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1.  A genome-wide association study of heparin-induced thrombocytopenia using an electronic medical record 
Thrombosis and haemostasis  2014;113(4):772-781.
Heparin-induced thrombocytopenia (HIT) is an unpredictable, potentially catastrophic adverse effect of heparin treatment resulting from an immune response to platelet factor 4 (PF4)/heparin complexes. No genome-wide evaluations have been performed to identify potential genetic influences on HIT. Here, we performed a genome-wide association study (GWAS) and candidate gene study using HIT cases and controls identified using electronic medical records (EMRs) coupled to a DNA biobank and attempted to replicate GWAS associations in an independent cohort. We subsequently investigated influences of GWAS-associated single nucleotide polymorphisms (SNPs) on PF4/heparin antibodies in non-heparin treated individuals. In a recessive model, we observed significant SNP associations (OR 18.52 [6.33–54.23], p=3.18×10−9) with HIT near the T-Cell Death-Associated Gene 8 (TDAG8). These SNPs are in linkage disequilibrium with a missense TDAG8 SNP. TDAG8 SNPs trended toward an association with HIT in replication analysis (OR 5.71 [0.47–69.22], p=0.17), and the missense SNP was associated with PF4/heparin antibody levels and positive PF4/heparin antibodies in non-heparin treated patients (OR 3.09 [1.14–8.13], p=0.02). In the candidate gene study, SNPs at HLA-DRA were nominally associated with HIT (OR 0.25 [0.15–0.44], p=2.06×10−6). Further study of TDAG8 and HLA-DRA SNPs is warranted to assess their influence on the risk of developing HIT.
doi:10.1160/TH14-08-0670
PMCID: PMC4433536  PMID: 25503805
2.  Examining Rare and Low-Frequency Genetic Variants Previously Associated with Lone or Familial Forms of Atrial Fibrillation in an Electronic Medical Record System: A Cautionary Note 
Background
Studies in individuals or small kindreds have implicated rare variants in 25 different genes in lone and familial atrial fibrillation (AF) using linkage and segregation analysis, functional characterization, and rarity in public databases. Here we used a cohort of 20,204 patients of European or African ancestry with electronic medical records (EMRs) and exome chip data to compare the frequency of AF among carriers and non-carriers of these rare variants.
Methods and Results
The exome chip included 19/115 rare variants, in 9 genes, previously associated with lone or familial AF. Using validated algorithms querying a combination of clinical notes, structured billing codes, ECG reports, and procedure codes, we identified 1,056 AF cases (>18 years) and 19,148 non-AF controls (>50 years) with available genotype data on the Illumina HumanExome BeadChip v.1.0 in the Vanderbilt electronic medical record-linked DNA repository, BioVU. Known correlations between AF and common variants at 4q25 were replicated. None of the 19 variants previously associated with AF were overrepresented among AF cases (P >0.1 for all), and the frequency of variant carriers among non-AF controls was >0.1% for 14/19. Repeat analyses using non-AF controls aged >60 (n=14,904) >70 (n=9,670), and >80 (n=4,729) years old did not influence these findings.
Conclusions
Rare variants previously implicated in lone or familial forms AF present on the exome chip are detected at low frequencies in a general population but are not associated with AF. These findings emphasize the need for caution when ascribing variants as pathogenic or causative.
doi:10.1161/CIRCGENETICS.114.000718
PMCID: PMC4334677  PMID: 25410959
Genome Wide Association Study; single nucleotide polymorphism; genetics; association studies; atrial fibrillation; gene mutation; family study; penetrance; exome; genome; GWAS
3.  Pharmacology and Toxicology of Nav1.5-Class 1 anti-arrhythmic drugs 
SYNOPSIS
Although cardiac sodium channel blocking drugs can exert antiarrhythmic actions, they can also provoke life-threatening arrhythmias through a variety of mechanisms. This review addresses the way in which drugs interact with the channel, and how these effects translate to clinical beneficial or detrimental effects. A further understanding of the details of channel function and of drug-channel interactions may lead to the development of safer and more effective antiarrhythmic therapies.
doi:10.1016/j.ccep.2014.07.003
PMCID: PMC4226533  PMID: 25395995
sodium channel; drugs; proarrhythmia
4.  Screening for Acute IKr Block is Insufficient to Detect Torsades de Pointes Liability: Role of Late Sodium Current 
Circulation  2014;130(3):224-234.
