condition were recruited to form 5 separate focus groups (n = 35). Three separate age ranges were used in the focus groups. A questioning route was developed and used in focus groups to determine participants' experiences with medication use and opinions on PGx (referred to as “Personalized Medicine”). Focus group discussions were transcribed by 2 separate investigators, and qualitative analysis, based on the framework approach, was applied to the data. Data were independently coded to identify key themes then compared both within and between focus groups.ResultsA common theme was a desire to have a holistic approach to disease diagnosis and medication selection. A wide range of views were expressed by the focus group participants. Concerns were raised regarding the current level of side effects experienced with medications. Storage and privacy of genetic information, and the costs involved, were also seen as potential barriers to implementation of PGx.ConclusionsPGx testing was seen as a potential positive contribution, but only if other factors were considered during the prescribing process. As participants desired a high level of information and effective communication from their health-care professionals, PGx education of clinicians and pharmacists will be essential to satisfy consumers' requirements.     

Pharmacogenetics: practices and opportunities for study design and data analysis

Pharmacogenetics (PGx) is increasingly used as a way to target treatment to patients who are most likely to benefit. To date, PGx has shown clinical significance across a few applications but widespread use has been limited by the need for further technical, methodological and practical advances and for educating clinical researchers on the value of PGx. Here, I describe the current scope of PGx research, including recent contributions to prospective study design. A case study is included to demonstrate the limitations of current practice and to describe some practical steps for improving the chances of identifying genetic effects. Additionally, I describe some opportunities for the integration and application of disparate data sources in exploratory PGx research.     

Therapeutic drug monitoring to adjust dosing in morbid obesity - a new use for an old methodology

The phenomena of hunger and need at one end of the spectrum and obesity and plenty on the other is an anomaly of the 21(st) century, likely to be due to a combination of distributive inequities in food, social justice, access to education and other socio-economic factors. Both are major problems worldwide, although obesity has more media coverage due to the exponentially increasing incidence and the huge social and economic burden this is placing on Western society. For example, prevalence rates of obesity are currently exceeding 30% of adults in the USA with direct morbidity and mortality complications, in addition to the additional obesity-related health problems and death. Obesity is also rising in children. Obese people are thus a sizable group, and as with those with altered renal or liver function, require specific consideration with respect to the appropriate dosing of medications. However guidelines for how to do this in obesity are not currently available, due to the paucity of literature and regulatory rules for new medications which usually only request the demonstration of average population effectiveness. We believe it is timely for regulatory agencies worldwide to mandate studies involving consideration of body size, particularly obesity, in approving new medications across the therapeutic spectrum. This will drive the pharmaceutical industry to consider these groups in studies and will encourage investigator-initiated research using therapeutic drug monitoring (TDM), target concentration therapy (TCI) and pharmacogenetic (PGx) studies to optimize drug dosing.     

Clinical Utility of Pharmacogenomic Data Collected by a Health-System Biobank to Predict and Prevent Adverse Drug Events

Introduction

Medication-related harm represents a significant issue for patient safety and quality of care. One strategy to avoid preventable adverse drug events is to utilize patient-specific factors such as pharmacogenomics (PGx) to individualize therapy.

Objective

We measured the number of patients enrolled in a health-system biobank with actionable PGx results who received relevant medications and assessed the incidence of adverse drug events (ADEs) that might have been prevented had the PGx results been used to inform prescribing.

Methods

Patients with actionable PGx results in the following four genes with Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines were identified: HLA-A*31:01, HLA-B*15:02, TPMT, and VKORC1. The patients who received interacting medications (carbamazepine, oxcarbazepine, thiopurines, or warfarin) were identified, and electronic health records were reviewed to determine the incidence of potentially preventable ADEs.

Results

Of 36,424 patients with PGx results, 2327 (6.4%) were HLA-A*31:01 positive; 3543 (9.7%) were HLA-B*15:02 positive; 2893 (7.9%) were TPMT intermediate metabolizers; and 4249 (11.7%) were homozygous for the VKORC1 c.1639 G>A variant. Among patients positive for one of the HLA variants who received carbamazepine or oxcarbazepine (n = 92), four (4.3%) experienced a rash that warranted drug discontinuation. Among the TPMT intermediate metabolizers who received a thiopurine (n = 56), 11 (19.6%) experienced severe myelosuppression that warranted drug discontinuation. Among patients homozygous for the VKORC1 c.1639 G>A variant who received warfarin (n = 379), 85 (22.4%) experienced active bleeding and/or international normalized ratio (INR) > 5 that warranted drug discontinuation or dose reduction.

Conclusion

Patients with actionable PGx results from a health-system biobank who received relevant medications experienced predictable ADEs. These ADEs may have been prevented if the patients’ PGx results were available in the electronic health record with clinical decision support prior to prescribing.