A pharmacogenetic versus a clinical algorithm for warfarin dosing.

BACKGROUND: The clinical utility of genotype-guided (pharmacogenetically based) dosing of warfarin has been tested only in small clinical trials or observational studies, with equivocal results. METHODS: We randomly assigned 1015 patients to receive doses of warfarin during the first 5 days of therapy that were determined according to a dosing algorithm that included both clinical variables and genotype data or to one that included clinical variables only. All patients and clinicians were unaware of the dose of warfarin during the first 4 weeks of therapy. The primary outcome was the percentage of time that the international normalized ratio (INR) was in the therapeutic range from day 4 or 5 through day 28 of therapy. RESULTS: At 4 weeks, the mean percentage of time in the therapeutic range was 45.2% in the genotype-guided group and 45.4% in the clinically guided group (adjusted mean difference, [genotype-guided group minus clinically guided group], -0.2; 95% confidence interval, -3.4 to 3.1; P=0.91). There also was no significant between-group difference among patients with a predicted dose difference between the two algorithms of 1 mg per day or more. There was, however, a significant interaction between dosing strategy and race (P=0.003). Among black patients, the mean percentage of time in the therapeutic range was less in the genotype-guided group than in the clinically guided group. The rates of the combined outcome of any INR of 4 or more, major bleeding, or thromboembolism did not differ significantly according to dosing strategy. CONCLUSIONS: Genotype-guided dosing of warfarin did not improve anticoagulation control during the first 4 weeks of therapy. (Funded by the National Heart, Lung, and Blood Institute and others; COAG ClinicalTrials.gov number, NCT00839657.).

Relational machine learning for electronic health record-driven phenotyping.

OBJECTIVE: Electronic health records (EHR) offer medical and pharmacogenomics research unprecedented opportunities to identify and classify patients at risk. EHRs are collections of highly inter-dependent records that include biological, anatomical, physiological, and behavioral observations. They comprise a patient's clinical phenome, where each patient has thousands of date-stamped records distributed across many relational tables. Development of EHR computer-based phenotyping algorithms require time and medical insight from clinical experts, who most often can only review a small patient subset representative of the total EHR records, to identify phenotype features. In this research we evaluate whether relational machine learning (ML) using inductive logic programming (ILP) can contribute to addressing these issues as a viable approach for EHR-based phenotyping. METHODS: Two relational learning ILP approaches and three well-known WEKA (Waikato Environment for Knowledge Analysis) implementations of non-relational approaches (PART, J48, and JRIP) were used to develop models for nine phenotypes. International Classification of Diseases, Ninth Revision (ICD-9) coded EHR data were used to select training cohorts for the development of each phenotypic model. Accuracy, precision, recall, F-Measure, and Area Under the Receiver Operating Characteristic (AUROC) curve statistics were measured for each phenotypic model based on independent manually verified test cohorts. A two-sided binomial distribution test (sign test) compared the five ML approaches across phenotypes for statistical significance. RESULTS: We developed an approach to automatically label training examples using ICD-9 diagnosis codes for the ML approaches being evaluated. Nine phenotypic models for each ML approach were evaluated, resulting in better overall model performance in AUROC using ILP when compared to PART (p=0.039), J48 (p=0.003) and JRIP (p=0.003). DISCUSSION: ILP has the potential to improve phenotyping by independently delivering clinically expert interpretable rules for phenotype definitions, or intuitive phenotypes to assist experts. CONCLUSION: Relational learning using ILP offers a viable approach to EHR-driven phenotyping.

SNPs previously associated with Dupuytren's disease replicated in a North American cohort.

OBJECTIVE: Dupuytren's disease is a progressive fibrosis of the hand that often results in debilitating flexion contractures. Its etiology is not completely understood but likely involves both genetic and environmental factors. A recent study performed in Europe identified DNA variants that associate with Dupuytren's disease. Given the likelihood for genetic variation among populations, we planned to validate the genetic variants identified by this study in a North American population. METHODS: In the Marshfield Clinic's Personalized Medicine Research Project, 296 cases with Dupuytren's disease were identified and matched 3-to-1 to controls without Dupuytren's disease. Clinical data were abstracted from the electronic medical record. The top 12 single nucleotide polymorphisms (SNPs) from the European study were selected and tested in a multiplex assay using the MassArray Analyzer 4 (Sequenom, Inc., San Diego, CA). Differences in allele frequency were determined, and variants with a P value of <0.004 were considered significant. RESULTS: We replicated 5 of the 12 SNPs previously reported to be associated with Dupuytren's disease. CONCLUSION: Our findings support a role for the Wnt signaling pathway in the development of Dupuytren's disease, and suggest that further study of this pathway may result in early diagnosis and non-surgical treatments for Dupuytren's disease.

