Race and Drug Toxicity: A Study of Three Cardiovascular Drugs with Strong Pharmacogenetic Recommendations.

The Clinical Pharmacogenetics Implementation Consortium (CPIC®) establishes evidence-based guidelines for utilizing pharmacogenetic information for certain priority drugs. Warfarin, clopidogrel and simvastatin are cardiovascular drugs that carry strong prescribing guidance by CPIC. The respective pharmacogenes for each of these drugs exhibit considerable variability amongst different ethnic/ancestral/racial populations. Race and ethnicity are commonly employed as surrogate biomarkers in clinical practice and can be found in many prescribing guidelines. This is controversial due to the large variability that exists amongst different racial/ethnic groups, lack of detailed ethnic information and the broad geographic categorization of racial groups. Using a retrospective analysis of electronic health records (EHR), we sought to determine the degree to which self-reported race/ethnicity contributed to the probability of adverse drug reactions for these drugs. All models used individuals self-reporting as White as the comparison group. The majority of apparent associations between different racial groups and drug toxicity observed in the "race only" model failed to remain significant when we corrected for covariates. We did observe self-identified Asian race as a significant predictor (p = 0.016) for warfarin hemorrhagic events in all models. In addition, patients identifying as either Black/African-American (p = 0.001) or Other/Multiple race (p = 0.019) had a lower probability of reporting an adverse reaction than White individuals while on simvastatin even after correcting for other covariates. In both instances where race/ethnicity was predictive of drug toxicity (i.e., warfarin, simvastatin), the findings are consistent with the known global variability in the pharmacogenes described in the CPIC guidelines for these medications. These results confirm that the reliability of using self-identified race/ethnic information extracted from EHRs as a predictor of adverse drug reactions is likely limited to situations where the genes influencing drug toxicity display large, distinct ethnogeographic variability.

Genome Wide Epistasis Study of On-Statin Cardiovascular Events with Iterative Feature Reduction and Selection.

Predicting risk for major adverse cardiovascular events (MACE) is an evidence-based practice that incorporates lifestyle, history, and other risk factors. Statins reduce risk for MACE by decreasing lipids, but it is difficult to stratify risk following initiation of a statin. Genetic risk determinants for on-statin MACE are low-effect size and impossible to generalize. Our objective was to determine high-level epistatic risk factors for on-statin MACE with GWAS-scale data. Controlled-access data for 5890 subjects taking a statin collected from Vanderbilt University Medical Center's BioVU were obtained from dbGaP. We used Random Forest Iterative Feature Reduction and Selection (RF-IFRS) to select highly informative genetic and environmental features from a GWAS-scale dataset of patients taking statin medications. Variant-pairs were distilled into overlapping networks and assembled into individual decision trees to provide an interpretable set of variants and associated risk. 1718 cases who suffered MACE and 4172 controls were obtained from dbGaP. Pathway analysis showed that variants in genes related to vasculogenesis (FDR = 0.024), angiogenesis (FDR = 0.019), and carotid artery disease (FDR = 0.034) were related to risk for on-statin MACE. We identified six gene-variant networks that predicted odds of on-statin MACE. The most elevated risk was found in a small subset of patients carrying variants in COL4A2, TMEM178B, SZT2, and TBXAS1 (OR = 4.53, p < 0.001). The RF-IFRS method is a viable method for interpreting complex "black-box" findings from machine-learning. In this study, it identified epistatic networks that could be applied to risk estimation for on-statin MACE. Further study will seek to replicate these findings in other populations.

The ACCOuNT Consortium: A Model for the Discovery, Translation, and Implementation of Precision Medicine in African Americans.

The majority of pharmacogenomic (PGx) studies have been conducted on European ancestry populations, thereby excluding minority populations and impeding the discovery and translation of African American-specific genetic variation into precision medicine. Without accounting for variants found in African Americans, clinical recommendations based solely on genetic biomarkers found in European populations could result in misclassification of drug response in African American patients. To address these challenges, we formed the Transdisciplinary Collaborative Center (TCC), African American Cardiovascular Pharmacogenetic Consortium (ACCOuNT), to discover novel genetic variants in African Americans related to clinically actionable cardiovascular phenotypes and to incorporate African American-specific sequence variations into clinical recommendations at the point of care. The TCC consists of two research projects focused on discovery and translation of genetic findings and four cores that support the projects. In addition, the largest repository of PGx information on African Americans is being established as well as lasting infrastructure that can be utilized to spur continued research in this understudied population.

Teaching students in clinical programs about pharmacogenomics: do they understand drug-drug interactions?

