Inconsistency in race and ethnic classification in pharmacogenetics studies and its potential clinical implications

Neighborhood matters: An exploration of neighborhood-level disadvantage and cancer preventive behaviors in Hispanic youth with unhealthy weight

OBJECTIVES

The present study aimed to assess the associations between the youth's cancer preventive behaviors (CPB) (i.e., healthy dietary intake and physical activity), parent stress, parent socio-demographic characteristics (i.e., education, household income, and marital status), and neighborhood influences measured by the Area Deprivation Index (ADI) in a sample of Hispanic families who have youth with unhealthy weight. Additionally, we examined whether parent stress mediated the relationship between ADI and youth CPB.

METHODS

Baseline data from 280 Hispanic youth (Mage = 13.01 ± 0.83; 52.1 % females; MBody Mass Index (BMI) Percentile = 94.55 ± 4.15) and their parents (Mage = 41.87 ± 6.49; 88.2 % females) who enrolled in an RCT were used. Self-reported data on youth dietary intake and physical activity, parent stress, and parent socio-demographic characteristics were collected. Neighborhood impact was examined using ADI, a validated measure to classify neighborhood disadvantage (e.g., housing quality and neighborhood income) using data from the US Census Bureau. Structural Equation Modeling was used (CPB as a latent variable) to evaluate the study model.

RESULTS

Our findings indicated significant associations between ADI and youth CPB (b = -0.17, p = .019), and parent stress (b = 0.23, p = .001). However, parent stress did not mediate the relationship between youth ADI and CPB.

CONCLUSION

Youth living in disadvantaged neighborhoods report less engagement in cancer preventive behaviors including poorer food intake quality and less physical activity, which may increase their risk of cancer. Future research should evaluate neighborhood resources to encourage physical activity and healthy eating.

Online database of clinical algorithms with race and ethnicity

Some clinical algorithms incorporate an individual's race, ethnicity, or both as an input variable or predictor in determining diagnoses, prognoses, treatment plans, or risk assessments. Inappropriate use of race and ethnicity in clinical algorithms at the point of care may exacerbate health disparities and promote harmful practices of race-based medicine. Using database analysis primarily, we identified 42 risk calculators that use race and ethnicity as predictors, five laboratory test results with reference ranges that differed based on race and ethnicity, one therapy recommendation based on race and ethnicity, 15 medications with race- and ethnicity-based initiation and monitoring guidelines, and five medical devices with differential racial and ethnic performances. Information on these clinical algorithms is freely available at https://www.clinical-algorithms-with-race-and-ethnicity.org/ . This resource aims to raise awareness about the use of race and ethnicity in clinical algorithms and track progress toward eliminating their inappropriate use. The database is actively updated to include clinical algorithms that were missed and additional characteristics of these algorithms.

Online Database of Clinical Algorithms with Race and Ethnicity

Some clinical algorithms incorporate an individual's race, ethnicity, or both as an input variable or predictor in determining diagnoses, prognoses, treatment plans, or risk assessments. Inappropriate use of race and ethnicity in clinical algorithms at the point of care may exacerbate health disparities and promote harmful practices of race-based medicine. We identified 42 risk calculators that use race as a predictor, five laboratory test results with different reference ranges recommended for different races, one therapy recommendation based on race, 15 medications with guidelines for initiation and monitoring based on race, and four medical devices with differential racial performance. Information on these clinical algorithms are freely available at http://www.clinical-algorithms-with-race-and-ethnicity.org. This resource aims to raise awareness about the use of race in clinical algorithms and to track the progress made toward eliminating its inappropriate use. The database will be actively updated to include clinical algorithms based on race that were missed, along with additional characteristics of these algorithms.

Ethno-racial categorisations for biomedical studies: the fair selection of research participants and population stratification

We argue that there are neither scientific nor social reasons to require gathering ethno-racial data, as defined in the US legal regulations if researchers have no prior hypotheses as to how to connect this type of categorisation of human participants of clinical trials with any mechanisms that could explain alleged interracial health differences and guide treatment choice. Although we agree with the normative perspective embedded in the calls for the fair selection of participants for biomedical research, we demonstrate that current attempts to provide and elucidate the criteria for the fair selection of participants, in particular, taking into account ethno-racial categories, overlook important epistemic and normative challenges to implement the results of such race-sorting requirements. We discuss existing arguments for and against gathering ethno-racial statistics for biomedical research and present a new one that refers to the assumption that prediction is epistemically superior to accommodation. We also underline the importance of closer interaction between research ethics and the methodology of biomedicine in the case of population stratifications for medical research, which requires weighing non-epistemic values with methodological constraints.

The Role of Pharmacogenomics Studies for Precision Medicine Among Ethiopian Patients and Their Clinical Implications: A Scoping Review

Background

Pharmacogenomics research is currently revolutionizing treatment optimization by discovering molecular markers. Medicines are the cornerstone of treatment for both acute and chronic diseases. Pharmacogenomics associated treatment response varies from 20% to 95%, resulting in from lack of efficacy to serious toxicity. Pharmacogenomics has emerged as a useful tool for therapy optimization and plays a bigger role in clinical care going forward. However, in Africa, in particular in Ethiopia, such studies are scanty and not generalizing. Therefore, the objective of this review was to outline such studies, generating comprehensive evidence and identify studied variants' association with treatment responses in Ethiopian patients.