Rationale and design of the Clarification of Optimal Anticoagulation through Genetics trial.

BACKGROUND: Current dosing practices for warfarin are empiric and result in the need for frequent dose changes as the international normalized ratio gets too high or too low. As a result, patients are put at increased risk for thromboembolism, bleeding, and premature discontinuation of anticoagulation therapy. Prior research has identified clinical and genetic factors that can alter warfarin dose requirements, but few randomized clinical trials have examined the utility of using clinical and genetic information to improve anticoagulation control or clinical outcomes among a large, diverse group of patients initiating warfarin. METHODS: The COAG trial is a multicenter, double-blind, randomized trial comparing 2 approaches to guiding warfarin therapy initiation: initiation of warfarin therapy based on algorithms using clinical information plus an individual's genotype using genes known to influence warfarin response ("genotype-guided dosing") versus only clinical information ("clinical-guided dosing") (www.clinicaltrials.gov Identifier: NCT00839657). RESULTS: The COAG trial design is described. The study hypothesis is that, among 1,022 enrolled patients, genotype-guided dosing relative to clinical-guided dosing during the initial dosing period will increase the percentage of time that patients spend in the therapeutic international normalized ratio range in the first 4 weeks of therapy. CONCLUSION: The COAG will determine if genetic information provides added benefit above and beyond clinical information alone.

Evaluation of a mitochondrial DNA mutation in maternally inherited and sporadic cases of Dupuytren disease.

OBJECTIVE: The purpose was to test the hypothesis that Dupuytren disease (DD) is associated with a previously reported mutation in mitochondrial DNA at position 2839. METHODS: Two hundred sixty-nine cases of DD and an equal number of matched controls were identified in Marshfield Clinic's Personalized Medicine Research Project (PMRP). Clinical data used to describe the cohort were abstracted from the electronic medical records of the population. Genetic analysis of all the cases and controls was done using a custom synthesis TaqMan assay, while genetic analysis of sixteen of the above cases with a familial history of DD was performed by mitochondrial DNA sequencing at position C2839A. RESULTS: Cases and controls were evenly distributed with 167 (62%) men and 102 (38%) women. The majority, 264 (98%) of the cases and controls were white non-Hispanic. Of the 269 cases, 16 were found to have a familial history of DD. Two cases had a maternal history, eight a paternal history, five an affected sibling, and one a paternal grandfather. All cases and controls were found to have only the C allele at the site of the reported mitochondrial C2839A polymorphism. CONCLUSIONS: The previously reported mitochondrial mutation was not present in our small, maternally inherited cohort or in the total population of 538 cases and controls. This finding does not support the reported incidence of this polymorphism in 90% of the affected population with a maternal inheritance, and calls into question the role of the C2839A mitochondrial DNA polymorphism in familial or sporadic cases of DD.

Numerical investigation of air intrusion and aerobic reactions in municipal solid waste landfills.

Air intrusion into municipal solid waste landfills can cause a localized switch from anaerobic to aerobic biodegradation adjacent to the intrusion. The purpose of this study was to explore the effects on temperature and gas composition of air intrusion into an idealized anaerobic landfill. Two scenarios of air intrusion and injection were simulated using a mechanistic landfill model built into TOUGH2. The modeled landfill geometry and properties are based on an actual U.S. landfill. The simulation results show that air intrusion can cause a quick switch from anaerobic to aerobic conditions and as a result, cause a fast increase in temperature of up to 30 °C associated with stimulation of aerobic biodegradation reactions. Associated with the change to aerobic conditions is a decrease in CH4/CO2 (v/v) ratio in the landfill gas. Depending on the air flow rate intruding or injecting into the landfill, localized aerobic biodegradation is stimulated and as a result heat generation rate of 10 to 150 W/m3 leads to temperature increase. Temperature increase near a temporary air intrusion lasts no longer than a few weeks while the high temperatures in deep layers could last up to one year.