Teaching the clinical implementation of pharmacogenomics to students in clinical programs first requires careful consideration of their aptitude in basic clinical pharmacologic concepts. Prior to developing training exercises on drug-gene interactions, educators must first assess student competency in identifying and managing drug-drug interactions given the similarities in identifying and managing these sources of medication error.

Genetic Variation in CYP2R1 and GC Genes Associated With Vitamin D Deficiency Status.

This cross-sectional study enrolled 180 patients at a private family practice in Virginia. Total serum vitamin D concentrations were obtained weekly from January 30, 2013, through March 30, 2013, in consecutive patients regularly scheduled for laboratory work at the practice. Patients were categorized into 2 groups and analyzed for variant alleles in vitamin D receptor ( VDR; rs2228570), cytochrome P450 2R1 ( CYP2R1; rs10741657), 7-dehydrocholesterol reductase ( DHCR7; rs12785878), and group-specific component ( GC; rs2282679) to determine whether variants of those alleles influenced total serum 25(OH)D concentrations. One-hundred and eighty patients were enrolled, with 40 (22%) being sufficient, 25-hydroxy vitamin D level 25(OH)D ≥ 30 ng/mL, and 140 (78%) being insufficient, 25(OH)D < 30 ng/mL. Of the 4 genes, 2 genes, CYP2R1 (rs10741657) and GC (rs2282679), demonstrated a significant association related to vitamin D status. Subjects with 1 or more variant alleles at rs10741657 were almost 3.7 (odds ratio [OR] 3.67; 95% confidence interval [CI]: 1.35-9.99) times more likely be insufficient in vitamin D and subjects with 1 or more variant alleles at rs2282679 were about half (OR 0.42; 95% CI: 0.18-0.93) as likely to be insufficient in vitamin D. Allelic variations in CYP2R1 (rs10741657) and GC (rs2282679) affect vitamin D levels, but variant alleles on VDR (rs2228570) and DHCR7 (rs12785878) were not correlated with vitamin D deficiency, 25(OH)D < 30 ng/mL.

Impact of a personal CYP2D6 testing workshop on physician assistant student attitudes toward pharmacogenetics.

AIM: We assessed the impact of personal CYP2D6 testing on physician assistant student competency in, and attitudes toward, pharmacogenetics (PGx). MATERIALS & METHODS: Buccal samples were genotyped for CYP2D6 polymorphisms. Results were discussed during a 3-h PGx workshop. PGx knowledge was assessed by pre- and post-tests. Focus groups assessed the impact of the workshop on attitudes toward the clinical utility of PGx. RESULTS: Both student knowledge of PGx, and its perceived clinical utility, increased immediately following the workshop. However, exposure to PGx on clinical rotations following the workshop seemed to influence student attitudes toward PGx utility. CONCLUSION: Personal CYP2D6 testing improves both knowledge and comfort with PGx. Continued exposure to PGx concepts is important for transfer of learning.

Novel genetic predictors of venous thromboembolism risk in African Americans.

Venous thromboembolism (VTE) is the third most common life-threatening cardiovascular condition in the United States, with African Americans (AAs) having a 30% to 60% higher incidence compared with other ethnicities. The mechanisms underlying population differences in the risk of VTE are poorly understood. We conducted the first genome-wide association study in AAs, comprising 578 subjects, followed by replication of highly significant findings in an independent cohort of 159 AA subjects. Logistic regression was used to estimate the association between genetic variants and VTE risk. Through bioinformatics analysis of the top signals, we identified expression quantitative trait loci (eQTLs) in whole blood and investigated the messenger RNA expression differences in VTE cases and controls. We identified and replicated single-nucleotide polymorphisms on chromosome 20 (rs2144940, rs2567617, and rs1998081) that increased risk of VTE by 2.3-fold (P< 6 × 10(-7)). These risk variants were found in higher frequency among populations of African descent (>20%) compared with other ethnic groups (<10%). We demonstrate that SNPs on chromosome 20 are cis-eQTLs for thrombomodulin (THBD), and the expression of THBD is lower among VTE cases compared with controls (P= 9.87 × 10(-6)). We have identified novel polymorphisms associated with increased risk of VTE in AAs. These polymorphisms are predominantly found among populations of African descent and are associated with THBD gene expression. Our findings provide new molecular insight into a mechanism regulating VTE susceptibility and identify common genetic variants that increase the risk of VTE in AAs, a population disproportionately affected by this disease.

Targeted single molecule sequencing methodology for ovarian hyperstimulation syndrome.

