Background: Tobacco dependence is a chronic, relapsing condition that may require extended treatment.
Objective: To assess whether extended transdermal nicotine therapy increases abstinence from tobacco more than standard duration therapy in adult smokers.
Design: Parallel randomized placebo-controlled trial from September 2004 to February 2008 (small block randomization scheme, not stratified). Study participants and all research personnel except for the database manager were blinded to randomization. (NCT00364156)
Setting: Academic center.
Participants: 568 adult smokers.
Intervention: Participants were randomized to: standard (8 weeks 21mg Nicoderm CQ, 16 weeks placebo) or extended (24 weeks 21mg Nicoderm CQ) therapy.
Measurements: The primary outcome was biochemically-verified point prevalence abstinence at weeks 24 and 52. Secondary outcomes were continuous and prolonged abstinence, lapse and recovery events, cost/additional quitter, and side effects and adherence.
Results: At 24 weeks, extended therapy produced higher rates of point prevalence abstinence (31.6% versus 20.3%; Odds Ratio [OR] = 1.81 [1.23-2.66], p = 0.002), prolonged abstinence (41.5% versus 26.9%; OR = 1.97 [1.38-2.82] p = 0.001), and continuous abstinence (19.2% versus 12.6%; OR = 1.64 [1.04-2.60] p = 0.032), versus standard therapy. Extended therapy reduced the risk for a lapse (Hazard Ratio [HR] = 0.77 [0.63-0.95], p = 0.013) and increased the chances of recovery from lapses (HR = 1.47 [1.17-1.84], p = 0.001). Time to relapse was slower with extended versus standard therapy (HR = 0.50 [0.35-0.73], p < 0.001). At week 52, extended therapy produced higher quit rates for prolonged abstinence only (p = 0.027). There were no group differences in side effects and adverse events at the extended treatment phase assessment.
Limitations: The generalizability of the findings may be limited because participants were treatment-seeking smokers without medical comorbidity and differences in adherence across treatment arms were detected.
Conclusion: Compared to 8 weeks of transdermal nicotine, 24 weeks of transdermal nicotine increased biochemically-confirmed point prevalence abstinence and continuous abstinence at week 24, reduced the risk of smoking lapses, and increased the likelihood of post-lapse recovery to abstinence.
We evaluated a neutralizing anti-TGFβ antibody (GC1008) in cancer patients with malignant pleura mesothelioma (MPM). The goal of this study was to assess immunoregulatory effects in relation to clinical safety and clinical response. Patients with progressive MPM and 1–2 prior systemic therapies received GC1008 at 3mg/kg IV over 90 min every 21 d as part of an open-label, two-center Phase II trial. Following TGFβ blockade therapy, clinical safety and patient survival were monitored along with the effects of anti-TGFβ antibodies on serum biomarkers and peripheral blood mononuclear cells (PBMC). Although designed as a larger trial, only 13 patients were enrolled when the manufacturer discontinued further development of the antibody for oncology indications. All participants tolerated therapy. Although partial or complete radiographic responses were not observed, three patients showed stable disease at 3 mo. GC1008 had no effect in the expression of NK, CD4+, or CD8+ T cell activating and inhibitory markers, other than a decrease in the expression of 2B4 and DNAM-1 on NK cells. However, serum from 5 patients showed new or enhanced levels of antibodies against MPM tumor lysates as measured by immunoblotting. Patients who produced anti-tumor antibodies had increased median overall survival (OS) (15 vs 7.5 mo, p < 0.03) compared with those who did not. To our knowledge, these data represent the first immune analysis of TGFβ- blockade in human cancer patients.
GC1008; anti-TGFβ antibody; antibody therapy; clinical trial; immunotherapy; malignant mesothelioma
The nicotine metabolite ratio (NMR or 3-hydroxycotinine/cotinine) has been used to phenotype CYP2A6-mediated nicotine metabolism. Our objectives were to analyze (a) the stability of NMR in plasma, saliva, and blood in various storage conditions, (b) the relationship between NMRs derived from blood, plasma, saliva, and urine, and (c) the reproducibility of plasma NMR in ad libitum cigarette smokers.