A randomized controlled trial of genotype-based Coumadin initiation.

PURPOSE: A randomized controlled trial was conducted in patients initiating warfarin to determine whether algorithms that incorporate genotypes affecting warfarin metabolism and function, and Vitamin K metabolism improve prediction of therapeutic warfarin dose and anticoagulation management. METHODS: A total of 230 patients were randomized to either a clinical arm where dosing algorithms considered only clinical information or an interventional arm where dosing algorithms used clinical and genotypic variables (CYP2C9, CYP4F2, and VKORC1). Subjects in the interventional arm were genotyped within 5 hours, and the initial dose was informed by genotype. Primary endpoints were absolute prediction error relative to therapeutic dose, and time in therapeutic target range during the first 14 days. Secondary endpoints included time to stable dose in therapeutic range, time to first international normalization ratio >4, and warfarin-related adverse events. RESULTS: The model including genetics more accurately identified therapeutic dose twice as often as the clinical model (65.3% vs. 34.7%) (P < 0.0001). Patients in the interventional arm did not achieve greater time in therapeutic range. Study arms were similar regarding time to international normalization ratio >4 and adverse events. CONCLUSION: Genotype-informed dosing clearly improved prediction of therapeutic dose beyond that available with clinical parameters. Genetic information did not affect time in therapeutic target range during the first 14 days of therapy. Current management practices with the vagaries in dose adjustment after warfarin initiation exert a strong influence on traditional clinical outcomes.

Absence of novel CYP4F2 and VKORC1 coding region DNA variants in patients requiring high warfarin doses.

OBJECTIVE: Warfarin is an FDA-approved oral anticoagulant for long-term prevention of thromboembolism. Substantial inter-individual variation in dosing requirements and the narrow therapeutic index of this widely-prescribed drug make safe initiation and dose stabilization challenging. Single nucleotide polymorphisms (SNPs) occurring in CYP2C9, VKORC1, and CYP4F2 genes are known to impact dose, and VKORC1 and CYP4F2 polymorphisms are associated with higher therapeutic dose requirements in our cohort. However, the most advanced regression models using personal, clinical, and genetic factors to predict individual stable dose account for only 50% to 60% of the observed variability in stable therapeutic dose in Caucasians. DESIGN AND METHODS: In this study, we used DNA sequence analysis to determine whether additional variants in CYP4F2 and VKORC1 gene coding regions contribute to variable dosing requirements among individuals for whom the actual dose was the highest relative to regression model- predicted dose. RESULTS AND CONCLUSIONS: No novel DNA variants in the coding regions of these genes were identified among subjects requiring high warfarin doses, suggesting that other factors yet to be defined contribute to variability in warfarin dose requirements in this subset of our cohort.

Understanding the pharmacogenetic approach to warfarin dosing.

Warfarin remains the drug of choice for long-term anticoagulation management in a variety of conditions. Despite an established role in prevention of thromboembolic events such as stroke, warfarin continues to be underutilized because of its association with serious drug-related adverse events. Lacking alternative therapeutic approaches, intensive research in the past decade has focused on making anticoagulation with warfarin safer. Much emphasis has been placed on defining factors associated with the wide individual variability in warfarin dose. Polymorphic sites in three genes, cytochrome P450 (CYP) 2C9, vitamin K 2,3 epoxide reductase complex 1 (VKORC1), and CYP4F2, have been shown to affect stable warfarin dose. An overview of the persistent issues related to warfarin therapy and our current understanding of the genetic and clinical factors affecting warfarin dosing is presented. Finally, unresolved issues in improving clinical care of warfarin patients and future directions are provided.

New adjuvants to enhance anticoagulant activity of warfarin.

New adjuvants of warfarin anticoagulant activity have been developed. These compounds, which are 1,4-methano-1,2,3,4-tetrahydroanthracene-9,10-diol derivatives, act synergistically with warfarin to potentiate its anticoagulant effect. None of the compounds tested is an effective oral anticoagulant in the absence of warfarin.