Background
New drugs are routinely screened for acute IKr blocking properties thought to predict QT prolonging and arrhythmogenic liability. However, recent data suggest that chronic (hours) drug exposure to PI3 kinase (PI3K) inhibitors used in cancer can prolong QT by inhibiting potassium currents and increasing late sodium current (INa-L) in cardiomyocytes. We tested the extent to which IKr blockers with known QT liability generate arrhythmias through this pathway.
Methods and Results
Acute exposure to dofetilide, an IKr blocker without other recognized electropharmacologic actions, produced no change in ion currents or action potentials in adult mouse cardiomyocytes, which lack IKr. By contrast, 2–48 hours’ exposure to the drug generated arrhythmogenic afterdepolarizations and up to 15-fold increases in INa-L. Including PIP3, a downstream effector for the PI3K pathway, in the pipette inhibited these effects. INa-L was also increased, and inhibitable by PIP3, with hours of dofetilide exposure in human iPSC-derived cardiomyocytes and in CHO cells transfected with SCN5A, encoding INa. Cardiomyocytes from dofetilide-treated mice similarly demonstrated increased INa-L and afterdepolarizations. Other agents with variable IKr blocking potencies and arrhythmia liability produced a range of effects on INa-L, from marked increases (E-4031, d-sotalol, thioridazine, erythromycin) to little or no effect (haloperidol, moxifloxacin, verapamil).
Conclusions
Some but not all drugs designated as arrhythmogenic IKr blockers can generate arrhythmias by augmenting INa-L through the PI3K pathway. These data identify a potential mechanism for individual susceptibility to proarrhythmia and highlight the need for a new paradigm to screen drugs for QT prolonging and arrhythmogenic liability.
doi:10.1161/CIRCULATIONAHA.113.007765
PMCID: PMC4101031  PMID: 24895457
Late sodium current; IKr block; arrhythmogenic; phosphoinositide 3-kinase (PI3K) inhibition
5.  The AFFORD Clinical Decision Aid To Identify Emergency Department Patients With Atrial Fibrillation At Low Risk For 30-Day Adverse Events 
The American journal of cardiology  2015;115(6):763-770.
There is wide variation in the management of emergency department (ED) patients with atrial fibrillation (AF). We aimed to derive and internally validate the first prospective, ED-based clinical decision aid to identify patients with AF at low risk for 30-day adverse events. We performed a prospective cohort study at a university-affiliated, tertiary-care, ED. Patients were enrolled from June 9, 2010 to February 28, 2013 and followed for 30 days. We enrolled a convenience sample of ED patients presenting with symptomatic AF. Candidate predictors were based on ED data available in the first two hours. The decision aid was derived using model approximation (preconditioning) followed by strong bootstrap internal validation. We utilized an ordinal outcome hierarchy defined as the incidence of the most severe adverse event within 30 days of the ED evaluation. Of 497 patients enrolled, stroke and AF-related death occurred in 13 (3%) and 4 (<1%) patients, respectively. The decision aid included the following: age, triage vitals (systolic blood pressure, temperature, respiratory rate, oxygen saturation, supplemental oxygen requirement); medical history (heart failure, home sotalol use, prior percutaneous coronary intervention, electrical cardioversion, cardiac ablation, frequency of AF symptoms); ED data (2 hour heart rate, chest radiograph results, hemoglobin, creatinine, and brain natriuretic peptide). The decision aid’s c-statistic in predicting any 30-day adverse event was 0.7 (95% CI, 0.65, 0.76). In conclusion, among ED patients with AF, AFFORD provides the first evidence based decision aid for identifying patients who are at low risk for 30-day adverse events and candidates for safe discharge.
doi:10.1016/j.amjcard.2014.12.036
PMCID: PMC4346475  PMID: 25633190
atrial fibrillation; emergency treatment; decision aids
6.  Personalized medicine to treat arrhythmias 
The efficacy of antiarrhythmic drug therapy is incomplete, with responses ranging from efficacy to no effect to severe adverse effects, including paradoxical drug-induced arrhythmia. Most antiarrhythmic drugs were developed at a time when mechanism underlying arrhythmias were not well-understood. In the last decade, a range of experimental approaches have advanced our understanding of the molecular and genomic contributors to the generation of an arrhythmia-prone heart, and this information is directly informing targeted therapy with existing drugs or the development of new ones. The development of inexpensive whole genome sequencing holds the promise of identifying patients susceptible to arrhythmias in a presymptomatic phase, and thus implementing preventive therapies.
doi:10.1016/j.coph.2013.11.013
PMCID: PMC3984450  PMID: 24721655
genomics; pharmacogenomics; arrhythmia; long QT syndrome; atrial fibrillation
7.  Dantrolene: From Better Bacon to a Treatment for Ventricular Fibrillation 
Circulation  2014;129(8):834-836.
