Allele frequency misspecification: effect on power and Type I error of model-dependent linkage analysis of quantitative traits under random ascertainment

BACKGROUND: Studies of model-based linkage analysis show that trait or marker model misspecification leads to decreasing power or increasing Type I error rate. An increase in Type I error rate is seen when marker related parameters (e.g., allele frequencies) are misspecified and ascertainment is through the trait, but lod-score methods are expected to be robust when ascertainment is random (as is often the case in linkage studies of quantitative traits). In previous studies, the power of lod-score linkage analysis using the "correct" generating model for the trait was found to increase when the marker allele frequencies were misspecified and parental data were missing. An investigation of Type I error rates, conducted in the absence of parental genotype data and with misspecification of marker allele frequencies, showed that an inflation in Type I error rate was the cause of at least part of this apparent increased power. To investigate whether the observed inflation in Type I error rate in model-based LOD score linkage was due to sampling variation, the trait model was estimated from each sample using REGCHUNT, an automated segregation analysis program used to fit models by maximum likelihood using many different sets of initial parameter estimates. RESULTS: The Type I error rates observed using the trait models generated by REGCHUNT were usually closer to the nominal levels than those obtained when assuming the generating trait model. CONCLUSION: This suggests that the observed inflation of Type I error upon misspecification of marker allele frequencies is at least partially due to sampling variation. Thus, with missing parental genotype data, lod-score linkage is not as robust to misspecification of marker allele frequencies as has been commonly thought

Association between proton pump inhibitor therapy and clostridium difficile infection: a contemporary systematic review and meta-analysis.

Abstract Introduction Emerging epidemiological evidence suggests that proton pump inhibitor (PPI) acid-suppression therapy is associated with an increased risk of Clostridium difficile infection (CDI). Methods Ovid MEDLINE, EMBASE, ISI Web of Science, and Scopus were searched from 1990 to January 2012 for analytical studies that reported an adjusted effect estimate of the association between PPI use and CDI. We performed random-effect meta-analyses. We used the GRADE framework to interpret the findings. Results We identified 47 eligible citations (37 case-control and 14 cohort studies) with corresponding 51 effect estimates. The pooled OR was 1.65, 95% CI (1.47, 1.85), I2 = 89.9%, with evidence of publication bias suggested by a contour funnel plot. A novel regression based method was used to adjust for publication bias and resulted in an adjusted pooled OR of 1.51 (95% CI, 1.26–1.83). In a speculative analysis that assumes that this association is based on causality, and based on published baseline CDI incidence, the risk of CDI would be very low in the general population taking PPIs with an estimated NNH of 3925 at 1 year. Conclusions In this rigorously conducted systemic review and meta-analysis, we found very low quality evidence (GRADE class) for an association between PPI use and CDI that does not support a cause-effect relationship

Genetic variation in the pleiotropic association between physical activity and body weight in mice

<p>Abstract</p> <p>Background</p> <p>A sedentary lifestyle is often assumed to lead to increases in body weight and potentially obesity and related diseases but in fact little is known about the genetic association between physical activity and body weight. We tested for such an association between body weight and the distance, duration, and speed voluntarily run by 310 mice from the F₂generation produced from an intercross of two inbred lines that differed dramatically in their physical activity levels.</p> <p>Methods</p> <p>We used a conventional interval mapping approach with SNP markers to search for QTLs that affected both body weight and activity traits. We also conducted a genome scan to search for relationship QTLs (<it>rel</it>QTLs), or chromosomal regions that affected an activity trait variably depending on the phenotypic value of body weight.</p> <p>Results</p> <p>We uncovered seven quantitative trait loci (QTLs) affecting body weight, but only one co-localized with another QTL previously found for activity traits. We discovered 19 <it>rel</it>QTLs that provided evidence for a genetic (pleiotropic) association of physical activity and body weight. The three genotypes at each of these loci typically exhibited a combination of negative, zero, and positive regressions of the activity traits on body weight, the net effect of which was to produce overall independence of body weight from physical activity. We also demonstrated that the <it>rel</it>QTLs produced these varying associations through differential epistatic interactions with a number of other epistatic QTLs throughout the genome.</p> <p>Conclusion</p> <p>It was concluded that individuals with specific combinations of genotypes at the <it>rel</it>QTLs and <it>epi</it>QTLs might account for some of the variation typically seen in plots of the association of physical activity with body weight.</p

Toward a Quantitative Estimate of Future Heat Wave Mortality under Global Climate Change