We analyzed data from four clinical studies. In studies 1 and 2, we assessed NMR stability in saliva and plasma samples at room temperature (~22°C) over 14 days and in blood at 4°C for up to 72 hours. In studies 2 and 3, we used Bland-Altman analysis to assess agreement between blood, plasma, saliva, and urine NMRs. In study 4, plasma NMR was measured on 6 occasions over 44 weeks in 43 ad libitum smokers.
Reliability coefficients for stability tests of NMR in plasma and saliva at room temperature were 0.97 and 0.98, respectively, and 0.92 for blood at 4°C. Blood NMR agreed consistently with saliva and plasma NMRs but showed more variability in relation to urine NMR. The reliability coefficient for repeated plasma NMR measurements in smokers was 0.85.
The NMR is stable in blood, plasma, and saliva at the conditions tested. Blood, plasma, and saliva NMRs are similar while urine NMR is a good proxy for these NMR measures. Plasma NMR was reproducible over time in smokers.
One measurement may reliably estimate a smoker’s NMR for use as an estimate of the rate of nicotine metabolism.
Nicotine metabolite ratio (NMR); cotinine; 3-hydroxycotinine; biological stability; chemical stability
Comparative effectiveness research has become an integral part of health care planning in most developed countries. In a simulated cohort of women, aged 30–65, who tested positive for BRCA1 or BRCA2 mutations, we compared outcomes of mammography with and without MRI, prophylactic oophorectomy with and without mastectomy, mastectomy alone, and chemoprevention. Methods: Using Treeage 9.02 software, we developed Markov models with 25,000 Monte Carlo simulations and conducted probabilistic sensitivity analysis. We based mutation penetrance rates, breast and ovarian cancer incidence, and mortality rates, and costs in terms of 2009 dollars, on published studies and data from the Surveillance, Epidemiology, and End Results (SEER) Program and the Centers for Medicare and Medicaid Services. We used preference ratings obtained from mutation carriers and controls to adjust survival for quality of life (QALYs). Results: For BRCA1 mutation carriers, prophylactic oophorectomy at $1,741 per QALY, was more cost effective than both surgeries and dominated all other interventions. For BRCA2 carriers, prophylactic oophorectomy, at $4,587 per QALY, was more cost effective than both surgeries. Without quality adjustment, both mastectomy and BSO surgeries dominated all other interventions. In all simulations, preventive surgeries or chemoprevention dominated or were more cost effective than screening because screening modalities were costly. Conclusion: Our analysis suggested that among BRCA1/2 mutation carriers, prophylactic surgery would dominate or be cost effective compared to chemoprevention and screening. Annual screening with MRI and mammography was the most effective strategy because it was associated with the longest quality-adjusted survival, but it was also very expensive.
Comparative effectiveness; Cost-effectiveness; Mastectomy; Oophorectomy or both; Tamoxifen; Screening with MRI and mammography; BRCA1/BRCA2
Graft-versus-host disease (GVHD) is a major barrier to successful allogeneic hematopoietic stem-cell transplantation (HSCT). The chemokine receptor CCR5 appears to play a role in alloreactivity. We tested whether CCR5 blockade would be safe and limit GVHD in humans.
We tested the in vitro effect of the CCR5 antagonist maraviroc on lymphocyte function and chemotaxis. We then enrolled 38 high-risk patients in a single-group phase 1 and 2 study of reduced-intensity allogeneic HSCT that combined maraviroc with standard GVHD prophylaxis.
Maraviroc inhibited CCR5 internalization and lymphocyte chemotaxis in vitro without impairing T-cell function or formation of hematopoietic-cell colonies. In 35 patients who could be evaluated, the cumulative incidence rate (±SE) of grade II to IV acute GVHD was low at 14.7±6.2% on day 100 and 23.6±7.4% on day 180. Acute liver and gut GVHD were not observed before day 100 and remained uncommon before day 180, resulting in a low cumulative incidence of grade III or IV GVHD on day 180 (5.9±4.1%). The 1-year rate of death that was not preceded by disease relapse was 11.7±5.6% without excessive rates of relapse or infection. Serum from patients receiving maraviroc prevented CCR5 internalization by CCL5 and blocked T-cell chemotaxis in vitro, providing evidence of antichemotactic activity.