Bacteria and Antibiotics in Wound Healing.

This review of the literature concerning bacteria, antibiotics and tissue repair shows there are extensive data supporting microbial interference with wound healing once bacterial burden exceeds 104 CFU per unit of measure, The mechanism of bacterial interference lies largely in prolonging the inflammatory phase of tissue repair. Reducing the microbial bioburden allows tissue repair to continue. Systemic and topical antimicrobials appear critical to reducing the bioburden and facilitating repair. The current controversy over the use of antimicrobials in patients with chronically infected wounds, in particular, revolves around the definition of infection. The reliance on classic clinical signs of inflammation to support antimicrobial use in these patients is tenuous due to the lack of correlation of these signs with the microbial burden known to impair tissue repair.

Perioperative genomic profiles using structure-specific oligonucleotide probes.

OBJECTIVES: Many complications in the perioperative interval are associated with genetic susceptibilities that may be unknown in advance of surgery and anesthesia, including drug toxicity and inefficacy, thrombosis, prolonged neuromuscular blockade, organ failure and sepsis. The aims of this study were to design and validate the first genetic testing platform and panel designed for use in perioperative care, to establish allele frequencies in a target population, and to determine the number of mutant alleles per patient undergoing surgery. DESIGN/SETTING/PARTICIPANTS AND METHODS: One hundred fifty patients at Marshfield Clinic, Marshfield, Wisconsin, 100 patients at the Medical College of Wisconsin Zablocki Veteran's Administration Medical Center, Milwaukee, Wisconsin, and 200 patients at the University of Wisconsin Hospitals and Clinics, Madison, Wisconsin undergoing surgery and anesthesia were tested for 48 polymorphisms in 22 genes including ABC, BChE, ACE, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, beta2AR, TPMT, F2, F5, F7, MTHFR, TNFalpha, TNFbeta, CCR5, ApoE, HBB, MYH7, ABO and Gender (PRKY, PFKFB1). Using structure-specific cleavage of oligonucleotide probes (Invader, Third Wave Technologies, Inc., Madison, WI), 96-well plates were configured so that each well contained reagents for detection of both the wild type and mutant alleles at each locus. RESULTS: There were 21,600 genotypes confirmed in duplicate. After withdrawal of polymorphisms in non-pathogenic genes (i.e., the ABO blood group and gender-specific alleles), 376 of 450 patients were found to be homozygous for mutant alleles at one or more loci. Modes of two mutant homozygous loci and 10 mutant alleles in aggregate (i.e., the sum of homozygous and heterozygous mutant polymorphisms) were observed per patient. CONCLUSIONS: Significant genetic heterogeneity that may not be accounted for by taking a family medical history, or by obtaining routine laboratory test results, is present in most patients presenting for surgery and may be detected using a newly developed genotyping platform.

Modeling methane oxidation in landfill cover soils as indicator of functional stability with respect to gas management.

A performance-based method for evaluating methane (CH4) oxidation as the best available control technology (BACT) for passive management of landfill gas (LFG) was applied at a municipal solid waste (MSW) landfill in central Washington, USA, to predict when conditions for functional stability with respect to LFG management would be expected. The permitted final cover design at the subject landfill is an all-soil evapotranspirative (ET) cover system. Using a model, a correlation between CH4 loading flux and oxidation was developed for the specific ET cover design. Under Washington's regulations, a MSW landfill is functionally stable when it does not present a threat to human health or the environment (HHE) at the relevant point of exposure (POE), which was conservatively established as the cover surface. Approaches for modeling LFG migration and CH4 oxidation are discussed, along with comparisons between CH4 oxidation and biodegradation of non-CH4 organic compounds (NMOCs). The modeled oxidation capacity of the ET cover design is 15 g/m2/day under average climatic conditions at the site, with 100% oxidation expected on an annual average basis for fluxes up to 8 g/m2/day. This translates to a sitewide CH4 generation rate of about 260 m3/hr, which represents the functional stability target for allowing transition to cover oxidation as the BACT (subject to completion of a confirmation monitoring program). It is recognized that less than 100% oxidation might occur periodically if climate and/or cover conditions do not precisely match the model, but that residual emissions during such events would be de minimis in comparison with published limit values. Accordingly, it is also noted that nonzero net emissions may not represent a threat to HHE at a POE (i.e., a target flux between 8 and 15 g/m2/day might be appropriate for functional stability) depending on the site reuse plan and distance to potential receptors.Implications: This study provides a scientifically defensible method for estimating when methane oxidation in landfill cover soils may represent the best available control technology for residual landfill gas (LFG) emissions. This should help operators and regulators agree on the process of safely eliminating active LFG controls in favor of passive control measures once LFG generation exhibits asymptotic trend behavior below the oxidation capacity of the soil. It also helps illustrate the potential benefits of evolving landfill designs to include all-soil vegetated evapotranspirative (ET) covers that meet sustainability objectives as well as regulatory performance objectives for infiltration control.