doi:10.1161/CIRCULATIONAHA.113.007657
PMCID: PMC3959791  PMID: 24403562
dantrolene; Editorial; ventricular fibrillation; ryanodine receptor; excitation-contraction coupling
8.  A Combined Genetic and Clinical Risk Prediction Model for Postoperative Atrial Fibrillation 
Background
Postoperative atrial fibrillation (PoAF) is common after coronary artery bypass grafting (CABG). We previously showed that AF susceptibility single nucleotide polymorphisms (SNPs) at the chromosome 4q25 locus are associated with PoAF. Here, we tested the hypothesis that a combined clinical and genetic model incorporating AF risk SNPs would be superior to a clinical-only model.
Methods and Results
We developed and externally validated clinical and clinical/genetic risk models for PoAF. The discovery and validation cohorts included 556 and 1164 patients, respectively. Clinical variables previously associated with PoAF and 13 SNPs at loci associated with AF in genome wide association studies were considered. PoAF occurred in 30% and 29% of patients in the discovery and validation cohorts, respectively. In the discovery cohort, a logistic regression model with clinical factors had good discrimination, with an area under the receiver operator characteristic (ROC) curve of 0.76. The addition of 10 SNPs to the clinical model did not improve discrimination (area under ROC curve: 0.78, P=0.14 for difference between the two models). In the validation cohort, the clinical model had good discrimination (area under the ROC curve: 0.69) and addition of genetic variables resulted in a marginal improvement in discrimination (area under ROC curve: 0.72, P<0.0001).
Conclusions
We developed and validated a model for the prediction of PoAF containing common clinical variables. Addition of AF susceptibility SNPs did not improve model performance. Tools to accurately predict PoAF are needed to risk-stratify patients undergoing CABG and identify candidates for prophylactic therapies.
doi:10.1161/CIRCEP.114.002300
PMCID: PMC4334678  PMID: 25567478
atrial fibrillation; genetics; risk model; cardiac surgery; postoperative complication arrhythmia
9.  Common Genetic Variants and Response to Atrial Fibrillation Ablation 
Background
Common single nucleotide polymorphisms (SNPs) at chromosomes 4q25 (rs2200733, rs10033464 near PITX2), 1q21 (rs13376333 in KCNN3), and 16q22 (rs7193343 in ZFHX3) have consistently been associated with the risk of atrial fibrillation (AF). Single-center studies have shown that 4q25 risk alleles predict recurrence of AF after catheter ablation of AF. Here, we performed a meta-analysis to test the hypothesis that these 4 AF susceptibility SNPs modulate response to AF ablation.
Methods and Results
Patients underwent de novo AF ablation between 2008 and 2012 at Vanderbilt University, the Heart Center Leipzig, and Massachusetts General Hospital. The primary outcome was 12-month recurrence, defined as an episode of AF, atrial flutter, or atrial tachycardia lasting >30 seconds after a 3-month blanking period. Multivariable analysis of the individual cohorts using a Cox proportional hazards model was performed. Summary statistics from the 3 centers were analyzed using fixed effects meta-analysis. A total of 991 patients were included (Vanderbilt University, 245; Heart Center Leipzig, 659; and Massachusetts General Hospital, 87). The overall single procedure 12-month recurrence rate was 42%. The overall risk allele frequency for these SNPs ranged from 12% to 35%. Using a dominant genetic model, the 4q25 SNP, rs2200733, predicted a 1.4-fold increased risk of recurrence (adjusted hazard ratio, 1.3 [95% confidence intervals, 1.1–1.6]; P=0.011). The remaining SNPs, rs10033464 (4q25), rs13376333 (1q21), and rs7193343 (16q22) were not significantly associated with recurrence.
Conclusions
Among the 3 genetic loci most strongly associated with AF, the chromosome 4q25 SNP rs2200733 is significantly associated with recurrence of atrial arrhythmias after catheter ablation for AF.
doi:10.1161/CIRCEP.114.001909
PMCID: PMC4731871  PMID: 25684755
ablation techniques; atrial fibrillation; genomics
10.  A Genome-Wide Association Study to Identify Genomic Modulators of Rate Control Therapy in Patients with Atrial Fibrillation 
The American journal of cardiology  2014;114(4):593-600.