In this study, inhibition of lymphocyte trafficking was a specific and potentially effective new strategy to prevent visceral acute GVHD. (Funded by Pfizer and others; ClinicalTrials.gov number, NCT00948753.)
New therapeutic strategies are needed for malignant pleural mesothelioma (MPM). We conducted a single-center, open-label, nonrandomized, pilot and feasibility trial using two intrapleural doses of an adenoviral vector encoding human IFN-α (Ad.IFN-α2b). Nine subjects were enrolled at two dose levels. The first three subjects had very high pleural and systemic IFN-α concentrations resulting in severe “flu-like” symptoms necessitating dose de-escalation. The next six patients had reduced (but still significant) pleural and serum IFN-α levels, but with tolerable symptoms. Repeated vector administration appeared to prolong IFN-α expression levels. Anti-tumor humoral immune responses against mesothelioma cell lines were seen in seven of the eight subjects evaluated. No clinical responses were seen in the four subjects with advanced disease. However, evidence of disease stability or tumor regression was seen in the remaining five patients, including one dramatic example of partial tumor regression at sites not in contiguity with vector infusion. These data show that Ad.IFN-α2b has potential therapeutic benefit in MPM and that it generates anti-tumor immune responses that may induce anatomic and/or metabolic reductions in distant tumor.
Clinical trial registered with www.clinicaltrials.gov (NCT 01212367).
clinical trials; immunotherapy; gene therapy
Obesity has implications for chemotherapy dosing and selection of patients for therapy. Autologous hematopoietic stem cell transplant (AutoHCT) improves outcomes for patients with multiple myeloma, but optimal chemotherapy dosing for obese patients is poorly defined. We analyzed the outcomes of 1087 recipients of AutoHCT for myeloma reported to the CIBMTR between 1995 and 2003 receiving high-dose melphalan conditioning, with or without total body irradiation (TBI). We categorized patients by body mass index (BMI) as normal, overweight, obese, or severely obese. There was no overall effect of BMI on progression-free survival (PFS), overall survival (OS), progression, or non-relapse mortality (NRM). In patients receiving melphalan and TBI conditioning, obese and severely obese patients had superior PFS and OS compared with normal and overweight patients, but the clinical significance of this finding is unclear. More obese patients were more likely to receive a reduced dose of melphalan, but there was no evidence that melphalan or TBI dosing variability affected PFS.
Therefore, current common strategies of dosing melphalan do not impair outcomes for obese patients, and obesity should not exclude patients from consideration of autologous transplantation. Further research is necessary to optimize dosing of both chemotherapy and radiation in obese patients.
obesity; myeloma; autologous transplantation; chemotherapy; radiation therapy; melphalan
Smoking cessation trials generally record information on daily smoking behavior, but base analyses on measures of smoking status at the end of treatment (EOT). We present an alternative approach that analyzes the entire sequence of daily smoking status observations.
We analyzed daily abstinence data from a smoking cessation trial, using two longitudinal logistic regression methods: A mixed-effects (ME) model and a generalized estimating equations (GEE) model. We compared results to a standard analysis that takes as outcome abstinence status at EOT. We evaluated time-varying covariates (smoking history and time-varying drug effect) in the longitudinal analysis and compared ME and GEE approaches.
We observed some differences in the estimated treatment effect odds ratios across models, with narrower confidence intervals under the longitudinal models. GEE yields similar results to ME when only baseline factors appear in the model, but gives biased results when one includes time-varying covariates. The longitudinal models indicate that the quit probability declines and the drug effect varies over time. Both the previous day’s smoking status and recent smoking history predict quit probability, independently of the drug effect.
When analysing outcomes of studies from smoking cessation interventions, longitudinal models with multiple outcome data points, rather than just end of treatment, can makes efficient use of the data and incorporate time-varying covariates. The generalized estimating equations approach should be avoided when using time-varying predictors.
Generalized estimating equations; longitudinal analysis; mixed-effects model
Molecular epidemiology studies commonly exhibit missing observations. Methods for extracting correct and efficient analyses from incomplete data are well known in statistics, but relatively few such methods have diffused into applications. I review some areas of incomplete-data research that are relevant to molecular epidemiology, and appeal for greater efforts by statisticians to translate their methods into practice.