Methods

The Joanna Briggs Institute's updated 2020 methodological guidelines for conducting and guidance for scoping reviews were used. We meticulously adhered to the systemic review reporting items checklist and scoping review meta-analyses extension.

Results

Two hundred twenty-nine possibly relevant studies were searched. These include: 64, 54, 21, 48 and 42 from PubMed, Scopus, Google Scholar, EMBASE, and manual search, respectively. Seventy-seven duplicate studies were removed. Thirty-nine papers were rejected with justification, whereas 58 studies were qualified for full-text screening. Finally 19 studies were examined. The primary pharmacogene that was found to have a significant influence on the pharmacokinetics of efavirenz was CYP2B6. Drug-induced liver injury has frequently identified toxicity among studied medications.

Conclusion and Future Perspectives

Pharmacogenomics studies in Ethiopian populations are less abundant. The studies conducted focused on infectious diseases, specifically on HAART commonly efavirenz and backbone first-line anti-tuberculosis drugs. There is a high need for further pharmacogenomics research to verify the discrepancies among the studies and for guiding precision medicine. Systematic review and meta-analysis are also recommended for pooled effects of different parameters in pharmacogenomics studies.

Can pharmacogenetics impact the therapeutic effect of cytarabine and anthracyclines in adult acute myeloid leukaemia patients?: A Serbian experience

Background

Cytarabine-anthracycline-based induction chemotherapy remains the standard of care for remission induction among patients with newly diagnosed acute myeloid leukaemia (AML). There are remarkable differences in therapy response among AML patients. This fact could be partly explained by the patients' genetic variability related to the metabolic paths of cytarabine and anthracyclines. This study aims to evaluate the effect of variants in pharmacogenes SLC29A1, DCK, ABCB1, GSTM1, and GSTT1, as well as laboratory and AML-related parameters on clinical outcomes in adult AML patients.

Methods

A total of 100 AML patients were included in the study. Pharmacogenetic variants SLC29A1 rs9394992, DCK rs12648166, ABCB1 rs2032582, and GSTM1 and GSTT1 gene deletions were detected by methodology based on PCR, fragment analysis and direct sequencing. The methods of descriptive and analytic statistics were used. Survival analysis was done using the Kaplan-Meier method using the Log-Rank test.

Results

This is the first study of adult AML pharmacogenetics in the Serbian population. Clinical outcomes in our cohort of AML patients were not impacted by analysed variants in SLC29A1, DCK, ABCB1 and GSTT1, and GSTM1 genes, independently or in combinations. Achievement of complete remission was identified as an independent prognostic indicator of clinical outcome.

Conclusions

The population-specific genomic profile has to be considered in pharmacogenetics. Since the data on AML pharmacogenetics in European populations is limited, our results contribute to knowledge in this field and strongly indicate that a high-throughput approach must be applied to find particular pharmacogenetic markers of AML in the European population.

Genetic diversity of variants involved in drug response among Tunisian and Italian populations toward personalized medicine

Adverse drug reactions (ADR) represent a significant contributor to morbidity and mortality, imposing a substantial financial burden. Genetic ancestry plays a crucial role in drug response. The aim of this study is to characterize the genetic variability of selected pharmacogenes involved with ADR in Tunisians and Italians, with a comparative analysis against global populations. A cohort of 135 healthy Tunisians and 737 Italians were genotyped using a SNP array. Variants located in 25 Very Important Pharmacogenes implicated in ADR were extracted from the genotyping data. Distribution analysis of common variants in Tunisian and Italian populations in comparison to 24 publicly available worldwide populations was performed using PLINK and R software. Results from Principle Component and ADMIXTURE analyses showed a high genetic similarity among Mediterranean populations, distinguishing them from Sub-Saharan African and Asian populations. The Fst comparative analysis identified 27 variants exhibiting significant differentiation between the studied populations. Among these variants, four SNPs rs622342, rs3846662, rs7294, rs5215 located in SLC22A1, HMGCR, VKORC1 and KCNJ11 genes respectively, are reported to be associated with ethnic variability in drug responses. In conclusion, correlating the frequencies of genotype risk variants with their associated ADRs would enhance drug outcomes and the implementation of personalized medicine in the studied populations.

Assessment of the current status of real-world pharmacogenomic testing: informed consent, patient education, and related practices

Introduction: The practice of informed consent (IC) for pharmacogenomic testing in clinical settings varies, and there is currently no consensus on which elements of IC to provide to patients. This study aims to assess current IC practices for pharmacogenomic testing. Methods: An online survey was developed and sent to health providers at institutions that offer clinical germline pharmacogenomic testing to assess current IC practices. Results: Forty-six completed surveys representing 43 clinical institutions offering pharmacogenomic testing were received. Thirty-two (74%) respondents obtain IC from patients with variability in elements incorporated. Results revealed that twenty-nine (67%) institutions discuss the benefits, description, and purpose of pharmacogenomic testing with patients. Less commonly discussed elements included methodology and accuracy of testing, and laboratory storage of samples. Discussion: IC practices varied widely among survey respondents. Most respondents desire the establishment of consensus IC recommendations from a trusted pharmacogenomics organization to help address these disparities.