BACKGROUND: One of the most significant issues surrounding next generation sequencing is the cost and the difficulty assembling short read lengths. Targeted capture enrichment of longer fragments using single molecule sequencing (SMS) is expected to improve both sequence assembly and base-call accuracy but, at present, there are very few examples of successful application of these technologic advances in translational research and clinical testing. We developed a targeted single molecule sequencing (T-SMS) panel for genes implicated in ovarian response to controlled ovarian hyperstimulation (COH) for infertility. RESULTS: Target enrichment was carried out using droplet-base multiplex polymerase chain reaction (PCR) technology (RainDance®) designed to yield amplicons averaging 1 kb fragment size from candidate 44 loci (99.8% unique base-pair coverage). The total targeted sequence was 3.18 Mb per sample. SMS was carried out using single molecule, real-time DNA sequencing (SMRT® Pacific Biosciences®), average raw read length = 1178 nucleotides, 5% of the amplicons >6000 nucleotides). After filtering with circular consensus (CCS) reads, the mean read length was 3200 nucleotides (97% CCS accuracy). Primary data analyses, alignment and filtering utilized the Pacific Biosciences® SMRT portal. Secondary analysis was conducted using the Genome Analysis Toolkit for SNP discovery l and wANNOVAR for functional analysis of variants. Filtered functional variants 18 of 19 (94.7%) were further confirmed using conventional Sanger sequencing. CCS reads were able to accurately detect zygosity. Coverage within GC rich regions (i.e.VEGFR; 72% GC rich) was achieved by capturing long genomic DNA (gDNA) fragments and reading into regions that flank the capture regions. As proof of concept, a non-synonymous LHCGR variant captured in two severe OHSS cases, and verified by conventional sequencing. CONCLUSIONS: Combining emulsion PCR-generated 1 kb amplicons and SMRT DNA sequencing permitted greater depth of coverage for T-SMS and facilitated easier sequence assembly. To the best of our knowledge, this is the first report combining emulsion PCR and T-SMS for long reads using human DNA samples, and NGS panel designed for biomarker discovery in OHSS.

Kinase insert domain receptor/vascular endothelial growth factor receptor 2 (KDR) genetic variation is associated with ovarian hyperstimulation syndrome.

BACKGROUND: The objective of this investigation was to determine if kinase insert domain/vascular endothelial growth factor receptor 2 (KDR/VEGFR2) genetic variation was associated with the development of ovarian hyperstimulation syndrome (OHSS) in patients undergoing controlled ovarian hyperstimulation (COH). METHODS: This was a case-control study of 174 patients who underwent controlled ovarian stimulation. Patient blood samples were genotyped for single nucleotide polymorphisms (SNPs) spanning the KDR locus. OHSS development, clinical outcome variables, SNP and haplotype frequencies were compared between control (n = 155) and OHSS (n = 19) groups. RESULTS: Patients who developed OHSS had significantly higher response markers (estradiol levels of the day of hCG administration, number of follicles developed, number of eggs retrieved) than control patients. When adjusted for age and self-identified race, the rs2305945 G/T genotype was associated (P = 0.027) with a decreased risk (OR = 0.30; 95% CI = 0.10, 0.93) of developing OHSS using an overdominant model. The rs2305945 G/T variant was also associated with decreased COH response (number of follicles, number of eggs retrieved) in an overdominant model. The rs2305948, rs1870378, rs2305945 (C-T-G) haplotype was associated with both decreased COH response and OHSS risk (unadjusted OR = 0.10; 95% CI = 0.01, 0.80, P = 0.031). CONCLUSIONS: The KDR receptor is believed to play a central role OHSS development and is a target for pharmacological prevention of OHSS. These results indicate that genetic variation in the KDR gene may impact individual risk of developing OHSS from COH. In addition, the rs2305948 SNP and C-T-G haplotype might serve as potential biomarkers for poor ovarian response to COH.

Status of pharmacy practice experience education programs.

OBJECTIVE: To assess financial, personnel, and curricular characteristics of US pharmacy practice experiential education programs and follow-up on results of a similar survey conducted in 2001. METHODS: Experiential education directors at 118 accredited US pharmacy colleges and schools were invited to participate in a blinded, Web-based survey in 2011. Aggregate responses were analyzed using descriptive statistics and combined with data obtained from the American Association of Colleges of Pharmacy to assess program demographics, faculty and administrative organizational structure, and financial support. RESULTS: The number of advanced pharmacy practice experience (APPE) sites had increased by 24% for medium, 50% for large, and 55% for very large colleges and schools. Introductory pharmacy practice experience (IPPE) sites outnumbered APPEs twofold. The average experiential education team included an assistant/associate dean (0.4 full-time equivalent [FTE]), a director (1.0 FTE), assistant/associate director (0.5 FTE), coordinator (0.9 FTE), and multiple administrative assistants (1.3 FTE). Most faculty members (63%-75%) were nontenure track and most coordinators (66%) were staff members. Estimated costs to operate an experiential education program represented a small percentage of the overall expense budget of pharmacy colleges and schools. CONCLUSION: To match enrollment growth, pharmacy practice experiential education administrators have expanded their teams, reorganized responsibilities, and found methods to improve cost efficiency. These benchmarks will assist experiential education administrators to plan strategically for future changes.