Advances in statistical modeling and analysis technology have improved our ability to derive valid inferences from tumor xenograft experiments. Further challenges in this area include the modeling of inter-tumor heterogeneity and the development of robust statistical models that describe key parameters in the underlying tumor biology.
The role of serum uric acid as an independent risk factor for cardiovascular disease remains unclear although hyperuricemia is associated with cardiovascular disease such as coronary heart disease (CHD), stroke and hypertension.
A systematic review and meta-analysis using a random-effects model was conducted to determine the risk of CHD associated with hyperuricemia in adults. Studies of hyperuricemia and CHD were identified by searching major electronic databases using the Medical Subject Headings and keywords without language restriction (through February 2009). Only prospective cohort studies were included if they had data on CHD incidences or mortalities related to serum uric acid levels in adults.
26 eligible studies of 402,997 adults were identified. Hyperuricemia was associated with an increased risk of CHD incidence (unadjusted risk ratio (RR) 1.34; 95% confidence interval (CI) 1.19-1.49) and mortality (unadjusted RR 1.46; 95% CI 1.20-1.73). When adjusted for potential confounding, the pooled RR was 1.09 (95% CI: 1.03-1.16) for CHD incidence and 1.16 (95% CI: 1.01-1.30) for mortality. For each increase of 1 mg/dl in uric acid level, the pooled multivariate RR for CHD mortality was 1.12 (95% CI: 1.05-1.19). Subgroup analyses showed no significant association between hyperuricemia and CHD incidence/mortality in men, but an increased risk for CHD mortality in women (RR 1.67; 95% CI: 1.30-2.04).
Hyperuricemia may marginally increase the risk of CHD events, independently of traditional CHD risk factors. A more pronounced increased risk for CHD mortality in women should be investigated in future research.
hyperuricemia; coronary heart disease; meta-analysis
When testing multiple hypotheses simultaneously, there is a need to adjust the levels of the individual tests to effect control of the family-wise error rate (FWER). Standard frequentist adjustments control the error rate but are typically both conservative and oblivious to prior information. We propose a Bayesian testing approach—multiplicity-calibrated Bayesian hypothesis testing—that sets individual critical values to reflect prior information while controlling the FWER via the Bonferroni inequality. If the prior information is specified correctly, in the sense that those null hypotheses considered most likely to be false in fact are false, the power of our method is substantially greater than that of standard frequentist approaches. We illustrate our method using data from a pharmacogenetic trial and a preclinical cancer study. We demonstrate its error rate control and power advantage by simulation.
Bayes factor; Bonferroni inequality; Frequentist calibration; Multiplicity
Flaxseed (FS) is a dietary supplement known for its antioxidant and anti-inflammatory properties. Radiation exposure of lung tissues occurs either when given therapeutically to treat intrathoracic malignancies or incidentally, such as in the case of exposure from inhaled radioisotopes released after the detonation of a radiological dispersion devise (RDD). Such exposure is associated with pulmonary inflammation, oxidative tissue damage and irreversible lung fibrosis. We previously reported that dietary FS prevents pneumonopathy in a rodent model of thoracic X-ray radiation therapy (XRT). However, flaxseed's therapeutic usefulness in mitigating radiation effects post-exposure has never been evaluated.
We evaluated the effects of a 10%FS or isocaloric control diet given to mice (C57/BL6) in 2 separate experiments (n = 15-25 mice/group) on 0, 2, 4, 6 weeks post a single dose 13.5 Gy thoracic XRT and compared it to an established radiation-protective diet given preventively, starting at 3 weeks prior to XRT. Lungs were evaluated four months post-XRT for blood oxygenation levels, inflammation and fibrosis.
Irradiated mice fed a 0%FS diet had a 4-month survival rate of 40% as compared to 70-88% survival in irradiated FS-fed mouse groups. Additionally, all irradiated FS-fed mice had decreased fibrosis compared to those fed 0%FS. Lung OH-Proline content ranged from 96.5 ± 7.1 to 110.2 ± 7.7 μg/ml (Mean ± SEM) in all irradiated FS-fed mouse groups, as compared to 138 ± 10.8 μg/ml for mice on 0%FS. Concomitantly, bronchoalveolar lavage (BAL) protein and weight loss associated with radiation cachexia was significantly decreased in all FS-fed groups. Inflammatory cell influx to lungs also decreased significantly except when FS diet was delayed by 4 and 6 weeks post XRT. All FS-fed mice (irradiated or not), maintained a higher blood oxygenation level as compared to mice on 0%FS. Similarly, multiplex cytokine analysis in the BAL fluid revealed a significant decrease of specific inflammatory cytokines in FS-fed mice.