For many patients with atrial fibrillation (AF), ventricular rate control with atrioventricular (AV) nodal blockers is considered first-line therapy, though response to treatment is highly variable. Using an extreme phenotype of failure of rate control necessitating AV nodal ablation and pacemaker implantation, we conducted a genome wide association study (GWAS) to identify genomic modulators of rate control therapy. Cases included 95 patients who failed rate control therapy. Controls (N=190) achieved adequate rate control therapy with ≤2 AV nodal blockers using a conventional clinical definition. Genotyping was performed on the Illumina 610-Quad platform, and results were imputed to the 1000 Genomes reference haplotypes. 554,041 single nucleotide polymorphisms (SNPs) met criteria for minor allele frequency (>0.01), call rate (>95%), and quality control, and 6,055,224 SNPs were available after imputation. No SNP reached the canonical threshold for significance for GWAS of P<5 × 10−8. Sixty-three SNPs with P<10−5 at 6 genomic loci were genotyped in a validation cohort of 130 cases and 157 controls. These included 6q24.3 (near SAMD5/SASH1, P=9.36 × 10−8), 4q12 (IGFBP7, P=1.75 × 10−7), 6q22.33 (C6orf174, P=4.86 × 10−7), 3p21.31 (CDCP1, P=1.18 × 10−6), 12p12.1 (SOX5, P=1.62 × 10−6), and 7p11 (LANCL2, P=6.51 × 10−6). However, none of these were significant in the replication cohort or in a meta-analysis of both cohorts. In conclusion, we identified several potentially important genomic modulators of rate control therapy in AF, particularly SOX5, which was previously associated with resting heart rate and PR interval. However these failed to reach genome-wide significance.
doi:10.1016/j.amjcard.2014.05.040
PMCID: PMC4119836  PMID: 25015694
atrial fibrillation; genomics; rate control
11.  Novel Rare Variants in Congenital Cardiac Arrhythmia Genes are Frequent in Drug-induced Torsades de Pointes 
The pharmacogenomics journal  2012;13(4):325-329.
Marked prolongation of the QT interval and polymorphic ventricular tachycardia following medication (drug-induced long QT syndrome, diLQTS) is a severe adverse drug reaction (ADR) that phenocopies congenital long QT syndrome (cLQTS) and one of the leading causes for drug withdrawal and relabeling. We evaluated the frequency of rare non-synonymous variants in genes contributing to the maintenance of heart rhythm in cases of diLQTS using targeted capture coupled to next generation sequencing. Eleven of 31 diLQTS subjects (36%) carried a novel missense mutation in genes with known congenital arrhythmia associations or a known cLQTS mutation. In the 26 Caucasian subjects, 23% carried a highly conserved rare variant predicted to be deleterious to protein function in these genes compared with only 2-4% in public databases (p < 0.003). We conclude that rare variation in genes responsible for congenital arrhythmia syndromes is frequent in diLQTS. Our findings demonstrate that diLQTS is a pharmacogenomic syndrome predisposed by rare genetic variants.
doi:10.1038/tpj.2012.14
PMCID: PMC3422407  PMID: 22584458
pharmacogenomics; sudden cardiac death; adverse drug reaction; next generation sequencing
12.  Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality 
Objectives Drug repurposing, which finds new indications for existing drugs, has received great attention recently. The goal of our work is to assess the feasibility of using electronic health records (EHRs) and automated informatics methods to efficiently validate a recent drug repurposing association of metformin with reduced cancer mortality.
Methods By linking two large EHRs from Vanderbilt University Medical Center and Mayo Clinic to their tumor registries, we constructed a cohort including 32 415 adults with a cancer diagnosis at Vanderbilt and 79 258 cancer patients at Mayo from 1995 to 2010. Using automated informatics methods, we further identified type 2 diabetes patients within the cancer cohort and determined their drug exposure information, as well as other covariates such as smoking status. We then estimated HRs for all-cause mortality and their associated 95% CIs using stratified Cox proportional hazard models. HRs were estimated according to metformin exposure, adjusted for age at diagnosis, sex, race, body mass index, tobacco use, insulin use, cancer type, and non-cancer Charlson comorbidity index.
Results Among all Vanderbilt cancer patients, metformin was associated with a 22% decrease in overall mortality compared to other oral hypoglycemic medications (HR 0.78; 95% CI 0.69 to 0.88) and with a 39% decrease compared to type 2 diabetes patients on insulin only (HR 0.61; 95% CI 0.50 to 0.73). Diabetic patients on metformin also had a 23% improved survival compared with non-diabetic patients (HR 0.77; 95% CI 0.71 to 0.85). These associations were replicated using the Mayo Clinic EHR data. Many site-specific cancers including breast, colorectal, lung, and prostate demonstrated reduced mortality with metformin use in at least one EHR.
