The Epidemiologic Approach to Pharmacogenomics

A Decade of Pharmacogenetic Studies in Jordan: A Systemic Review

The aim of this study was to perform a systematic overview of the pharmacogenetic studies conducted in Jordan. A structured search of Medline was conducted for articles over the last decade (January 2010-July 2020). Studies were classified by design, sample size, drug-gene combination, and the significance of the results. Thirty-two studies met the criteria for review. Most pharmacogenomic studies had a case-only design (n = 23). Only five studies included >500 participants. The total number of genetic variants in all studies was one hundred fifteen, which were found in forty genes, including dynamic (n = 27), and kinetic (n = 9) genes. The most commonly studied drugs were within the hematology and cardiology therapeutic areas and included statins, warfarin, aspirin, and clopidogrel. Most studies (n = 18) reported results with mixed p values [<0.05 and >0.05]. Pharmacogenomic research in Jordan is still in its infancy and is limited mainly to replication attempts. The need for standardization is imperative, especially in developing countries with scarce funding resources.

Using Genetic Marginal Effects to Study Gene-Environment Interactions with GWAS Data

Gene-environment interactions (GxE) play a central role in the theoretical relationship between genetic factors and complex traits. While genome wide GxE studies of human behaviors remain underutilized, in part due to methodological limitations, existing GxE research in model organisms emphasizes the importance of interpreting genetic associations within environmental contexts. In this paper, we present a framework for conducting an analysis of GxE using raw data from genome wide association studies (GWAS) and applying the techniques to analyze gene-by-age interactions for alcohol use frequency. To illustrate the effectiveness of this procedure, we calculate genetic marginal effects from a GxE GWAS analysis for an ordinal measure of alcohol use frequency from the UK Biobank dataset, treating the respondent's age as the continuous moderating environment. The genetic marginal effects clarify the interpretation of the GxE associations and provide a direct and clear understanding of how the genetic associations vary across age (the environment). To highlight the advantages of our proposed methods for presenting GxE GWAS results, we compare the interpretation of marginal genetic effects with an interpretation that focuses narrowly on the significance of the interaction coefficients. The results imply that the genetic associations with alcohol use frequency vary considerably across ages, a conclusion that may not be obvious from the raw regression or interaction coefficients. GxE GWAS is less powerful than the standard "main effect" GWAS approach, and therefore require larger samples to detect significant moderated associations. Fortunately, the necessary sample sizes for a successful application of GxE GWAS can rely on the existing and on-going development of consortia and large-scale population-based studies.

A critical appraisal of pharmacogenetic inference

In essence, pharmacogenetic research is aimed at discovering variants of importance to gene-treatment interaction. However, epidemiological studies are rarely set up with this goal in mind. It is therefore of great importance that researchers clearly communicate which assumptions they have had to make, and which inherent limitations apply to the interpretation of their results. This review discusses considerations of, and the underlying assumptions for, utilizing different response phenotypes and study designs popular in pharmacogenetic research to infer gene-treatment interaction effects, with a special focus on those dealing with of clinical effects of drug treatment.

Opportunities for translational epidemiology: the important role of observational studies to advance precision oncology

Within current oncology practice, several genomic applications are being used to inform treatment decisions with molecularly targeted therapies in breast, lung, colorectal, melanoma, and other cancers. This commentary introduces a conceptual framework connecting the full spectrum of biomedical research disciplines, including fundamental laboratory research, clinical trials, and observational studies in the translation of genomic applications into clinical practice. The conceptual framework illustrates the contribution that well-designed observational epidemiologic studies provide to the successful translation of these applications, and characterizes the role observational epidemiology plays in driving the dynamic and iterative bench-to-bedside, and bedside-to-bench translation continuum. We also discuss how the principles of this conceptual model, emphasizing integration of multidisciplinary research, can be applied to the evolving paradigm in "precision oncology" focusing on multiplex tumor sequencing, and we identify opportunities for observational studies to contribute to the successful and efficient translation of this paradigm.Cancer Epidemiol Biomarkers Prev; 24(3); 484-9. ©2015 AACR.

Pharmacogenetic effects of 'candidate gene complexes' on stroke in the GenHAT study

OBJECTIVE

The aim of this study was to investigate whether there is a genotype-by-treatment interaction in patients experiencing stroke and treated with one of three antihypertensive drugs, that is chlorthalidone, amlodipine, or lisinopril.