Background: Climate change is anticipated to affect human health by changing the distribution of known risk factors. Heat waves have had debilitating effects on human mortality, and global climate models predict an increase in the frequency and severity of heat waves. The extent to which climate change will harm human health through changes in the distribution of heat waves and the sources of uncertainty in estimating these effects have not been studied extensively. Objectives: We estimated the future excess mortality attributable to heat waves under global climate change for a major U.S. city. Methods: We used a database comprising daily data from 1987 through 2005 on mortality from all nonaccidental causes, ambient levels of particulate matter and ozone, temperature, and dew point temperature for the city of Chicago, Illinois. We estimated the associations between heat waves and mortality in Chicago using Poisson regression models. Results: Under three different climate change scenarios for 2081–2100 and in the absence of adaptation, the city of Chicago could experience between 166 and 2,217 excess deaths per year attributable to heat waves, based on estimates from seven global climate models. We noted considerable variability in the projections of annual heat wave mortality; the largest source of variation was the choice of climate model. Conclusions: The impact of future heat waves on human health will likely be profound, and significant gains can be expected by lowering future carbon dioxide emissions

Field Assessment of a Novel Household-Based Water Filtration Device: A Randomised, Placebo-Controlled Trial in the Democratic Republic of Congo

BACKGROUND: Household water treatment can improve the microbiological quality of drinking water and may prevent diarrheal diseases. However, current methods of treating water at home have certain shortcomings, and there is evidence of bias in the reported health impact of the intervention in open trial designs. METHODS AND FINDINGS: We undertook a randomised, double-blinded, placebo-controlled trial among 240 households (1,144 persons) in rural Democratic Republic of Congo to assess the field performance, use and effectiveness of a novel filtration device in preventing diarrhea. Households were followed up monthly for 12 months. Filters and placebos were monitored for longevity and for microbiological performance by comparing thermotolerant coliform (TTC) levels in influent and effluent water samples. Mean longitudinal prevalence of diarrhea was estimated among participants of all ages. Compliance was assessed through self-reported use and presence of water in the top vessel of the device at the time of visit. Over the 12-month follow-up period, data were collected for 11,236 person-weeks of observation (81.8% total possible). After adjusting for clustering within the household, the longitudinal prevalence ratio of diarrhoea was 0.85 (95% confidence interval: 0.61-1.20). The filters achieved a 2.98 log reduction in TTC levels while, for reasons that are unclear, the placebos achieved a 1.05 log reduction (p<0.0001). After 8 months, 68% of intervention households met the study's definition of current users, though most (73% of adults and 95% of children) also reported drinking untreated water the previous day. The filter maintained a constant flow rate over time, though 12.4% of filters were damaged during the course of the study. CONCLUSIONS: While the filter was effective in improving water quality, our results provide little evidence that it was protective against diarrhea. The moderate reduction observed nevertheless supports the need for larger studies that measure impact against a neutral placebo. TRIAL REGISTRATION: Current Controlled Trials ISRCTN03844341

Determining initial and follow-up costs of cardiovascular events in a US managed care population

<p>Abstract</p> <p>Background</p> <p>Cardiovascular (CV) events are prevalent and expensive worldwide both in terms of direct medical costs at the time of the event and follow-up healthcare after the event. This study aims to determine initial and follow-up costs for cardiovascular (CV) events in US managed care enrollees and to compare to healthcare costs for matched patients without CV events.</p> <p>Methods</p> <p>A 5.5-year retrospective matched cohort analysis of claims records for adult enrollees in ~90 US health plans. Patients hospitalized for first CV event were identified from a database containing a representative sample of the commercially-insured US population. The CV-event group (n = 29,688) was matched to a control group with similar demographics but no claims for CV-related events. Endpoints were total direct medical costs for inpatient and outpatient services and pharmacy (paid insurance amount).</p> <p>Results</p> <p>Overall, mean initial inpatient costs were US dollars ($) 16,981 per case (standard deviation [SD] =$20,474), ranging from $6,699 for a transient ischemic attack (mean length of stay [LOS] = 3.7 days) to$56,024 for a coronary artery bypass graft (CABG) (mean LOS = 9.2 days). Overall mean health-care cost during 1-year follow-up was $16,582 (SD =$34,425), an excess of $13,792 over the mean cost of matched controls. This difference in average costs between CV-event and matched-control subjects was$20,862 and $26,014 after two and three years of follow-up. Mean overall inpatient costs for second events were similar to those for first events ($17,705/case; SD = $22,703). The multivariable regression model adjusting for demographic and clinical characteristics indicated that the presence of a CV event was positively associated with total follow-up costs (P < 0.0001).</p> <p>Conclusions</p> <p>Initial hospitalization and follow-up costs vary widely by type of CV event. The 1-year follow-up costs for CV events were almost as high as the initial hospitalization costs, but much higher for 2- and 3-year follow-up.</p