Conclusions EHR data suggested that the use of metformin was associated with decreased mortality after a cancer diagnosis compared with diabetic and non-diabetic cancer patients not on metformin, indicating its potential as a chemotherapeutic regimen. This study serves as a model for robust and inexpensive validation studies for drug repurposing signals using EHR data.
doi:10.1136/amiajnl-2014-002649
PMCID: PMC4433365  PMID: 25053577
drug repurposing; electronic health records; natural language processing; metformin
13.  A polymorphism in HLA-G modifies statin benefit in asthma 
The pharmacogenomics journal  2014;15(3):272-277.
Several reports have shown that statin treatment benefits patients with asthma, however inconsistent effects have been observed. The mir-152 family (148a, 148b and 152) has been implicated in asthma. These microRNAs suppress HLA-G expression, and rs1063320, a common SNP in the HLA-G 3’UTR which is associated with asthma risk, modulates miRNA binding. We report that statins up-regulate mir-148b and 152, and affect HLA-G expression in an rs1063320 dependent fashion. In addition, we found that individuals who carried the G minor allele of rs1063320 had reduced asthma related exacerbations (emergency department visits, hospitalizations or oral steroid use) compared to non-carriers (p=0.03) in statin users ascertained in the Personalized Medicine Research Project at the Marshfield Clinic (n=421). These findings support the hypothesis that rs1063320 modifies the effect of statin benefit in asthma, and thus may contribute to variation in statin efficacy for the management of this disease.
doi:10.1038/tpj.2014.55
PMCID: PMC4379135  PMID: 25266681
pharmacogenetics; HLA-G; statin; asthma; mir-148; mir-152
14.  Size matters: How population size influences genotype–phenotype association studies in anonymized data 
Objective
Electronic medical records (EMRs) data is increasingly incorporated into genome-phenome association studies. Investigators hope to share data, but there are concerns it may be “re-identified” through the exploitation of various features, such as combinations of standardized clinical codes. Formal anonymization algorithms (e.g., k-anonymization) can prevent such violations, but prior studies suggest that the size of the population available for anonymization may influence the utility of the resulting data. We systematically investigate this issue using a large-scale biorepository and EMR system through which we evaluate the ability of researchers to learn from anonymized data for genome- phenome association studies under various conditions.
Methods
We use a k-anonymization strategy to simulate a data protection process (on data sets containing clinical codes) for resources of similar size to those found at nine academic medical institutions within the United States. Following the protection process, we replicate an existing genome-phenome association study and compare the discoveries using the protected data and the original data through the correlation (r2) of the p-values of association significance.
Results
Our investigation shows that anonymizing an entire dataset with respect to the population from which it is derived yields significantly more utility than small study-specific datasets anonymized unto themselves. When evaluated using the correlation of genome-phenome association strengths on anonymized data versus original data, all nine simulated sites, results from largest-scale anonymizations (population ∼ 100;000) retained better utility to those on smaller sizes (population ∼ 6000—75;000). We observed a general trend of increasing r2 for larger data set sizes: r2 = 0.9481 for small-sized datasets, r2 = 0.9493 for moderately-sized datasets, r2 = 0.9934 for large-sized datasets.
Conclusions
This research implies that regardless of the overall size of an institution's data, there may be significant benefits to anonymization of the entire EMR, even if the institution is planning on releasing only data about a specific cohort of patients.
doi:10.1016/j.jbi.2014.07.005
PMCID: PMC4260994  PMID: 25038554
Privacy; Anonymization; Clinical codes; Data publishing
15.  Electrophysiologic Substrate in Congenital Long QT Syndrome: Noninvasive Mapping with Electrocardiographic Imaging (ECGI) 
Circulation  2014;130(22):1936-1943.
Background
Congenital Long QT syndrome (LQTS) is an arrhythmogenic disorder that causes syncope and sudden death. While its genetic basis has become well-understood, the mechanisms whereby mutations translate to arrhythmia susceptibility in the in situ human heart have not been fully defined. We used noninvasive ECG imaging (ECGI) to map the cardiac electrophysiologic substrate and examine whether LQTS patients display regional heterogeneities in repolarization, a substrate which promotes arrhythmogenesis.