Conflating race and ancestry: Tracing decision points about population descriptors over the precision medicine research life course

Responding to calls for human genomics to shift away from the use of race, genomic investigators are coalescing around the possibility of using genetic ancestry. This shift has renewed questions about the use of social and genetic concepts of difference in precision medicine research (PMR). Drawing from qualitative data on five PMR projects, we illustrate negotiations within and between research teams as genomic investigators deliberate on the relevance of race and genetic ancestry for different analyses and contexts. We highlight how concepts of both social and genetic difference are embedded within and travel through research practices, and identify multiple points across the research life course at which conceptual slippage and conflation between race and genetic ancestry occur. We argue that moving beyond race will require PMR investigators to confront the entrenched ways in which race is built into research practices and biomedical infrastructures.

Clinical Decision Support for Precision Dosing: Opportunities for Enhanced Equity and Inclusion in Health Care

Precision dosing aims to tailor doses to individual patients with the goal of improving treatment efficacy and avoiding toxicity. Clinical decision support software (CDSS) plays a crucial role in mediating this process, translating knowledge derived from clinical trials and real-world data (RWD) into actionable insights for clinicians to use at the point of care. However, not all patient populations are proportionally represented in clinical trials and other data sources that inform CDSS tools, limiting the applicability of these tools for underrepresented populations. Here, we review some of the limitations of existing CDSS tools and discuss methods for overcoming these gaps. We discuss considerations for study design and modeling to create more inclusive CDSS, particularly with an eye toward better incorporation of biological indicators in place of race, ethnicity, or sex. We also review inclusive practices for collection of these demographic data, during both study design and in software user interface design. Because of the role CDSS plays in both recording routine clinical care data and disseminating knowledge derived from data, CDSS presents a promising opportunity to continuously improve precision dosing algorithms using RWD to better reflect the diversity of patient populations.

Reductionist methodology and the ambiguity of the categories of race and ethnicity in biomedical research: an exploratory study of recent evidence

In this article, we analyse how researchers use the categories of race and ethnicity with reference to genetics and genomics. We show that there is still considerable conceptual "messiness" (despite the wide-ranging and popular debate on the subject) when it comes to the use of ethnoracial categories in genetics and genomics that among other things makes it difficult to properly compare and interpret research using ethnoracial categories, as well as draw conclusions from them. Finally, we briefly reconstruct some of the biases of reductionism to which geneticists (as well as other researchers referring to genetic methods and explanations) are particularly exposed to, and we analyse the problem in the context of the biologization of ethnoracial categories. Our work constitutes a novel, in-depth contribution to the debate about reporting race and ethnicity in biomedical and health research. First, we reconstruct the theoretical background assumptions about racial ontology which researchers implicitly presume in their studies with the aid of a sample of recent papers published in medical journals about COVID-19. Secondly, we use the typology of the biases of reductionism to the problem of biologization of ethnoracial categories with reference to genetics and genomics.

Population designations in biomedical research: Limitations and perspectives

In biomedical research, population differences are of central interest. Variations in the frequency and severity of diseases and in treatment effects among human subpopulation groups are common in many medical conditions. Unfortunately, the practices in terms of subpopulation labeling do not exhibit the level of rigor one would expect in biomedical research, especially when studying multifactorial diseases such as cancer or atherosclerosis. The reporting of population differences in clinical research is characterized by large disparities in practices, and fraught with methodological issues and inconsistencies. The actual designations such as "Black" or "Asian" refer to broad and heterogeneous groups, with a great discrepancy among countries. Moreover, the use of obsolete concepts such as "Caucasian" is unfortunate and imprecise. The use of adequate labeling to reflect the scientific hypothesis needs to be promoted. Furthermore, the use of "race/ethnicity" as a unique cause of human heterogeneity may distract from investigating other factors related to a medical condition, particularly if this label is employed as a proxy for cultural habits, diet, or environmental exposure. In addition, the wide range of opinions among researchers does not facilitate the attempts made for resolving this heterogeneity in labeling. "Race," "ethnicity," "ancestry," "geographical origin," and other similar concepts are saturated with meanings. Even if the feasibility of a global consensus on labeling seems difficult, geneticists, sociologists, anthropologists, and ethicists should help develop policies and practices for the biomedical field.

Towards the multileveled and processual conceptualisation of racialised individuals in biomedical research

In this paper, we discuss the processes of racialisation on the example of biomedical research. We argue that applying the concept of racialisation in biomedical research can be much more precise, informative and suitable than currently used categories, such as race and ethnicity. For this purpose, we construct a model of the different processes affecting and co-shaping the racialisation of an individual, and consider these in relation to biomedical research, particularly to studies on hypertension. We finish with a discussion on the potential application of our proposition to institutional guidelines on the use of racial categories in biomedical research.

PharmVar GeneFocus: CYP3A5

The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP3A5 gene. Genetic variation within the CYP3A5 gene locus impacts the metabolism of several clinically important drugs, including the immunosuppressants tacrolimus, sirolimus, cyclosporine, and the benzodiazepine midazolam. Variable CYP3A5 activity is of clinical importance regarding tacrolimus metabolism. This GeneFocus provides a CYP3A5 gene summary with a focus on aspects regarding standardized nomenclature. In addition, this review also summarizes recent changes and updates, including the retirement of several allelic variants and provides an overview of how PharmVar CYP3A5 star allele nomenclature is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).