Dietary FS given post-XRT mitigates radiation effects by decreasing pulmonary fibrosis, inflammation, cytokine secretion and lung damage while enhancing mouse survival. Dietary supplementation of FS may be a useful adjuvant treatment mitigating adverse effects of radiation in individuals exposed to inhaled radioisotopes or incidental radiation.
Flaxseed; radiation pneumonopathy; mitigation; lung fibrosis; antioxidant; flaxseed lignans; SDG; lung injury; ROS; inflammation; bronchoalveolar lavage; survival; cytokines; mouse model
The ability to quit smoking is heritable, yet few genetic studies have investigated prospective smoking cessation. We conducted a systems-based genetic association analysis in a sample of 472 treatment-seeking smokers of European ancestry after 8 weeks of transdermal nicotine therapy for smoking cessation. The genotyping panel included 169 single-nucleotide polymorphisms (SNPs) in 7 nicotinic acetylcholine receptor subunit genes and 4 genes in the endogenous cholinergic system. The primary outcome was smoking cessation (biochemically confirmed) at the end of treatment. SNPs clustered in the choline acetyltransferase (ChAT) gene were individually identified as nominally significant, and a 5-SNP haplotype (block 6) in ChAT was found to be significantly associated with quitting success. Single SNPs in ChAT haplotype block 2 were also associated with pretreatment levels of nicotine dependence in this cohort. To replicate associations of SNPs in haplotype blocks 2 and 6 of ChAT with nicotine dependence in a non-treatment-seeking cohort, we used data from an independent community-based sample of 629 smokers representing 200 families of European ancestry. Significant SNP and haplotype associations were identified for multiple measures of nicotine dependence. Although the effect sizes in both cohorts are modest, converging data across cohorts and phenotypes suggest that ChAT may be involved in nicotine dependence and ability to quit smoking. Additional sequencing and characterization of ChAT may reveal functional variants that contribute to nicotine dependence and smoking cessation.
nicotine; smoking cessation; choline acetyltransferase ChAT; pharmacogenetics; addiction; Pharmacogenetics/Pharmacogenomics; Addiction & Substance Abuse; Clinical Pharmacology/Trials; Psychiatry & Behavioral Sciences; Nicotine; Smoking Cessation; choline acetyltransferase ChAT
Since an immuno-inhibitory environment exists within tumors, successful vaccines will likely require additional approaches to alter the tumor microenvironment. Monocyte chemoattractant proteins (such as CCL2) are produced by many tumors and have both direct and indirect immuno-inhibitory effects. We hypothesized that CCL2 blockade would reduce immunosuppression and augment vaccine immunotherapy. Anti-murine-CCL2/CCL12 monoclonal antibodies were administered in three immunotherapy models: one aimed at the HPV-E7 antigen expressed by a non-small cell lung cancer line, one targeted to mesothelin expressed by a mesothelioma cell line, and one using an adenovirus expressing Interferon-α to treat a non-immunogenic, non-small cell lung cancer line. We evaluated the effect of the combination treatment on tumor growth and assessed the mechanism of these changes by evaluating cytotoxic T cells, immunosuppressive cells, and the tumor microenvironment. Administration of anti-CCL2/CCL12 antibodies along with the vaccines markedly augmented efficacy with enhanced reduction in tumor volume and cures of approximately half of the tumors. The combined treatment generated more total intra-tumoral CD8+ T-cells that were more activated and more anti-tumor antigen specific, as measured by tetramer evaluation. Another important potential mechanism was reduction in intratumoral T-regulatory (T-reg) cells. CCL2 appears to be a key proximal cytokine mediating immunosuppression in tumors. Its blockade augments CD8+ T cell immune response to tumors elicited by vaccines via multifactorial mechanisms. These observations suggest that combining CCL2 neutralization with vaccines should be considered in future immunotherapy trials.