Effect of CYP4F2, VKORC1, and CYP2C9 in Influencing Coumarin Dose: A Single-Patient Data Meta-Analysis in More Than 15,000 Individuals.

The cytochrome P450 (CYP)4F2 gene is known to influence mean coumarin dose. The aim of the present study was to undertake a meta-analysis at the individual patients level to capture the possible effect of ethnicity, gene-gene interaction, or other drugs on the association and to verify if inclusion of CYP4F2*3 variant into dosing algorithms improves the prediction of mean coumarin dose. We asked the authors of our previous meta-analysis (30 articles) and of 38 new articles retrieved by a systematic review to send us individual patients' data. The final collection consists of 15,754 patients split into a derivation and validation cohort. The CYP4F2*3 polymorphism was consistently associated with an increase in mean coumarin dose (+9% (95% confidence interval (CI) 7-10%), with a higher effect in women, in patients taking acenocoumarol, and in white patients. The inclusion of the CYP4F2*3 in dosing algorithms slightly improved the prediction of stable coumarin dose. New pharmacogenetic equations potentially useful for clinical practice were derived.

Case study comparison of functional vs. organic stability approaches for assessing threat potential at closed landfills in the USA.

Municipal solid waste (MSW) landfills in the USA are regulated under Subtitle D of the Resource Conservation and Recovery Act (RCRA), which includes the requirement to protect human health and the environment (HHE) during the post-closure care (PCC) period. Several approaches have been published for assessment of potential threats to HHE. These approaches can be broadly divided into organic stabilization, which establishes an inert waste mass as the ultimate objective, and functional stability, which considers long-term emissions in the context of minimizing threats to HHE in the absence of active controls. The objective of this research was to conduct a case study evaluation of a closed MSW landfill using long-term data on landfill gas (LFG) production, leachate quality, site geology, and solids decomposition. Evaluations based on both functional and organic stability criteria were compared. The results showed that longer periods of LFG and leachate management would be required using organic stability criteria relative to an approach based on functional stability. These findings highlight the somewhat arbitrary and overly stringent nature of assigning universal stability criteria without due consideration of the landfill's hydrogeologic setting and potential environmental receptors. This supports previous studies that advocated for transition to a passive or inactive control stage based on a performance-based functional stability framework as a defensible mechanism for optimizing and ending regulatory PCC.

Using Machine Learning Algorithms to Predict Risk for Development of Calciphylaxis in Patients with Chronic Kidney Disease.

Calciphylaxis is a disorder that results in necrotic cutaneous lesions with a high rate of mortality. Due to its rarity and complexity, the risk factors for and the disease mechanism of calciphylaxis are not fully understood. This work focuses on the use of machine learning to both predict disease risk and model the contributing factors learned from an electronic health record data set. We present the results of four modeling approaches on several subpopulations of patients with chronic kidney disease (CKD). We find that modeling calciphylaxis risk with random forests learned from binary feature data produces strong models, and in the case of predicting calciphylaxis development among stage 4 CKD patients, we achieve an AUC-ROC of 0.8718. This ability to successfully predict calciphylaxis may provide an excellent opportunity for clinical translation of the predictive models presented in this paper.

Relative impact of covariates in prescribing warfarin according to CYP2C9 genotype.