Hyper-responsiveness to warfarin in a young patient with the VKORC1 -1639GA/CYP2C9*1*46 genotype: a case report

BACKGROUND

Warfarin is the most widely used oral anticoagulant; nevertheless, dosing of warfarin is problematic for clinicians worldwide. Inter-individual variability in response to warfarin is attributed to genetic as well as non-genetic factors. Pharmacogenomics studies have identified variants in CYP2C9 and VKORC1 genes as significant predictors of warfarin dose, however, phenotypes of rare variants are not well characterized.

CASE PRESENTATION

We report a case of hyper-responsiveness to warfarin in a 22-year-old outpatient with Crohn's disease who presented with a swollen, red, and painful left calf. Deep venous thrombosis (DVT) in the left lower extremity was confirmed via ultrasonography, and hence, anticoagulation therapy of heparin and concomitant warfarin was initiated. Warfarin dose of 7.5 mg/day was estimated by the physician based on clinical factors. Higher than the expected international normalized ratio (INR) value of 4.5 necessitated the reduction of the warfarin dose to 5 and eventually to 2.5 mg/day to reach a therapeutic INR value of 2.6. Pharmacogenetic profiling of the VKORC1 -1639G > A and CYP2C9 *2, *3, *4, *5, *8, *14, *20, *24, *26, *33, *40, *41, *42, *43, *45, *46, *55, *62, *63, *66, *68, *72, *73 and *78 revealed a VKORC1-1639GA/CYP2C9*1*46 genotype. The lower catalytic activity of the CYP2C9*46 (A149T) variant was previously reported in in vitro settings.

CONCLUSIONS

This is the first report on a case of warfarin hyper-responsive phenotype of a patient with the heterozygous CYP2C9*1*46 polymorphism.

An Idealized Clinicogenomic Registry to Engage Underrepresented Populations Using Innovative Technology

Current best practices in tumor registries provide a glimpse into a limited time frame over the natural history of disease, usually a narrow window around diagnosis and biopsy. This creates challenges meeting public health and healthcare reimbursement policies that increasingly require robust documentation of long-term clinical trajectories, quality of life, and health economics outcomes. These challenges are amplified for underrepresented minority (URM) and other disadvantaged populations, who tend to view the institution of clinical research with skepticism. Participation gaps leave such populations underrepresented in clinical research and, importantly, in policy decisions about treatment choices and reimbursement, thus further augmenting health, social, and economic disparities. Cloud computing, mobile computing, digital ledgers, tokenization, and artificial intelligence technologies are powerful tools that promise to enhance longitudinal patient engagement across the natural history of disease. These tools also promise to enhance engagement by giving participants agency over their data and addressing a major impediment to research participation. This will only occur if these tools are available for use with all patients. Distributed ledger technologies (specifically blockchain) converge these tools and offer a significant element of trust that can be used to engage URM populations more substantively in clinical research. This is a crucial step toward linking composite cohorts for training and optimization of the artificial intelligence tools for enhancing public health in the future. The parameters of an idealized clinical genomic registry are presented.

Ethnic Diversity and Warfarin Pharmacogenomics

Warfarin has remained the most commonly prescribed vitamin K oral anticoagulant worldwide since its approval in 1954. Dosing challenges including having a narrow therapeutic window and a wide interpatient variability in dosing requirements have contributed to making it the most studied drug in terms of genotype-phenotype relationships. However, most of these studies have been conducted in Whites or Asians which means the current pharmacogenomics evidence-base does not reflect ethnic diversity. Due to differences in minor allele frequencies of key genetic variants, studies conducted in Whites/Asians may not be applicable to underrepresented populations such as Blacks, Hispanics/Latinos, American Indians/Alaska Natives and Native Hawaiians/other Pacific Islanders. This may exacerbate health inequalities when Whites/Asians have better anticoagulation profiles due to the existence of validated pharmacogenomic dosing algorithms which fail to perform similarly in the underrepresented populations. To examine the extent to which individual races/ethnicities are represented in the existing body of pharmacogenomic evidence, we review evidence pertaining to published pharmacogenomic dosing algorithms, including clinical utility studies, cost-effectiveness studies and clinical implementation guidelines that have been published in the warfarin field.

Pharmacogenomics and clinical cultural competency: pathway to overcome the limitations of race

Global migration trends are accelerating population admixture. Increasing population diversity met with minority health disparities necessitates thoughtful training of health professional students. Health professional accreditation standards emphasize pharmacogenomics and clinical cultural competency (CCC); however, published studies focus on students’ knowledge in pharmacogenomics alone. This report reviews considerations for integrating CCC into required pharmacogenomic education in pharmacy and other health disciplines. By coupling both topics during didactic training and active learning exercises repeated throughout the existing curriculum, students can become adept at these individualized patient care skills and retain their knowledge into their careers. Moving beyond race as a proxy for healthcare decision-making, the CCC of clinicians coupled with patients’ genetic test results could empower clinicians to address health disparities and facilitate discussions about the role of race in clinical practice. Ultimately, an integrated approach of teaching pharmacogenomics and CCC could dismantle race-norming or race-based clinical practices.

Effect of CYP2C19 genetic polymorphism on the pharmacodynamics and clinical outcomes for patients treated with ticagrelor: a systematic review with qualitative and quantitative meta-analysis

BACKGROUND

Studies show inconsistent results regarding the impact of CYP2C19 genotype on the pharmacodynamics (PD) and clinical outcomes of ticagrelor. With the implementation of genotype-guided individualized antiplatelet therapy, the association between CYP2C19 polymorphism and the efficacy and safety of ticagrelor for patients is still worthy of exploring and studying.