Out-of-school genomics program for young women demystifies genomics and fosters interest in biomedical sciences.

BACKGROUND: Pharmacogenomics (PGx) plays a critical role in personalized medicine; however, most healthcare practitioners lack the training and confidence in PGx required to fully utilize its potential. Although continuing education and inclusion of PGx into the professional curricula will begin to address this deficiency, PGx education at the secondary and postsecondary levels would demystify PGx and pique interest at an academic stage that is key to funneling PGx curious students into the science and healthcare pipeline earlier. METHODS: This article describes the development and evaluation of a genomics outreach program targeted at young women in high school with the ultimate goal of recruiting students into an undergraduate PGx program and school of pharmacy. RESULTS: This program increased participants' genomics knowledge, influenced their careers interests, and imparted positive feelings towards a genomics-based and/or biomedical career. CONCLUSION: Genomics-based educational outreach programs geared towards secondary school students can increase interest in and confidence to pursue a PGx-centric degree/career. Original submitted 3 July 2013; Revision submitted 6 January 2014.

Engaging the next generation of healthcare professionals in genomics: planning for the future.

There is broad agreement that healthcare professionals require fundamental training in genomics to keep pace with scientific advancement. Strong models that promote effective genomic education, however, are lacking. Furthermore, curricula at many institutions are now straining to adapt to the integration of additional material on next-generation sequencing and the bioethical and legal issues that will accompany clinical genomic testing. This article advocates for core competencies focused on job function, which will best prepare providers to be end-users of healthcare information. In addition, it argues in favor of online and blended learning models that incorporate student genotyping and specific training in the ethical, legal and social issues raised by genomic testing.

Association between the luteinizing hormone/chorionic gonadotropin receptor (LHCGR) rs4073366 polymorphism and ovarian hyperstimulation syndrome during controlled ovarian hyperstimulation.

BACKGROUND: The aim of this study was to determine the relationship between a purported luteinizing hormone/chorionic gonadotropin (LHCGR) high function polymorphism (rs4539842/insLQ) and outcome to controlled ovarian hyperstimulation (COH). METHODS: This was a prospective study of 172 patients undergoing COH at the Fertility and IVF Center at GWU. DNA was isolated from blood samples and a region encompassing the insLQ polymorphism was sequenced. We also investigated a polymorphism (rs4073366 G > C) that was 142 bp from insLQ. The association of the insLQ and rs4073366 alleles and outcome to COH (number of mature follicles, estradiol level on day of human chorionic gonadotropin (hCG) administration, the number of eggs retrieved and ovarian hyperstimulation syndrome (OHSS)) was determined. RESULTS: Increasing age and higher day 3 (basal) FSH levels were significantly associated with poorer response to COH. We found that both insLQ and rs4073366 were in linkage disequilibrium (LD) and no patients were homozygous for both recessive alleles (insLQ/insLQ; C/C). The insLQ variant was not significantly associated with any of the main outcomes to COH. Carrier status for the rs4073366 C variant was associated (P = 0.033) with an increased risk (OR 2.95, 95% CI = 1.09-7.96) of developing OHSS. CONCLUSIONS: While age and day 3 FSH levels were predictive of outcome, we found no association between insLQ and patient response to COH. Interestingly, rs4073366 C variant carrier status was associated with OHSS risk. To the best of our knowledge, this is the first report suggesting that LHCGR genetic variation might function in patient risk for OHSS.

First report of warfarin dose requirements in patients possessing the CYP2C9*12 allele.