Methods and Results
25 subjects (9 LQT1, 9 LQT2, 5 LQT3 and 2 LQT5) with genotype and phenotype positive LQTS underwent ECGI. Seven normal subjects provided control. Epicardial maps of activation, recovery times (RT), Activation-recovery intervals (ARI) and repolarization dispersion were constructed. Activation was normal in all patients. However, RT and ARI were prolonged relative to control, indicating delayed repolarization and abnormally long APD (312 ± 30 ms vs. 235 ± 21 ms in control). ARI prolongation was spatially heterogeneous, with repolarization gradients much steeper than control (119 ± 19 ms/cm vs. 2.0 ± 2.0 ms/cm). There was variability in steepness and distribution of repolarization gradients between and within LQTS types. Repolarization gradients were steeper in symptomatic patients (130 ± 27 ms/cm in 12 symptomatic patients vs. 98 ± 19 ms/cm in 13 asymptomatic patients; P < 0.05).
Conclusions
LQTS patients display regions with steep repolarization dispersion caused by localized APD prolongation. This defines a substrate for reentrant arrhythmias, not detectable by surface ECG. Steeper dispersion in symptomatic patients suggests a possible role for ECGI in risk stratification.
doi:10.1161/CIRCULATIONAHA.114.011359
PMCID: PMC4245321  PMID: 25294783
congenital long-QT syndrome; arrhythmia (mechanisms); electrophysiology mapping; noninvasive imaging; ECGI
16.  SCN10A/Nav1.8 modulation of peak and late sodium currents in patients with early onset atrial fibrillation 
Cardiovascular Research  2014;104(2):355-363.
Aims
To test the hypothesis that vulnerability to atrial fibrillation (AF) is associated with rare coding sequence variation in the SCN10A gene, which encodes the voltage-gated sodium channel isoform NaV1.8 found primarily in peripheral nerves and to identify potentially disease-related mechanisms in high-priority rare variants using in-vitro electrophysiology.
Methods and results
We re-sequenced SCN10A in 274 patients with early onset AF from the Vanderbilt AF Registry to identify rare coding variants. Engineered variants were transiently expressed in ND7/23 cells and whole-cell voltage clamp experiments were conducted to elucidate their functional properties. Resequencing SCN10A identified 18 heterozygous rare coding variants (minor allele frequency ≤1%) in 18 (6.6%) AF probands. Four probands were carriers of two rare variants each and 14 were carriers of one coding variant. Based on evidence of co-segregation, initial assessment of functional importance, and presence in ≥1 AF proband, three variants (417delK, A1886V, and the compound variant Y158D-R814H) were selected for functional studies. The 417delK variant displayed near absent current while A1886V and Y158D-R814H exhibited enhanced peak and late (INa-L) sodium currents; both Y158D and R818H individually contributed to this phenotype.
Conclusion
Rare SCN10A variants encoding Nav1.8 were identified in 6.6% of patients with early onset AF. In-vitro electrophysiological studies demonstrated profoundly altered function in 3/3 high-priority variants. Collectively, these data strongly support the hypothesis that rare SCN10A variants may contribute to AF susceptibility.
doi:10.1093/cvr/cvu170
PMCID: PMC4271018  PMID: 25053638
Atrial fibrillation; SCN10A; Nav1.8; Late sodium current; Cardiac electrophysiology
17.  Exome Sequencing Implicates an Increased Burden of Rare Potassium Channel Variants in the Risk of Drug Induced Long QT Syndrome 
Objectives
To test the hypothesis that rare variants are associated with Drug-induced long QT syndrome (diLQTS) and torsade de pointes (TdP).
Background
diLQTS is associated with the potentially fatal arrhythmia TdP. The contribution of rare genetic variants to the underlying genetic framework predisposing diLQTS has not been systematically examined.
Methods
We performed whole exome sequencing (WES) on 65 diLQTS cases and 148 drug-exposed controls of European descent. We employed rare variant analyses (variable threshold [VT] and sequence kernel association test [SKAT]) and gene-set analyses to identify genes enriched with rare amino-acid coding (AAC) variants associated with diLQTS. Significant associations were reanalyzed by comparing diLQTS cases to 515 ethnically matched controls from the NHLBI GO Exome Sequencing Project (ESP).
Results
Rare variants in 7 genes were enriched in the diLQTS cases according to SKAT or VT compared to drug exposed controls (p<0.001). Of these, we replicated the diLQTS associations for KCNE1 and ACN9 using 515 ESP controls (p<0.05). A total of 37% of the diLQTS cases also had ≥1 rare AAC variant, as compared to 21% of controls (p=0.009), in a predefined set of seven congenital LQTS (cLQTS) genes encoding potassium channels or channel modulators (KCNE1,KCNE2,KCNH2,KCNJ2, KCNJ5,KCNQ1,AKAP9).