METHODS

This systematic review protocol has been registered in the PROSPERO network (No. CRD 42020158920). Electronic databases of PubMed, EmBase, and the Cochrane Library were systematically searched from inception to January 6th, 2022 to select studies investigating the impact of CYP2C19 genotype on PD and clinical outcomes of ticagrelor. The results were presented as odds ratio (OR) or weight mean difference with its 95% confidence interval (CI) by using the random-effects model. Trial sequential analysis (TSA) was used to control risk of random errors and detect the robustness of outcomes.

RESULTS

Eight studies recruited a total of 6405 patients treated with ticagrelor. Mostly trials reported no significant effect of any or no CYP2C19 loss-of-function (LOF) allele (*2 or *3) on all the endpoints. Compared with no LOF allele carriers, subgroup analysis suggested any LOF allele in Asian patients was associated with a significant decreased risk of bleeding events (OR: 0.41; 95% CI: 0.22-0.75; P = 0.004). Furthermore, any LOF allele carriers didn't yield any impact on the risk of MACEs (OR: 1.11; 95% CI: 0.76-1.64; P = 0.586), stroke (OR: 1.71; 95% CI: 0.99-2.96; P = 0.054), definite stent thrombosis (OR: 0.88; 95% CI: 0.17-4.60; P = 0.882), bleeding (OR: 0.63; 95% CI: 0.27-1.46; P = 0.281), myocardial infarction (OR: 0.81; 95% CI: 0.30-2.20; P = 0.682), and revascularization (OR: 0.81; 95% CI: 0.33-2.00; P = 0.649) in all patients. The results of TSA were indicated that more further trials would be required.

CONCLUSIONS

This qualitative and quantitative study suggested Asian patients carrying any CYP2C19 LOF allele might have a lower risk of bleeding events comparing with no LOF allele carriers when treated with ticagrelor. However, we did not prove an important role of CYP2C19 genotype on the risk of PD and clinical endpoints in the whole cohort. In future, more large-scale prospective studies and more different ethnic populations should be included.

Integration of liquid biopsy and pharmacogenomics for precision therapy of EGFR mutant and resistant lung cancers

The advent of molecular profiling has revolutionized the treatment of lung cancer by comprehensively delineating the genomic landscape of the epidermal growth factor receptor (EGFR) gene. Drug resistance caused by EGFR mutations and genetic polymorphisms of drug metabolizing enzymes and transporters impedes effective treatment of EGFR mutant and resistant lung cancer. This review appraises current literature, opportunities, and challenges associated with liquid biopsy and pharmacogenomic (PGx) testing as precision therapy tools in the management of EGFR mutant and resistant lung cancers. Liquid biopsy could play a potential role in selection of precise tyrosine kinase inhibitor (TKI) therapies during different phases of lung cancer treatment. This selection will be based on the driver EGFR mutational status, as well as monitoring the development of potential EGFR mutations arising during or after TKIs treatment, since some of these new mutations may be druggable targets for alternative TKIs. Several studies have identified the utility of liquid biopsy in the identification of EGFR driver and acquired resistance with good sensitivities for various blood-based biomarkers. With a plethora of sequencing technologies and platforms available currently, further evaluations using randomized controlled trials (RCTs) in multicentric, multiethnic and larger patient cohorts could enable optimization of liquid-based assays for the detection of EGFR mutations, and support testing of CYP450 enzymes and drug transporter polymorphisms to guide precise dosing of EGFR TKIs.

Genetic markers for non-syndromic orofacial clefts in populations of European ancestry: a meta-analysis

To date, the involvement of various genetic markers in the aetiopathogenesis of non-syndromic orofacial cleft (nsOFC) has been extensively studied. In the present study, we focused on studies performed on populations of European ancestry to systematically review the available literature to define relevant genetic risk factors for nsOFC. Eligible studies were obtained by searching Ovid Medline and Ovid Embase. We gathered the genetic markers from population-based case–control studies on nsOFC, and conducted meta-analysis on the repeatedly reported markers. Whenever possible, we performed stratified analysis based on different nsOFC phenotypes, using allelic, dominant, recessive and overdominant genetic models. Effect sizes were expressed as pooled odds ratios (ORs) with 95% confidence intervals (CIs), and p ≤ 0.05 were considered statistically significant. A total of 84 studies were eligible for this systematic review, with > 700 markers included. Of these, 43 studies were included in the meta-analysis. We analysed 47 genetic variants in 30 genes/loci, which resulted in 226 forest plots. There were statistically significant associations between at least one of the nsOFC phenotypes and 19 genetic variants in 13 genes/loci. These data suggest that IRF6, GRHL3, 8q24, VAX1, TGFA, FOXE1, ABCA4, NOG, GREM1, AXIN2, DVL2, WNT3A and WNT5A have high potential as biomarkers of nsOFC in populations of European descent. Although other meta-analyses that included European samples have been performed on a limited number of genetic variants, this study represents the first meta-analysis of all genetic markers that have been studied in connection with nsOFC in populations of European ancestry.

Health equality, race and pharmacogenomics

Pharmacogenomics is increasingly moving into mainstream clinical practice. Careful consideration must be paid to inclusion of diverse populations in research, translation and implementation, in the historical and social context of population stratification, to ensure that this leads to improvements in healthcare for all rather than increased health disparities. This review takes a broad and critical approach to the current role of diversity in pharmacogenomics and addresses potential pitfalls in order to raise awareness for prescribers. It also emphasizes evidence gaps and suggests approaches that may minimize negative consequences and promote health equality.

