Testing Genetic Association by Regressing Genotype over Multiple Phenotypes

Complex disorders are typically characterized by multiple phenotypes. Analyzing these phenotypes jointly is expected to be more powerful than dealing with one of them at a time. A recent approach (O''Reilly et al. 2012) is to regress the genotype at a SNP marker on multiple phenotypes and apply the proportional odds model. In the current research, we introduce an explicit expression for the score test statistic and its non-centrality parameter that determines its power. Same simulation studies as those reported in Galesloot et al. (2014) were conducted to assess its performance. We demonstrate by theoretical arguments and simulation studies that, despite its potential usefulness for multiple phenotypes, the proportional odds model method can be less powerful than regular methods for univariate traits. We also introduce an implementation of the proposed score statistic in an R package named iGasso.     

Decision-Making in Research Tasks with Sequential Testing

Background

In a recent controversial essay, published by JPA Ioannidis in PLoS Medicine, it has been argued that in some research fields, most of the published findings are false. Based on theoretical reasoning it can be shown that small effect sizes, error-prone tests, low priors of the tested hypotheses and biases in the evaluation and publication of research findings increase the fraction of false positives. These findings raise concerns about the reliability of research. However, they are based on a very simple scenario of scientific research, where single tests are used to evaluate independent hypotheses.

Methodology/Principal Findings

In this study, we present computer simulations and experimental approaches for analyzing more realistic scenarios. In these scenarios, research tasks are solved sequentially, i.e. subsequent tests can be chosen depending on previous results. We investigate simple sequential testing and scenarios where only a selected subset of results can be published and used for future rounds of test choice. Results from computer simulations indicate that for the tasks analyzed in this study, the fraction of false among the positive findings declines over several rounds of testing if the most informative tests are performed. Our experiments show that human subjects frequently perform the most informative tests, leading to a decline of false positives as expected from the simulations.

Conclusions/Significance

For the research tasks studied here, findings tend to become more reliable over time. We also find that the performance in those experimental settings where not all performed tests could be published turned out to be surprisingly inefficient. Our results may help optimize existing procedures used in the practice of scientific research and provide guidance for the development of novel forms of scholarly communication.     

Conditional Inference Following Group Sequential Testing

The work of Fisher (1959) and Buehler (1959) discuss the importance of conditioning on recognizable subsets of the sample space. The stopping time yields an easily identifiable partition of the sample space when considering group sequential testing. We first present confidence intervals that are correct when conditioning on the subset of data for which a trial stopped at a particular analysis. These intervals have very desirable properties for observations that are highly unusual (given any value of the mean). In addition, they provide insight into how information about the mean is distributed between the two sufficient statistics. We then use conditional coverage probabilities to compare the sample mean, stagewise, and repeated confidence intervals. We find that none of these intervals outperforms the others when conditioning on stopping time, and no interval is a uniformly acceptable performer.     

Sequential Metabolic Events During Encystment of Azobacter vinelandii

Cells of Azotobacter vinelandii are specifically induced to encyst by beta-hydroxybutyrate (BHB). The process of differentiation, which occurs over a period of 36 h, was characterized by an ordered sequence of biochemical events. Upon initiation of encystment, nitrogen fixation and glucose-6-phosphate dehydrogenase activities decreased immediately to very low levels. This was followed by an increase in the specific activities of BHB dehydrogenase, isocitrate dehydrogenase, isocitrate lyase, and malate synthase first at 3 h and then again at 21 h. The peak activity of fructose 1,6-diphosphate aldolase occurred at 6 h, and the enzyme activity then decreased gradually. Fructose 1,6-diphosphatase had peak activities at 9 and 27 h. Deoxyribonucleic acid synthesis ceased just prior to the final cell division at 4 to 6 h, but ribonucleic acid synthesis continued until the 12th h. From labeling studies and the appearance of new enzyme activities, it appeared that protein synthesis continued throughout encystment.     

Methods for Estimating Center Effects on Recurrent Events

In this article, we develop methods for quantifying center effects with respect to recurrent event data. In the models of interest, center effects are assumed to act multiplicatively on the recurrent event rate function. When the number of centers is large, traditional estimation methods that treat centers as categorical variables have many parameters and are sometimes not feasible to implement, especially with large numbers of distinct recurrent event times. We propose a new estimation method for center effects which avoids including indicator variables for centers. We then show that center effects can be consistently estimated by the center-specific ratio of observed to expected cumulative numbers of events. We also consider the case where the recurrent event sequence can be stopped permanently by a terminating event. Large-sample results are developed for the proposed estimators. We assess the finite-sample properties of the proposed estimators through simulation studies. The methods are then applied to national hospital admissions data for end stage renal disease patients.     