Conclusions
By combining WES with aggregated rare variant analyses, we implicate rare variants in KCNE1 and ACN9 as risk factors for diLQTS. Moreover, diLQTS cases were more burdened by rare AAC variants in cLQTS genes encoding potassium channel modulators, supporting the idea that multiple rare variants, notably across cLQTS genes, predispose to diLQTS.
doi:10.1016/j.jacc.2014.01.031
PMCID: PMC4018823  PMID: 24561134
exome; torsade des pointes; long QT syndrome; genetics, adverse drug event
18.  Genome- and Phenome-Wide Analysis of Cardiac Conduction Identifies Markers of Arrhythmia Risk 
Circulation  2013;127(13):1377-1385.
Background
Electrocardiographic QRS duration, a measure of cardiac intraventricular conduction, varies ~2-fold in individuals without cardiac disease. Slow conduction may promote reentrant arrhythmias.
Methods and Results
We performed a genome-wide association study (GWAS) to identify genomic markers of QRS duration in 5,272 individuals without cardiac disease selected from electronic medical record (EMR) algorithms at five sites in the Electronic Medical Records and Genomics (eMERGE) network. The most significant loci were evaluated within the CHARGE consortium QRS GWAS meta-analysis. Twenty-three single nucleotide polymorphisms in 5 loci, previously described by CHARGE, were replicated in the eMERGE samples; 18 SNPs were in the chromosome 3 SCN5A and SCN10A loci, where the most significant SNPs were rs1805126 in SCN5A with p=1.2×10−8 (eMERGE) and p=2.5×10−20 (CHARGE) and rs6795970 in SCN10A with p=6×10−6 (eMERGE) and p=5×10−27 (CHARGE). The other loci were in NFIA, near CDKN1A, and near C6orf204. We then performed phenome-wide association studies (PheWAS) on variants in these five loci in 13,859 European Americans to search for diagnoses associated with these markers. PheWAS identified atrial fibrillation and cardiac arrhythmias as the most common associated diagnoses with SCN10A and SCN5A variants. SCN10A variants were also associated with subsequent development of atrial fibrillation and arrhythmia in the original 5,272 “heart-healthy” study population.
Conclusions
We conclude that DNA biobanks coupled to EMRs provide a platform not only for GWAS but may also allow broad interrogation of the longitudinal incidence of disease associated with genetic variants. The PheWAS approach implicated sodium channel variants modulating QRS duration in subjects without cardiac disease as predictors of subsequent arrhythmias.
doi:10.1161/CIRCULATIONAHA.112.000604
PMCID: PMC3713791  PMID: 23463857
cardiac conduction; QRS duration; atrial fibrillation; genome-wide association study; phenome-wide association study; electronic medical records
19.  Stem Cell–Derived Cardiomyocytes as a Tool for Studying Proarrhythmia 
Circulation  2013;127(16):1641-1643.
doi:10.1161/CIRCULATIONAHA.113.002127
PMCID: PMC3954984  PMID: 23519759
Editorials; arrhythmias; cardiac; genetics; humans; pharmacology; stem cells
20.  Genotype and risk of major bleeding during warfarin treatment 
Pharmacogenomics  2014;15(16):1973-1983.
Aim
To determine whether genetic variants associated with warfarin dose variability were associated with increased risk of major bleeding during warfarin therapy.
Materials & methods
Using Vanderbilt’s DNA biobank we compared the prevalence of CYP2C9, VKORC1 and CYP4F2 variants in 250 cases with major bleeding and 259 controls during warfarin therapy.
Results
CYP2C9*3 was the only allele that differed significantly among cases (14.2%) and controls (7.8%; p = 0.022). In the 214 (85.6%) cases with a major bleed 30 or more days after warfarin initiation, CYP2C9*3 was the only variant associated with bleeding (adjusted odds ratio: 2.05; 95% CI: 1.04, 4.04).
Conclusion
The CYP2C9*3 allele may double the risk of major bleeding among patients taking warfarin for 30 or more days.
doi:10.2217/pgs.14.153
PMCID: PMC4304738  PMID: 25521356
CYP2C9; CYP4F2; pharmacogenetics; risk of major bleeding; VKORC1; warfarin
21.  Design and Anticipated Outcomes of the eMERGE-PGx Project: A Multi-Center Pilot for Pre-Emptive Pharmacogenomics in Electronic Health Record Systems 
We describe here the design and initial implementation of the eMERGE-PGx project. eMERGE-PGx, a partnership of the eMERGE and PGRN consortia, has three objectives : 1) Deploy PGRNseq, a next-generation sequencing platform assessing sequence variation in 84 proposed pharmacogenes, in nearly 9,000 patients likely to be prescribed drugs of interest in a 1–3 year timeframe across several clinical sites; 2) Integrate well-established clinically-validated pharmacogenetic genotypes into the electronic health record with associated clinical decision support and assess process and clinical outcomes of implementation; and 3) Develop a repository of pharmacogenetic variants of unknown significance linked to a repository of EHR-based clinical phenotype data for ongoing pharmacogenomics discovery. We describe site-specific project implementation and anticipated products, including genetic variant and phenotype data repositories, novel variant association studies, clinical decision support modules, clinical and process outcomes, approaches to manage incidental findings, and patient and clinician education methods.