BACKGROUND: Warfarin is the most frequently prescribed anticoagulant in North America and Europe. It is administered as a racemate, but S-warfarin is principally responsible for its anticoagulant activity. Cytochrome P450 (CYP) 2C9 is the enzyme primarily responsible for the metabolism of S-warfarin. Numerous variant alleles of CYP2C9 have been identified. The CYP2C9*12 (rs9332239) allele harbors a P489S substitution in CYP2C9 which has been shown to result in a 40% decline in catalytic activity in vitro. CASES: Four Caucasian patients with a low mean weekly warfarin dose (MWWD) were genotyped for CYP2C9, VKORC1 and APOE variant alleles. None of the four patients carried the common CYP2C9 variant alleles (*2, *3, *5, *6, *7, *8, *9, *11, *13) despite a relatively low MWWD (23.4±7.94 mg) compared to 208 patients carrying the CYP29C9*1 genotype (32.2±12.65 mg). Given that CYP2C9*12 confers decreased in vitro activity to the enzyme, we investigated whether these patients carried this allele. All four patients were CYP2C9*12 CT heterozygotes. Individual comparisons with patients possessing the same VKORC1 and APOE genotypes also demonstrated lower dose requirements in the patients that possessed CYP2C9*12 allele. CONCLUSIONS: There are no reports of the clinical impact of rs9332239 on CYP2C9 substrates. This is the first report of patients with the rare CYP2C9*12 genotype and lower warfarin dose requirements.

Adjunctive sitagliptin therapy in postoperative cardiac surgery patients: a pilot study.

Aim. We aimed to determine if sitagliptin added to standard postoperative standardized sliding-scale insulin regimens improved blood glucose. Methods. A prospective, randomized, double-blind, placebo-controlled pilot study was conducted in diabetic cardiac surgery patients. Patients received sitagliptin or placebo after surgery for 4 days. The primary endpoint was to estimate the effect of adjunctive sitagliptin versus placebo on overall mean blood glucose in the 4-day period after surgery. Results. Sixty-two patients participated. Repeated measures tests indicated no significant difference between the groups in the overall mean blood glucose level with a mean of 147.2 ± 4.8 mg/dL and 153.0 ± 4.6 mg/dL for the test and the control group, respectively (P = 0.388). Conclusions. Sitagliptin added to normal postoperative glucose management practices did not improve overall mean blood glucose control in diabetic patients in the postoperative setting.

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.

Pharmacogenomics instruction in US and Canadian medical schools: implications for personalized medicine.

AIMS: To determine the extent of pharmacogenomics instruction at US and Canadian medical schools, characterize perceptions of curricular coverage, identify curricular resources and compare responses with similar studies conducted in US pharmacy schools and British medical schools. MATERIALS & METHODS: A survey was sent to the pharmacology department chairs of US and Canadian medical schools accredited by the Liaison Committee on Medical Education or the American Osteopathic Association's Commission on Osteopathic College Accreditation. Data were collected from July 2009 to February 2010. RESULTS: A total of 56% of eligible medical schools responded (90 out of 160). Of these schools, 82% (74 out of 90) incorporated pharmacogenomics into their curriculum. However, only 28% (21 out of 74) had more than 4 h of the required didactic pharmacogenomic coursework, and only 29% (22 out of 75) were planning to increase the number of pharmacogenomic coursework hours in the next 3 years. Pharmacogenomics coursework was most often contained within a required pharmacology course (66%; 49 out of 74) taught in the second professional year (72%; 53 out of 74). A total of 57% (44 out of 77) considered pharmacogenomics instruction at their own school as 'poor' or 'not at all adequate' while 76% (54 out of 71) considered it 'poor' or 'not at all adequate' at most medical schools. CONCLUSION: Most US and Canadian medical schools have begun to incorporate pharmacogenomics material into their curriculum; however, the extent of instruction is less than that of US pharmacy schools. To adequately prepare physicians to practice in the era of personalized medicine, medical schools should be encouraged to incorporate greater pharmacogenomic material in their curriculum.

Frequency of CYP3A4, CYP3A5, CYP2C9, and CYP2C19 variant alleles in patients receiving clopidogrel that experience repeat acute coronary syndrome.

The presence of cytochrome P450 (CYP) variant alleles may reduce the activation of the prodrug clopidogrel to its active state. This research evaluated the frequency of variant alleles in the genes coding for CYP3A4, CYP3A5, CYP2C9, and CYP2C19 enzymes in patients on clopidogrel therapy and experiencing repeat acute coronary syndrome (ACS) compared to a control group with a matching ethnic composition. Real-time polymerase chain reaction was used for allelic discrimination. Complete data were obtained for 92 patients enrolled over a 3-month period. There were no significant differences in the presence of the examined CYP3A4, CYP3A5, CYP2C9, or CYP2C19 variant alleles between the two groups. The present data indicate that patients currently receiving clopidogrel therapy who present with repeat ACS do not have higher frequency of the examined variant alleles compared to a control group.