Joint Models of Longitudinal Data and Recurrent Events with Informative Terminal Event

This article presents semiparametric joint models to analyze longitudinal data with recurrent events (e.g. multiple tumors, repeated hospital admissions) and a terminal event such as death. A broad class of transformation models for the cumulative intensity of the recurrent events and the cumulative hazard of the terminal event is considered, which includes the proportional hazards model and the proportional odds model as special cases. We propose to estimate all the parameters using the nonparametric maximum likelihood estimators (NPMLE). We provide the simple and efficient EM algorithms to implement the proposed inference procedure. Asymptotic properties of the estimators are shown to be asymptotically normal and semiparametrically efficient. Finally, we evaluate the performance of the method through extensive simulation studies and a real-data application.     

Testing Hypotheses about Linkage Disequilibrium with Multiple Alleles

For loci with multiple alleles, hypotheses about linkage disequilibrium may be tested on the complete set of gametic data, or on various collapsed sets of data. Collapsing data into a few alleles at each locus can change the power of the tests, as implied in a recent paper by Zouros, Golding and Mackay (1977). We show that the nature of such changes can be found from properties of the noncentral chi-square distribution, and that the magnitude and direction of these changes depend on the levels of linkage disequilibria, allelic frequencies and degrees of freedom.     

Semiparametric Transformation Models with Time‐Varying Coefficients for Recurrent and Terminal Events

Summary In this article, we propose a family of semiparametric transformation models with time‐varying coefficients for recurrent event data in the presence of a terminal event such as death. The new model offers great flexibility in formulating the effects of covariates on the mean functions of the recurrent events among survivors at a given time. For the inference on the proposed models, a class of estimating equations is developed and asymptotic properties of the resulting estimators are established. In addition, a lack‐of‐fit test is provided for assessing the adequacy of the model, and some tests are presented for investigating whether or not covariate effects vary with time. The finite‐sample behavior of the proposed methods is examined through Monte Carlo simulation studies, and an application to a bladder cancer study is also illustrated.     

The Design of Intervention Trials Involving Recurrent and Terminal Events

Clinical trials are often designed to assess the effect of therapeutic interventions on the incidence of recurrent events in the presence of a dependent terminal event such as death. Statistical methods based on multistate analysis have considerable appeal in this setting since they can incorporate changes in risk with each event occurrence, a dependence between the recurrent event and the terminal event, and event-dependent censoring. To date, however, there has been limited development of statistical methods for the design of trials involving recurrent and terminal events. Based on the asymptotic distribution of regression coefficients from a multiplicative intensity Markov regression model, we derive sample size formulas to address power requirements for both the recurrent and terminal event processes. We consider the design of trials for which separate marginal hypothesis tests are of interest for the recurrent and terminal event processes and deal with both superiority and non-inferiority tests. Simulation studies confirm that the designs satisfy the nominal power requirements in both settings, and an application to a trial evaluating the effect of a bisphosphonate on skeletal complications is given for illustration.     

Recurrent Mild Drought Events Increase Resistance Toward Extreme Drought Stress

The frequency and magnitude of extreme weather events such as drought are expected to increase in the future. At present, plant responses to recurrent extreme events have been sparsely examined and the role of stress history on subsequent stress response has been widely neglected. In a long-term field experiment, we investigated the response of grassland and heath communities to a very severe drought event, which exceeded the duration of projected drought scenarios. During the preceding 6 years, the plant communities experienced scenarios of varying water supply, including annually recurring drought, heavy rain, regular watering, and natural drought periods. Single species and plant communities that were regularly watered in the preceding years revealed the highest tissue die-back under a very severe drought when compared to plants that experienced mild or severe drought stress before. Contrary to expectations, the root to shoot ratio did not increase due to previous recurrent drought occurrences. Furthermore, pre-exposure effects on Vaccinium myrtillus and Plantago lanceolata tissue die-back and reproductive biomass (P. lanceolata) were altered by community composition. Recurrent mild drought stress seems to improve drought resistance of plant communities and species. Potential reasons could be epigenetic changes or soil biotic legacies. Morphological legacies such as altered root to shoot ratio did not play a role in our study. Imprinting events which trigger this ecological stress memory do not have to be extreme themselves. Thresholds, longevity of effects, and the role of biodiversity shown by the importance of community composition require further attention.     