PARTICIPANTS AND METHODS

A population of 436 African Americans and 539 whites who had experienced stroke in the GenHAT study were genotyped for 768 single nucleotide polymorphisms (SNPs) in 280 candidate genes. To detect a genotype-by-treatment interaction, we used the Pearson's χ-test to assess whether the genotype frequencies differed at the single SNP level for the three drug treatment groups. From these single SNP analyses, we derived a summary statistic for the degree of association at the gene and gene complex levels. This was done by grouping SNPs using information on gene locations and defining gene complexes on the basis of protein-protein interactions. To assess the statistical significance of the observed test statistic, we derived an empirical P-value by simulating data under the null hypothesis.

RESULTS

We found that, in patients who have experienced stroke, there is a significant genetic difference between hypertension drug treatment groups. In African Americans, SNP rs12143842 showed a significant association (P<0.001) with drug treatment. At the gene level, HNRNPA1P4 and NOS1AP in African Americans and PRICKLE1 and NINJ2 in non-Hispanic whites were significantly associated (P<0.01) with drug treatment, whereas none of the gene complexes tested showed significance.

CONCLUSION

On the basis of the genetic differences between drug treatment groups, we conclude that there may be an interaction between certain genotypes and antihypertensive treatment in stroke patients. This needs to be replicated in other studies.

Prescription of psychiatric medications and polypharmacy in the LAMS cohort

OBJECTIVE

This study evaluated demographic and clinical correlates and predictors of polypharmacy at baseline assessment in the Longitudinal Assessment of Manic Symptoms (LAMS) sample, a cohort of children age six to 12 years at their first outpatient mental health visit at university-affiliated clinics.

METHODS

Use of medications in four classes (mood stabilizers, antidepressants, antipsychotics, and stimulants) was assessed, and the Service Assessment for Children and Adolescents classified lifetime and current use of various services. Analyses examined correlates of the number of medications prescribed and odds of polypharmacy, defined as use of two or more concurrent medications.

RESULTS

In the total sample, 201 of 698 participants (29%) were prescribed two or more medications. These participants had lower Children's Global Assessment Scale scores, more comorbid disorders, and higher baseline parent-reported mood symptoms than those prescribed no or one medication. White youths were three times as likely as nonwhite youths to be receiving two or more psychotropics, even after adjustment for other demographic and clinical characteristics. Of 262 participants (38% of sample) not being treated with medications, 252 (96%) had a diagnosis of at least one psychiatric disorder (74% had two or more).

CONCLUSIONS

Findings suggest that patients with greater severity and comorbidity were more likely to receive two or more medications. However, 38% of these children with serious disorders were not receiving psychotropic medication at the time of this assessment. Results counter findings suggesting overtreatment with medications of children with psychiatric disorders in the community.

The success of pharmacogenomics in moving genetic association studies from bench to bedside: study design and implementation of precision medicine in the post-GWAS era

Pharmacogenomics is emerging as a popular type of study for human genetics in recent years. This is primarily due to the many success stories and high potential for translation to clinical practice. In this review, the strengths and limitations of pharmacogenomics are discussed as well as the primary epidemiologic, clinical trial, and in vitro study designs implemented. A brief discussion of molecular and analytic approaches will be reviewed. Finally, several examples of bench-to-bedside clinical implementations of pharmacogenetic traits will be described. Pharmacogenomics continues to grow in popularity because of the important genetic associations identified that drive the possibility of precision medicine.

Mitochondrial genomics and CD4 T-cell count recovery after antiretroviral therapy initiation in AIDS clinical trials group study 384

BACKGROUND

Mitochondrial DNA (mtDNA) variation has been associated with time to progression to AIDS and adverse effects from antiretroviral therapy (ART). In this study, full mitochondrial DNA (mtDNA) sequence data from US-based adult participants in the AIDS Clinical Trials Group study 384 was used to assess associations between mtDNA variants and CD4 T-cell recovery with ART.

METHODS

Full mtDNA sequence was determined using chip-based array sequencing. Sequence and CD4 cell count data was available at baseline and after ART initiation for 423 subjects with HIV RNA levels <400 copies per milliliter plasma. The primary outcome was change in CD4 count of ≥100 cells per cubic millimeter from baseline. Analyses were adjusted for baseline age, CD4 cell count, HIV RNA, and naive:memory CD4 cell ratio.