Twelve-Month Results From the First-in-China Prospective, Multi-Center, Randomized, Controlled Study of the FREEWAY Paclitaxel-Coated Balloon for Femoropopliteal Treatment

Background: Several paclitaxel-coated balloons have been proved to provide better efficacy results than uncoated balloons in femoropopliteal lesions. But the efficacy and safety of FREEWAY balloons have not been investigated in Chinese patients. This study aimed to evaluate the efficacy and safety performance of FREEWAY paclitaxel-coated balloons vs. uncoated balloons in Chinese femoropopliteal artery lesions.

Methods: In this prospective multi-center randomized controlled FREEWAY-CHINA study, 311 patients with symptomatic lower limb ischemia (Rutherford category 2–5) and femoropopliteal lesions of 14 Chinese centers were randomly assigned in a 1:1 ratio to endovascular treatment with either FREEWAY paclitaxel-coated balloons or uncoated balloons (control). The primary endpoint was the 6-month clinically-driven target lesion revascularization (CD-TLR) rate. Secondary endpoints included the device and technical success rate, the ankle-brachial indexes (ABIs), Rutherford category change, the 6-month primary and secondary patency rates, severe adverse effects, and the 12-month CD-TLR rate.

Results: The two groups were comparable in terms of their demographic and lesion characteristics. Patients' mean age was 70 years, and 70% were men. The mean lesion length was 71 mm. The 6-month CD-TLR rate was 2.6% in the FREEWAY group and 11.7% in the control group (P = 0.001). The 12-month CD-TLR rate was 2.7% in the FREEWAY group and 13.2% in the control group (P = 0.0005). Other endpoints, including patency rates, major adverse events, and ABI or Rutherford change, did not differ between the two groups.

Conclusion: The FREEWAY balloon resulted in an effective decrease in CD-TLR rates and had similar safety results compared to the uncoated balloon in Chinese femoropopliteal artery patients at the 12-month follow-up appointment.

PharmVar GeneFocus: CYP2C9

The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C9 gene. Genetic variation within the CYP2C9 gene locus impacts the metabolism or bioactivation of many clinically important drugs, including nonsteroidal anti-inflammatory drugs, phenytoin, antidiabetic agents, and angiotensin receptor blockers. Variable CYP2C9 activity is of particular importance regarding efficacy and safety of warfarin and siponimod as indicated in their package inserts. This GeneFocus provides a comprehensive overview and summary of CYP2C9 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium.

Applying an equity lens to pharmacogenetic research and translation to under-represented populations

Since the publication of the Human Genome Project, genetic information has been used as an accepted, evidence-based biomarker to optimize patient care through the delivery of precision health. Pharmacogenetics (PGx) uses information about genes that encode proteins involved in pharmacokinetics, pharmacodynamics, and hypersensitivity reactions to guide clinical decision making to optimize medication therapy selection. Clinical PGx implementation is growing from the dramatic increase in PGx studies over the last decade. However, an overwhelming lack of genetic diversity in current PGx studies is evident. This lack of diverse representation in PGx studies will impede equitable clinical implementation through potentially inappropriate application of gene-based dosing algorithms, whereas representing a missed opportunity for identification of population specific single nucleotide variants and alleles. In this review, we discuss the challenges of studying PGx in under-represented populations, highlight two successful PGx studies conducted in non-European populations, and propose a path forward through community-based participatory research for equitable PGx research and clinical translation.

Developing mass spectrometry for the quantitative analysis of neuropeptides

INTRODUCTION

Neuropeptides are signaling molecules originating in the neuroendocrine system that can act as neurotransmitters and hormones in many biochemical processes. Their exact function is difficult to characterize, however, due to dependence on concentration, post-translational modifications, and the presence of other comodulating neuropeptides. Mass spectrometry enables sensitive, accurate, and global peptidomic analyses that can profile neuropeptide expression changes to understand their roles in many biological problems, such as neurodegenerative disorders and metabolic function.

AREAS COVERED

We provide a brief overview of the fundamentals of neuropeptidomic research, limitations of existing methods, and recent progress in the field. This review is focused on developments in mass spectrometry and encompasses labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements.

EXPERT OPINION

Neuropeptidomics is critical for future clinical research with impacts in biomarker discovery, receptor identification, and drug design. While advancements are being made to improve sensitivity and accuracy, there is still room for improvement. Better quantitative strategies are required for clinical analyses, and these methods also need to be amenable to mass spectrometry imaging, post-translational modification analysis, and multi-omics to facilitate understanding and future treatment of many diseases.

Undercutting efforts of precision medicine: roadblocks to minority representation in breast cancer clinical trials

Precision (or personalized) medicine holds great promise in the treatment of breast cancer. The success of personalized medicine is contingent upon inclusivity and representation for minority groups in clinical trials. In this article, we focus on the roadblocks for the African American demographic, including the barriers to access and enrollment in breast oncology trials, the prevailing classification of race and ethnicity, and the need to refine monolithic categorization by employing genetic ancestry mapping tools for a more accurate determination of race or ethnicity.