Feasibility of Performing Multiple Point of Care Testing for HIV Anti-Retroviral Treatment Initiation and Monitoring from Multiple or Single Fingersticks

Background

Point of Care testing (POCT) provides on-site, rapid, accessible results. With current South African anti-retroviral treatment guidelines, up to 4 fingersticks /patient/clinic visit could be required if utilizing POC. We determined the feasibility and accuracy of a nurse performing multiple POCT on multiple fingersticks followed by simplification of the process by performance of multiple POC on a single fingerstick.

Method and Findings

Random HIV positive adult patients presenting at a HIV treatment clinic in South Africa, for ART initiation/ monitoring, were approached to participate in the study between April-June 2012. Phase I: n=150 patients approached for multiple POCT on multiple fingersticks. Phase II: n=150 patients approached for multiple POCT on a single fingerstick. The following POC tests were performed by a dedicated nurse: PIMA (CD4), HemoCue (hemoglobin), Reflotron (alanine aminotransferase, creatinine). A venepuncture specimen was taken for predicate laboratory methodology. Normal laboratory ranges and Royal College of Pathologists Australasia (RCPA) allowable differences were used as guidelines for comparison. In 67% of participants, ≥3 tests were requested per visit. All POCT were accurate but ranged in variability. Phase I: Hemoglobin was accurate (3.2%CV) while CD4, alanine aminotransferase and creatinine showed increased variability (16.3%CV; 9.3%CV; 12.9%CV respectively). PIMA generated a misclassification of 12.4%. Phase II: Hemoglobin, alanine aminotransferase and creatinine showed good accuracy (3.2%CV, 8.7%CV, 6.4%CV respectively) with increased variability on CD4 (12.4%CV) but low clinical misclassification (4.1%). No trends were observed for the sequence in which POC was performed on a single fingerstick. Overall, PIMA CD4 generated the highest error rate (16-19%).

Conclusions

Multiple POCT for ART initiation and/or monitoring can be performed practically by a dedicated nurse on multiple fingersticks. The process is as accurate as predicate methodology and can be simplified using a single fingerstick.     

Estimating Treatment Effects for Recurrent Events in the Presence of Rescue Medications: An Application to the Immune Thrombocytopenia Study

In many clinical studies, patients may experience the same type of event of interest repeatedly over time. However, the assessment of treatment effects is often complicated by the rescue medication uses due to ethical reasons. For example, in the motivating trial in studying the Immune Thrombocytopenia (ITP), when the interest lies in evaluating the treatment benefit of investigational product (IP) on reducing patient’s repeated bleeding, rescue medication such as platelet transfusions may be allowed to raise platelet counts. Both the intention-to-treat analysis and treating the intermediate rescue medication as covariate tend to attenuate the treatment benefit, and the estimates can be biased if interpreted as causal. In this paper, we propose a general causal framework when intermediate rescue medications are informative. We adopt the inverse weighted estimation approach to estimate the treatment effect, where weights are constructed to reflect time-dependent medication use probabilities. The proposed estimators are shown to be asymptotically normal and are demonstrated to perform well in small-sample simulation studies. The application to the ITP studies reveals a stronger benefit of using IP in reducing bleeding.     

Statistical Testing for Seasonality in Data with Multiple Peaks and Troughs

EDWARDS'S test for seasonality is extended to multiple peaks and troughs. It is shown how the extended statistic may be adjusted for the population at risk and for unequal lengths of time intervals in the cycle of seasons. A simulation study shows that the extended test statistic is, for sample sizes N ≧ 100, very specific in detecting the number of peaks and troughs for which it is intended. The associated method of parameter estimation is also assessed; for N ≦ 100, the amplitude of a possibly adequate simple harmonic model is estimated well, but the initial value of the phase angle is not. Estimated percentage points for the extended test statistic are tabulated, and some recommendations are offered regarding usage of this method.     

Endonasal Endoscopic Treatment of Recurrent Dacryocystitis

This report assessed clinical conditions leading to recurrent dacryocystitis and success rates of its treatment by endonasal endoscopic dacryocystorhinostomy. Forty-eight patients with recurrent dacryocystitis underwent endonasal endoscopic surgery and were followed up for at least 6 months. High bone windows, small bone window openings, small lacrimal sac stomas, scar tissues, and organic diseases of the nasal cavity led to fistula closure. Out of 48 patients, 45 (93.8 %) patients were cured by endonasal endoscopic surgery. Endonasal endoscopic dacryocystorhinostomy is beneficial for recurrent dacryocystitis.     

Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods

Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (Na), allelic richness (Rs), Nei’s genetic diversity index (He), observed heterozygosity (Ho) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (Fst) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s.