Patients on warfarin anticoagulant therapy demonstrate wide variation in maintenance dose. Patients possessing variants (*2 and *3) of the cytochrome P450 2C9 gene require reduced maintenance doses compared to those having wild-type alleles (*1). Many other clinical factors have been shown to affect warfarin dose as well. To determine the relative impact of CYP2C9 genotype, age, gender, body surface area, concomitant medication, treatment indication and comorbidity, we conducted a retrospective cohort study in 453 patients managed by the anticoagulation service of a large, horizontally integrated, multispecialty group practice. In this largely Caucasian patient population, the CYP2C9 gene frequencies for *1/*1, *1/*2, *1/*3, *2/*2, *2/*3 and *3/*3 were 65.1%, 19.0%, 12.1%, 1.6%, 1.8% and 0.4%, respectively, approximating Hardy-Weinberg equilibrium. Mean maintenance doses for these genotypes were 36.5, 29.1, 23.5, 28.0, 18.1 and 5.5 mg/week, respectively. In univariate analyses, genotype alone accounted for 19.8% of the variability in maintenance dose. Age, body surface area and male gender accounted for 14.6%, 7.5% and 4.7%, respectively, while cardiac valve replacement as the indication for warfarin accounted for 5.4% of the variability. Collectively, these factors accounted for 33.7% of all dosing variability according to multiple regression. These results will help strengthen the mathematical models that are currently being developed for prospective gene-based warfarin dosing.

Longitudinal data analysis in support of functional stability concepts for leachate management at closed municipal landfills.

Landfill functional stability provides a target that supports no environmental threat at the relevant point of exposure in the absence of active control systems. With respect to leachate management, this study investigates "gateway" indicators for functional stability in terms of the predictability of leachate characteristics, and thus potential threat to water quality posed by leachate emissions. Historical studies conducted on changes in municipal solid waste (MSW) leachate concentrations over time (longitudinal analysis) have concentrated on indicator compounds, primarily chemical oxygen demand (COD) and biochemical oxygen demand (BOD). However, validation of these studies using an expanded database and larger constituent sets has not been performed. This study evaluated leachate data using a mixed-effects regression model to determine the extent to which leachate constituent degradation can be predicted based on waste age or operational practices. The final dataset analyzed consisted of a total of 1402 samples from 101 MSW landfills. Results from the study indicated that all leachate constituents exhibit a decreasing trend with time in the post-closure period, with 16 of the 25 target analytes and aggregate classes exhibiting a statistically significant trend consistent with well-studied indicators such as BOD. Decreasing trends in BOD concentration after landfill closure can thus be considered representative of trends for many leachate constituents of concern.

Pharmacogenetic warfarin dose refinements remain significantly influenced by genetic factors after one week of therapy.

By guiding initial warfarin dose, pharmacogenetic (PGx) algorithms may improve the safety of warfarin initiation. However, once international normalised ratio (INR) response is known, the contribution of PGx to dose refinements is uncertain. This study sought to develop and validate clinical and PGx dosing algorithms for warfarin dose refinement on days 6-11 after therapy initiation. An international sample of 2,022 patients at 13 medical centres on three continents provided clinical, INR, and genetic data at treatment days 6-11 to predict therapeutic warfarin dose. Independent derivation and retrospective validation samples were composed by randomly dividing the population (80%/20%). Prior warfarin doses were weighted by their expected effect on S-warfarin concentrations using an exponential-decay pharmacokinetic model. The INR divided by that "effective" dose constituted a treatment response index . Treatment response index, age, amiodarone, body surface area, warfarin indication, and target INR were associated with dose in the derivation sample. A clinical algorithm based on these factors was remarkably accurate: in the retrospective validation cohort its R(2) was 61.2% and median absolute error (MAE) was 5.0 mg/week. Accuracy and safety was confirmed in a prospective cohort (N=43). CYP2C9 variants and VKORC1-1639 G→A were significant dose predictors in both the derivation and validation samples. In the retrospective validation cohort, the PGx algorithm had: R(2)= 69.1% (p<0.05 vs. clinical algorithm), MAE= 4.7 mg/week. In conclusion, a pharmacogenetic warfarin dose-refinement algorithm based on clinical, INR, and genetic factors can explain at least 69.1% of therapeutic warfarin dose variability after about one week of therapy.