CCL2; Cancer immunotherapy; Lung Cancer; Mesothelioma; T-lymphocytes
Uncertainty exists about how best to measure daily cigarette consumption. Two common measures are timeline followback (TLFB), which involves structured, prompted recall, and ecological momentary assessment (EMA), which involves recording consumption, as it occurs, on a handheld electronic device.
We evaluated the agreement between TLFB and EMA measures collected for 14 days prior to the target quit date from 236 smokers in a smoking cessation program. We performed a Bland–Altman analysis to assess agreement of TLFB and EMA using a regression-based model that allows for a nonuniform difference between methods and limits of agreement that can vary with the number of cigarettes smoked.
For pairs of measurements taken on the same smoker, TLFB counts were on average 3.2 cigarettes higher than EMA counts; this difference increased for larger numbers of cigarettes. Using a model that allows for variable limits of agreement, the width of the 95% interval ranged from 8.7 to 61.8 cigarettes, with an average of 26.4 cigarettes. Variation between the methods increased substantially for larger cigarette counts, leading to wider limits and poorer agreement for heavy smokers.
Throughout the measurement range, the estimated limits of agreement were far wider than the limits of clinical significance, defined a priori to be 20% of the number of cigarettes smoked. We conclude that TLFB and EMA cannot be considered equivalent for the assessment of daily cigarette consumption, especially for heavy smokers.
Hyperuricemia is hypothesized to be a risk factor for stroke and other cardiovascular disease, but to date results from observational studies are conflicting.
We conducted a systematic review and meta-analysis to assess the association between hyperuricemia and risk of stroke incidence and mortality. Studies were identified by searching major electronic databases using the Medical Subject Headings and keywords without restriction in languages. Only prospective cohort studies were included if they had data on stroke incidences or mortalities related to serum uric acid levels in adults. Pooled risk ratios (RRs) for the association of stroke incidence and mortality with serum uric acid levels were calculated.
A total of 16 studies including 238,449 adults were eligible and abstracted. Hyperuricemia was associated with a significantly higher risk of both stroke incidence [N=6 studies, RR 1.41, 95% confidence interval (CI): 1.05–1.76] and mortality [N=6 studies, RR 1.36, 95% CI: 1.03–1.69] in our meta-analyses of unadjusted study estimates. Subgroup analyses of studies adjusting for known risk factors such as age, hypertension, diabetes, and cholesterol still showed that hyperuricemia was significantly associated with both stroke incidence [N=4 studies, RR 1.47, 95% CI: 1.19–1.76] and mortality [N=6 studies, RR 1.26, 95% CI: 1.12–1.39]. The pooled estimate of multivariate RRs did not differ much by gender.
Our study suggests that hyperuricemia may modestly increase the risks of both stroke incidence and mortality. Future research is needed to determine whether lowering uric acid level has any beneficial effects on stroke.
hyperuricemia; stroke; systematic review; meta-analysis
Nicotine deprivation symptoms, including fatigue and attentional deficits, predict relapse following smoking cessation. Modafinil (Provigil), a wakefulness medication shown to have efficacy for the treatment of cocaine addiction, was tested as a novel therapy for nicotine dependence in a double-blind placebo-controlled trial.
157 treatment-seeking smokers received brief smoking cessation counseling and were randomized to: 1) 8 weeks of modafinil (200mg/day), or 2) 8 weeks of placebo. The primary outcome was biochemically verified 7-day point prevalence abstinence at the end of treatment. Secondary outcomes included cigarette smoking rate and post-quit nicotine deprivation symptoms (e.g., negative affect, withdrawal).
In this interim study analysis, end of treatment (EOT) quit rates did not differ between treatment arms (42% for placebo vs. 34% for modafinil; OR = 0.67 [0.34 – 1.31], p = .24). Further, from the target quit date to EOT, the daily smoking rate was 44% higher among non-abstainers in the modafinil arm, compared to non-abstainers in the placebo arm (IRR = 1.44, CI95 = 1.09–1.89, p < .01). Modafinil-treated participants also reported greater increases in negative affect and withdrawal symptoms, vs. participants randomized to placebo (ps < .05).