Meta-analysis of probability estimates of worldwide variation of CYP2D6 and CYP2C19

Extensive migration has led to the necessity of knowledge regarding the treatment of migrants with different ethnical backgrounds. This is especially relevant for pharmacological treatment, because of the significant variation between migrant groups in their capacity to metabolize drugs. For psychiatric medications, CYP2D6 and CYP2C19 enzymes are clinically relevant. The aim of this meta-analysis was to analyze studies reporting clinically useful information regarding CYP2D6 and CYP2C19 genotype frequencies, across populations and ethnic groups worldwide. To that end, we conducted a comprehensive meta-analysis using Embase, PubMed, Web of Science, and PsycINFO (>336,000 subjects, 318 reports). A non-normal metabolizer (non-NM) probability estimate was introduced as the equivalent of the sum-prevalence of predicted poor, intermediate, and ultrarapid metabolizer CYP2D6 and CYP2C19 phenotypes. The probability of having a CYP2D6 non-NM predicted phenotype was highest in Algeria (61%) and lowest in Gambia (2.7%) while the probability for CYP2C19 was highest in India (80%) and lowest in countries in the Americas, particularly Mexico (32%). The mean total probability estimates of having a non-NM predicted phenotype worldwide were 36.4% and 61.9% for CYP2D6 and CYP2C19, respectively. We provide detailed tables and world maps summarizing clinically relevant data regarding the prevalence of CYP2D6 and CYP2C19 predicted phenotypes and demonstrating large inter-ethnic differences. Based on the documented probability estimates, pre-emptive pharmacogenetic testing is encouraged for every patient who will undergo therapy with a drug(s) that is metabolized by CYP2D6 and/or CYP2C19 pathways and should be considered in case of treatment resistance or serious side effects.

Physiologically-Based Pharmacokinetic-Pharmacodynamics Model Characterizing CYP2C19 Polymorphisms to Predict Clopidogrel Pharmacokinetics and Its Anti-Platelet Aggregation Effect Following Oral Administration to Coronary Artery Disease Patients With or Without Diabetes

Background and Objective: Clopidogrel (CLOP) is commonly used in coronary artery disease (CAD) patients with or without diabetes (DM), but these patients often suffer CLOP resistance, especially those with diabetes. This study was aimed to develop a physiologically-based pharmacokinetic-pharmacodynamic (PBPK-PD) model to describe the pharmacokinetics and pharmacodynamics of clopidogrel active metabolite (CLOP-AM) in CAD patients with or without DM.

Methods: The PBPK-PD model was first established and validated in healthy subjects and then in CAD patients with or without DM. The influences of CYP2C19, CYP2C9, CYP3A4, carboxylesterase 1 (CES1), gastrointestinal transit rates (K_t,i) and platelets response to CLOP-AM (k_irre) on predicted pharmacokinetics and pharmacodynamics were investigated, followed with their individual and integrated effects on CLOP-AM pharmacokinetics due to changes in DM status.

Results: Most predictions fell within 0.5–2.0 folds of observations, indicating successful predictions. Sensitivity analysis showed that contributions of interested factors to pharmacodynamics were CES1> k_irre> K_t,i> CYP2C19 > CYP3A4> CYP2C9. Mimicked analysis showed that the decreased exposure of CLOP-AM by DM was mainly attributed to increased CES1 activity, followed by decreased CYP2C19 activity.

Conclusion: The pharmacokinetics and pharmacodynamics of CLOP-AM were successfully predicted using the developed PBPK-PD model. Clopidogrel resistance by DM was the integrated effects of altered K_t,i, CYP2C19, CYP3A4, CES1 and k_irre.

PharmVar GeneFocus: CYP2C19

The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the metabolism of many drugs and has been associated with both efficacy and safety issues for several commonly prescribed medications. This GeneFocus provides a comprehensive overview and summary of CYP2C19 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC).

Pharmacogenomics in Asian Subpopulations and Impacts on Commonly Prescribed Medications

Asians as a group comprise > 60% the world's population. There is an incredible amount of diversity in Asian and admixed populations that has not been addressed in a pharmacogenetic context. The known pharmacogenetic differences in Asian subgroups generally represent previously known variants that are present at much lower or higher frequencies in Asians compared with other populations. In this review we summarize the main drugs and known genes that appear to have differences in their pharmacogenetic properties in certain Asian populations. Evidence-based guidelines and summary statistics from the US Food and Drug Administration and the Clinical Pharmacogenetics Implementation Consortium were analyzed for ethnic differences in outcomes. Implicated drugs included commonly prescribed drugs such as warfarin, clopidogrel, carbamazepine, and allopurinol. The majority of these associations are due to Asians more commonly being poor metabolizers of cytochrome P450 (CYP) 2C19 and carriers of the human leukocyte antigen (HLA)-B*15:02 allele. The relative risk increase was shown to vary between genes and drugs, but could be > 100-fold higher in Asians. Specifically, there was a 172-fold increased risk of Stevens-Johnson syndrome and toxic epidermal necrolysis with carbamazepine use among HLA-B*15:02 carriers. The effects ranged from relatively benign reactions such as reduced drug efficacy to severe cutaneous skin reactions. These reactions are severe and prevalent enough to warrant pharmacogenetic testing and appropriate changes in dose and medication choice for at-risk populations. Further studies should be done on Asian cohorts to more fully understand pharmacogenetic variants in these populations and to clarify how such differences may influence drug response.