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

A randomized trial of mail vs. telephone invitation to a community-based cardiovascular health awareness program for older family practice patients [ISRCTN61739603]

BACKGROUND: Family physicians can play an important role in encouraging patients to participate in community-based health promotion initiatives designed to supplement and enhance their in-office care. Our objectives were to determine effective approaches to invite older family practice patients to attend cardiovascular health awareness sessions in community pharmacies, and to assess the feasibility and acceptability of a program incorporating invitation by physicians and feedback to physicians. METHODS: We conducted a prospective randomized trial with 1 family physician practice and 5 community pharmacies in Dundas, Ontario. Regular patients 65 years or older (n = 235) were randomly allocated to invitation by mail or telephone to attend pharmacy cardiovascular health awareness sessions led by volunteer peer health educators. A health record review captured blood pressure status, monitoring and control. At the sessions, volunteers helped patients to measure blood pressure using in-store machines and a validated portable device (BPM-100), and recorded blood pressure readings and self-reported cardiovascular risk factors. We compared attendance rates in the mail and telephone invitation groups and explored factors potentially associated with attendance. RESULTS: The 119 patients invited by mail and 116 patients contacted by telephone had a mean age of 75.7 (SD, 6.4) years and 46.8% were male. Overall, 58.3% (137/235) of invitees attended a pharmacy cardiovascular health awareness session. Patients invited by telephone were more likely to attend than those invited by mail (72.3% vs. 44.0%, OR 3.3; 95%CI 1.9–5.7; p < 0.001). CONCLUSION: While the attendance in response to a telephone invitation was higher, response to a single letter was substantial. Attendance rates indicated considerable interest in community-based cardiovascular health promotion activities. A large-scale trial of a pharmacy cardiovascular health awareness program for older primary care patients is feasible

Dose-dense adjuvant chemotherapy for primary breast cancer

Adjuvant chemotherapy has been proven to reduce significantly the risk for relapse and death in women with operable breast cancer. Nevertheless, the prognosis for patients presenting with extensive axillary lymph node involvement remains suboptimal. In an attempt to improve on the efficacy of existing chemotherapy, a phase III intergroup trial led by the Cancer and Leukemia Group B (CALGB 97-41) was designed, which tested a mathematical model of tumor growth based on the Norton–Simon hypothesis. This hypothesis, developed about 3 decades ago, and the kinetic model derived from it, created the basis of the concepts of dose density and sequential therapy, both of which were tested in CALGB 97-41. This large prospective randomized trial demonstrated that shortening the time interval between each chemotherapy cycle while maintaining the same dose size resulted in significant improvements in disease-free and overall survival in patients with node-positive breast carcinoma. This finding is highly relevant and has immediate implications for clinical practice

A search for quantitative trait loci controlling within-individual variation of physical activity traits in mice

<p>Abstract</p> <p>Background</p> <p>In recent years it has become increasingly apparent that physical inactivity can predispose individuals to a host of health problems. While many studies have analyzed the effect of various environmental factors on activity, we know much less about the genetic control of physical activity. Some studies in mice have discovered quantitative trait loci (QTL) influencing various physical activity traits, but mostly have analyzed inter-individual variation rather than variation in activity within individuals over time. We conducted a genome scan to identify QTLs controlling the distance, duration, and time run by mice over seven consecutive three-day intervals in an F₂population created by crossing two inbred strains (C57L/J and C3H/HeJ) that differed widely (average of nearly 300%) in their activity levels. Our objectives were (a) to see if we would find QTLs not originally discovered in a previous investigation that assessed these traits over the entire 21-day period and (b) to see if some of these QTLs discovered might affect the activity traits only in the early or in the late time intervals.</p> <p>Results</p> <p>This analysis uncovered 39 different QTLs, over half of which were new. Some QTLs affected the activity traits only in the early time intervals and typically exhibited significant dominance effects whereas others affected activity only in the later age intervals and exhibited less dominance. We also analyzed the regression slopes of the activity traits over the intervals, and found several QTLs affecting these traits that generally mapped to unique genomic locations.</p> <p>Conclusions</p> <p>It was concluded that the genetic architecture of physical activity in mice is much more complicated than has previously been recognized, and may change considerably depending on the age at which various activity measures are assessed.</p