These data do not support the use of modafinil for the treatment of nicotine dependence and, as a consequence, this trial was discontinued. Cigarette smoking should be considered when modafinil is prescribed, particularly among those with psychiatric conditions that have high comorbidity with nicotine dependence.
nicotine dependence; smoking cessation; addiction; modafinil
Pharmacogenetic clinical trials seek to identify genetic modifiers of treatment effects. When a trial has collected data on many potential genetic markers, a first step in analysis is to screen for evidence of pharmacogenetic effects by testing for treatment-by-marker interactions in a statistical model for the outcome of interest. This approach is potentially problematic because i) individual significance tests can be overly sensitive, particularly when sample sizes are large; and ii) standard significance tests fail to distinguish between markers that are likely, on biological grounds, to have an effect, and those that are not. One way to address these concerns is to perform Bayesian hypothesis tests (Berger 1985; Kass and Raftery 1995), which are typically more conservative than standard uncorrected frequentist tests, less conservative than multiplicity-corrected tests, and make explicit use of relevant biological information through specification of the prior distribution. In this article we use a Bayesian testing approach to screen a panel of genetic markers recorded in a randomized clinical trial of bupropion versus placebo for smoking cessation. From a panel of 59 single-nucleotide polymorphisms (SNPs) located on 11 candidate genes, we identify four SNPs (one each on CHRNA5 and CHRNA2 and two on CHAT) that appear to have pharmacogenetic relevance. Of these, the SNP on CHRNA5 is most robust to specification of the prior. An unadjusted frequentist test identifies seven SNPs, including these four, none of which remains significant upon correction for multiplicity. In a panel of 43 randomly selected control SNPs, none is significant by either the Bayesian or the corrected frequentist test.
Bayes factor; Bayesian hypothesis test; bupropion; importance sampling; pharmacogenomics; single-nucleotide polymorphism
In studies of smoking behavior, some subjects report exact cigarette counts, whereas others report rounded-off counts, particularly multiples of 20, 10 or 5. This form of data reporting error, known as heaping, can bias the estimation of parameters of interest such as mean cigarette consumption. We present a model to describe heaped count data from a randomized trial of bupropion treatment for smoking cessation. The model posits that the reported cigarette count is a deterministic function of an underlying precise cigarette count variable and a heaping behavior variable, both of which are at best partially observed. To account for an excess of zeros, as would likely occur in a smoking cessation study where some subjects successfully quit, we model the underlying count variable with zero-inflated count distributions. We study the sensitivity of the inference on smoking cessation by fitting various models that either do or do not account for heaping and zero inflation, comparing the models by means of Bayes factors. Our results suggest that sufficiently rich models for both the underlying distribution and the heaping behavior are indispensable to obtaining a good fit with heaped smoking data. The analyses moreover reveal that bupropion has a significant effect on the fraction abstinent, but not on mean cigarette consumption among the non-abstinent.
Bayesian inference; heaped data; rounded data; smoking cessation; zero-inflated negative binomial; zero-inflated Poisson
Adoptive cellular immunotherapy has promise as an approach to eradicate established tumors. However, a significant hurdle in the success of cellular immunotherapy involves recently identified mechanisms of immune suppression on cytotoxic T-cells at the effector phase.
Transforming growth factor-β (TGF-β) is one of the most important of these immunosuppressive factors because it affects both T-cell and macrophage functions. We thus hypothesized that systemic blockade of TGF-β signaling combined with adoptive T-cell transfer would enhance the effectiveness of the therapy.
Flank tumors were generated in mice using the OVA-albumin (OA) expressing thymoma cell line, EG7. Splenocytes from transgenic OT-1 mice (whose CD8 T-cells recognize an immunodominant peptide in OA) were activated in vitro and adoptively transferred into mice bearing large tumors in the presence or absence of an orally available TGF-β receptor-I kinase blocker (SM16).