doi:10.1038/clpt.2014.137
PMCID: PMC4169732  PMID: 24960519
pharmacogenetics; pharmacogenomics; next generation sequencing; study design; pre-emptive genotyping
22.  Refining repolarization reserve 
doi:10.1016/j.hrthm.2011.06.024
PMCID: PMC3923504  PMID: 21708111
23.  Whole-exome sequencing in familial atrial fibrillation 
European Heart Journal  2014;35(36):2477-2483.
Aims
Positional cloning and candidate gene approaches have shown that atrial fibrillation (AF) is a complex disease with familial aggregation. Here, we employed whole-exome sequencing (WES) in AF kindreds to identify variants associated with familial AF.
Methods and results
WES was performed on 18 individuals in six modestly sized familial AF kindreds. After filtering very rare variants by multiple metrics, we identified 39 very rare and potentially pathogenic variants [minor allele frequency (MAF) ≤0.04%] in genes not previously associated with AF. Despite stringent filtering >1 very rare variants in the 5/6 of the kindreds were identified, whereas no plausible variants contributing to familial AF were found in 1/6 of the kindreds. Two candidate AF variants in the calcium channel subunit genes (CACNB2 and CACNA2D4) were identified in two separate families using expression data and predicted function.
Conclusion
By coupling family data with exome sequencing, we identified multiple very rare potentially pathogenic variants in five of six families, suggestive of a complex disease mechanism, whereas none were identified in the remaining AF pedigree. This study highlights some important limitations and challenges associated with performing WES in AF including the importance of having large well-curated multi-generational pedigrees, the issue of potential AF misclassification, and limitations of WES technology when applied to a complex disease.
doi:10.1093/eurheartj/ehu156
PMCID: PMC4169871  PMID: 24727801
Atrial fibrillation; Genetics; Exome; Family study; Calcium signalling
24.  Cardiovascular Pharmacogenomics: The Future of Cardiovascular Therapeutics? 
Responses to drug therapy vary from benefit to no effect to adverse effects which can be serious or occasionally fatal. Increasing evidence supports the idea that genetic variants can play a major role in this spectrum of responses. Well-studied examples in cardiovascular therapeutics include predictors of steady-state warfarin dosage, predictors of reduced efficacy among patients receiving clopidogrel for drug eluting stents, and predictors of some serious adverse drug effects. This review summarizes contemporary approaches to identifying and validating genetic predictors of variability in response to drug treatment. Approaches to incorporating this new knowledge into clinical care, and the barriers to this concept, are addressed.
doi:10.1016/j.cjca.2012.07.845
PMCID: PMC3529768  PMID: 23200096
25.  Genetic determinants of response to cardiovascular drugs 
Current opinion in cardiology  2012;27(3):10.1097/HCO.0b013e32835220e3.
Purpose of review
To survey genetic variation contributing to variable responsiveness and toxicity to important cardiovascular drugs and highlight recent developments in the field of cardiovascular pharmacogenomics and personalized medicine.
Recent findings
Previously recognized pharmacogenomic associations with drug efficacy have been further validated (e.g. with clopidogrel and warfarin) and shown to influence clinically important outcomes. The clinical significance of variants modulating toxicity (e.g. SLCO1B1 with simvastatin) has also been confirmed. The genetic contribution to variable efficacy and toxicity of other important classes of cardiovascular drugs, such as beta-blockers, is becoming increasingly recognized. Prospective trials testing whether the use of genomic information improves clinical care are underway. Guidance based on the most well-established pharmacogenomic findings has appeared in prescribing labeling and is in the early stages of being implemented into routine clinical care.
Summary
Clinically validated gene variants that modulate responsiveness to cardiovascular drugs continue to be discovered and validated. Early steps are underway to translate these discoveries into clinical care.
doi:10.1097/HCO.0b013e32835220e3
PMCID: PMC3874723  PMID: 22382501
personalized medicine; pharmacogenomics; variable drug response

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