Interethnic differences in the prevalence of main cardiovascular pharmacogenetic biomarkers

Background: The aim of this study was to determine the prevalence of CYP2C9, VKORC1, CYP2C19, ABCB1, CYP2D6 and SLCO1B1 genes polymorphisms among residents of the Volga region (Chuvash and Mari) and northern Caucasus (Kabardins and Ossetians). Materials & methods: The study involved 845 apparently healthy volunteers of both sexes of the four different ethnic groups living in the Russian Federation: 238 from the Chuvash ethnic group, 206 Mari, 157 Kabardins and 244 Ossetians. Results: Significant differences were identified in allele frequency of CYP2C9, VKORC1, CYP2C19, ABCB1, CYP2D6 and SLCO1B1 genes polymorphisms between the Chuvash and Kabardins, Chuvash and Ossetians, Mari and Kabardians, Mari and Ossetians.

The Identification of Admixture Patterns Could Refine Pharmacogenetic Counseling: Analysis of a Population-Based Sample in Mexico

Pharmacogenetic analysis has generated translational data that could be applied to guide treatments according to individual genetic variations. However, pharmacogenetic counseling in some mestizo (admixed) populations may require tailoring to different patterns of admixture. The identification and clustering of individuals with related admixture patterns in such populations could help to refine the practice of pharmacogenetic counseling. This study identifies related groups in a highly admixed population-based sample from Mexico, and analyzes the differential distribution of actionable pharmacogenetic variants. A subsample of 1728 individuals from the Mexican Genomic Database for Addiction Research (MxGDAR/Encodat) was analyzed. Genotyping was performed with the commercial PsychArray BeadChip, genome-wide ancestry was estimated using EIGENSOFT, and model-based clustering was applied to defined admixture groups. Actionable pharmacogenetic variants were identified with a query to the Pharmacogenomics Knowledge Base (PharmGKB) database, and functional prediction using the Variant Effect Predictor (VEP). Allele frequencies were compared with chi-square tests and differentiation was estimated by F_ST. Seven admixture groups were identified in Mexico. Some, like Group 1, Group 4, and Group 5, were found exclusively in certain geographic areas. More than 90% of the individuals, in some groups (Group 1, Group 4 and Group 5) were found in the Central-East and Southeast region of the country. MTRR p.I49M, ABCG2 p.Q141K, CHRNA5 p.D398N, SLCO2B1 rs2851069 show a low degree of differentiation between admixture groups. ANKK1 p.G318R and p.H90R, had the lowest allele frequency of Group 1. The reduction in these alleles reduces the risk of toxicity from anticancer and antihypercholesterolemic drugs. Our analysis identified different admixture patterns and described how they could be used to refine the practice of pharmacogenetic counseling for this admixed population.

A review of clinical pharmacogenetics Studies in African populations

Effective interventions and treatments for complex diseases have been implemented globally, however, coverage in Africa has been comparatively lower due to lack of capacity, clinical applicability and knowledge on the genetic contribution to disease and treatment. Currently, there is a scarcity of genetic data on African populations, which have enormous genetic diversity. Pharmacogenomics studies have the potential to revolutionise treatment of diseases, therefore, African populations are likely to benefit from these approaches to identify likely responders, reduce adverse side effects and optimise drug dosing. This review discusses clinical pharmacogenetics studies conducted in African populations, focusing on studies that examined drug response in complex diseases relevant to healthcare. Several pharmacogenetics associations have emerged from African studies, as have gaps in knowledge.

PharmVar GeneFocus: CYP2D6

The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus. CYP2D6 genetic variation impacts the metabolism of numerous drugs and, thus, can impact drug efficacy and safety. This GeneFocus provides a comprehensive overview and summary of CYP2D6 genetic variation and describes how the information provided by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).

Fewer actionable mutations but higher tumor mutational burden characterizes NSCLC in black patients at an urban academic medical center

Background: Black patients have been historically underrepresented in studies investigating molecular patterns in non-small cell lung cancer (NSCLC). We aimed to investigate differences in actionable mutations among patients at our urban, diverse medical center.

Results: 146 patients were included (59 black, 76 white, 7 Asian, 3 Hispanic, 1 mixed). 35 patients had a targetable mutation. Seven black patients (11.8%) had a targetable mutation compared to 28 non-black patients (32.2%, p = 0.005). 15 black patients had PD-L1 expression ≥50% compared to 19 non-black (25.4% vs 21.8%, p = 0.69). Black patients had a higher TMB compared to non-black (15.3 mutations/Mb compared to 11.5 mutations/Mb, p = 0.001). In a multivariate analysis, TMB was driven by smoking (p < 0.01), without any additive interaction in black patients who smoke (p = 0.8).

Conclusion: NSCLC tumors from black patients had a higher TMB and were less likely to carry a targetable mutation. The higher TMB seen was driven by a higher prevalence of smoking among black patients in our study, which may not reflect nationwide trends. Our results serve as a proof of concept that differences in molecular markers exist between black and non-black patients, and that these differences may impact the treatment options available to black patients.

Methods: Retrospective chart review of patients with a diagnosis of NSCLC who underwent both PD-L1 testing and massively parallel sequencing (UCM-OncoPlus) was conducted. We examined whether high PD-L1 expression, tumor mutational burden (TMB), and presence of targetable mutations (EGFR, BRAF, ERBB2, RET or ALK translocations, ROS1 rearrangements) occur at different frequencies in tumors from black patients compared to non-black patients.