We observed markedly smaller tumors in the group receiving the combination of SM16 chow and adoptive transfer. Additional investigation revealed that TGF-β receptor blockade increased the persistence of adoptively transferred T-cells in the spleen and lymph nodes, increased numbers of adoptively transferred T-cells within tumors, increased activation of these infiltrating T-cells, and altered the tumor microenvironment with a significant increase in TNF-α and decrease in arginase mRNA expression
We found that systemic blockade of TGF-β receptor activity augmented the anti-tumor activity of adoptively transferred T-cells and may thus be a useful adjunct in future clinical trials.
tumor immunology; immunosuppression; TGFβ; Cytotoxic T-cells; cytokines; adoptive transfer
In medical informatics research, study questions frequently involve individuals who are grouped into clusters. For example, an intervention may be aimed at a clinician (who treats a cluster of patients) with the intention of improving the health of individual patients. Correlation among individuals within a cluster can lead to incorrect estimates of the sample size required to detect an effect and inappropriate estimates of the confidence intervals and the statistical significance of the intervention effects. Contamination, which is the spread of the effect of an intervention or control treatment to the opposite group, often occurs between individuals within clusters. It leads to an attenuation of the effect of the intervention and reduced power to detect a difference. If individuals are randomized in a clinical trial (individual-randomized trial), then correlation must be taken into account in the analysis, and the sample size may need to be increased to compensate for contamination. Randomizing clusters rather than individuals (cluster-randomized trials) can eliminate contamination and may be preferred for logistical reasons. Cluster-randomized trials are generally less efficient than individual-randomized trials, so the tradeoffs must be assessed. Correlation must be taken into account in the analysis and in the sample-size calculations for cluster-randomized trials.
Goal: To assess the reliability of a reference standard for an information extraction task.
Setting: Twenty-four physician raters from two sites and two specialities judged whether clinical conditions were present based on reading chest radiograph reports.
Methods: Variance components, generalizability (reliability) coefficients, and the number of expert raters needed to generate a reliable reference standard were estimated.
Results: Per-rater reliability averaged across conditions was 0.80 (95% CI, 0.79-0.81). Reliability for the nine individual conditions varied from 0.67 to 0.97, with central line presence and pneumothorax the most reliable, and pleural effusion (excluding CHF) and pneumonia the least reliable. One to two raters were needed to achieve a reliability of 0.70, and six raters, on average, were required to achieve a reliability of 0.95. This was far more reliable than a previously published per-rater reliability of 0.19 for a more complex task. Differences between sites were attributable to changes to the condition definitions.
Conclusion: In these evaluations, physician raters were able to judge very reliably the presence of clinical conditions based on text reports. Once the reliability of a specific rater is confirmed, it would be possible for that rater to create a reference standard reliable enough to assess aggregate measures on a system. Six raters would be needed to create a reference standard sufficient to assess a system on a case-by-case basis. These results should help evaluators design future information extraction studies for natural language processors and other knowledge-based systems.
Objective: The prevalence of hepatitis B and hepatitis C in a sexually
transmitted disease (STD) clinic population was studied, along with the prevalence of
various STD agents, in an attempt to identify possible STD markers for the hepatitis C
virus and help delineate the role of hepatitis C as an STD. The hepatitis C antibody rates
found in the STD clinic were also compared with those found among patients attending a
local OB/GYN clinic and those enrolled in a blood donor program, all from the same
Methods: A total of 150 women attending an STD clinc were examined
for each of the following agents: Chlamyadia trachomatis, Neisseria gonorrhoeae, syphilis,
hepatitis B surface antigen, hepatitis B core antibody, hepatitis B surface antibody,
and hepatitis C virus antibody. Additionally, several patients who signed informed
consent to be evaluated for human immunodeficiency virus (HIV) antibody were tested by
an enzyme immunoassay (EIA) screen method. The prevalence of each agent was then
compared with the other agents.
Results: The overall prevalence rates detected were as follows:
hepatitis B 16%, hepatitis C 4%, chlamydia 18.7%, gonorrhea 7.4%, syphilis 0.7%, and
HIV 0%. Hepatitis C antibody was detected in 4% of patients in the STD clinic, 0.76% of
volunteer blood donors from central Pennsylvania, and 0% of patiants studied from the
Harrisburg Hospital (Harrisburg, PA) prentatal population.
Conclusions: This screening study reveals an association between
attending a Harrisburg, PA, area STD clinic and having an increased prevalence of hepatitis
C antibody, but larger matched control studies will be needed to help clarify sexual
transmission as a mode of transmission for the hepatitis C virus.