RESULTS

Race-stratified analysis of mtDNA variants with a minor allele frequency >1% revealed multiple mtDNA variants marginally associated (P < 0.05 before Bonferroni correction) with CD4 cell recovery. The most significant single nucleotide polymorphism associations were those tagging the African L2 haplogroup, which was associated with a decreased likelihood of ≥100 cells per cubic millimeter CD4 count increase at week 48 in non-Hispanic blacks (adjusted odds ratio = 0.17; 95% confidence interval = 0.06 to 0.53; P = 0.002).

CONCLUSIONS

An African mtDNA haplogroup was associated with CD4 cell recovery after ART in this clinical trial population. These initial findings warrant replication and further investigation to confirm the role of mtDNA variation in CD4 cell recovery during ART.

Pharmacogenetics in randomized controlled trials: considerations for trial design

Pharmacogenetic analyses of clinical trials aim to either detect whether a subgroup of patients identified by genetic characteristics responds differently to the treatment or to verify whether a proposed genotype-guided treatment is beneficial over standard care. This article describes three different trial designs, differing in the timing of randomization and genotyping. Each design has its own advantages, and the objectives and conditions under which each one is most suited are discussed.

Statistical Optimization of Pharmacogenomics Association Studies: Key Considerations from Study Design to Analysis

Research in human genetics and genetic epidemiology has grown significantly over the previous decade, particularly in the field of pharmacogenomics. Pharmacogenomics presents an opportunity for rapid translation of associated genetic polymorphisms into diagnostic measures or tests to guide therapy as part of a move towards personalized medicine. Expansion in genotyping technology has cleared the way for widespread use of whole-genome genotyping in the effort to identify novel biology and new genetic markers associated with pharmacokinetic and pharmacodynamic endpoints. With new technology and methodology regularly becoming available for use in genetic studies, a discussion on the application of such tools becomes necessary. In particular, quality control criteria have evolved with the use of GWAS as we have come to understand potential systematic errors which can be introduced into the data during genotyping. There have been several replicated pharmacogenomic associations, some of which have moved to the clinic to enact change in treatment decisions. These examples of translation illustrate the strength of evidence necessary to successfully and effectively translate a genetic discovery. In this review, the design of pharmacogenomic association studies is examined with the goal of optimizing the impact and utility of this research. Issues of ascertainment, genotyping, quality control, analysis and interpretation are considered.

Quality of consent forms in pharmacogenetic studies: a survey of research ethics committees in Spain

OBJECTIVES

To know the quality of consent forms in pharmacogenetic studies submitted for evaluation to Research Ethics Committees (RECs).

METHODS

A mail survey to RECs in Spain was conducted; this survey contained questions on the frequency with which different items were included in the consent forms of pharmacogenetic studies reviewed by each REC.

RESULTS

A total of 40 out of 69 RECs that answered the questionnaire had reviewed pharmacogenetic studies. RECs considered that information was always or almost always comprehensible in approximately 50% of the forms received. Information regarding reimbursement of patients and commercial interests of the research was scarcely incorporated in the consent forms. In general, RECs estimated that aspects related to the use of samples and genetic information were included in the consent forms with a frequency lower than 50%. The quality of consent forms was considered to be lower by those RECs which had reviewed a higher number of pharmacogenetic studies.

CONCLUSION

Significant deficiencies have been found in the consent forms of pharmacogenetic studies reviewed by Spanish RECs.

Pharmacogenetics in ovarian stimulation - current concepts and future options

Tailoring ovarian stimulation to the individual patient can be challenging because the ovarian response varies substantially between patients. Pharmacogenetics has emerged as a new area of research to improve the balance between desired and undesired actions of drugs, based upon the genetic predisposition of the individual patient. Clinical studies have demonstrated that the p.N680S polymorphism of the FSH-receptor gene determines the ovarian response to FSH stimulation in patients undergoing IVF. In homozygous Ser(680)/Ser(680) type women, the FSH receptor appears to be more resistant to FSH action even in normal menstrual cycles. Therefore, genotyping of patients scheduled for ovarian stimulation could be an attractive tool to individualize FSH dosing according to genetic differences in ovarian sensitivity. More clinical studies are warranted to investigate the usefulness of genotyping for the p.N680S polymorphism as a routine diagnostic test before ovarian stimulation.