Bayesian meta-analysis models for cross cancer genomic investigation of pleiotropic effects using group structure.

An increasing number of genome-wide association studies (GWAS) summary statistics is made available to the scientific community. Exploiting these results from multiple phenotypes would permit identification of novel pleiotropic associations. In addition, incorporating prior biological information in GWAS such as group structure information (gene or pathway) has shown some success in classical GWAS approaches. However, this has not been widely explored in the context of pleiotropy. We propose a Bayesian meta-analysis approach (termed GCPBayes) that uses summary-level GWAS data across multiple phenotypes to detect pleiotropy at both group-level (gene or pathway) and within group (eg, at the SNP level). We consider both continuous and Dirac spike and slab priors for group selection. We also use a Bayesian sparse group selection approach with hierarchical spike and slab priors that enables us to select important variables both at the group level and within group. GCPBayes uses a Bayesian statistical framework based on Markov chain Monte Carlo (MCMC) Gibbs sampling. It can be applied to multiple types of phenotypes for studies with overlapping or nonoverlapping subjects, and takes into account heterogeneity in the effect size and allows for the opposite direction of the genetic effects across traits. Simulations show that the proposed methods outperform benchmark approaches such as ASSET and CPBayes in the ability to retrieve pleiotropic associations at both SNP and gene-levels. To illustrate the GCPBayes method, we investigate the shared genetic effects between thyroid cancer and breast cancer in candidate pathways.

Quantifying the relative effect of environmental contamination on surgical ward MRSA incidence: An exploratory analysis.

BACKGROUND: To investigate and quantify the contribution of environmental contamination towards methicillin-resistant Staphylococcus aureus (MRSA) incidence observed in a hospital ward using stochastic modelling. METHODS: A non-homogeneous Poisson process model was developed to investigate the relationship between environmental contamination and MRSA incidence in a UK surgical ward during a cleaning intervention study. The model quantified the fractional risks (FRs) from colonised patients, environmental contamination and a generic background source as a measure of their relative importance in describing the observed MRSA incidence. RESULTS: While the background source remained the most likely MRSA acquisition source for this ward (as measured by the FRs), environmental contamination was the second most likely source, ahead of colonised patients in the ward. The relative importance of environmental contamination was smaller in the enhanced cleaning period compared with the normal cleaning period, albeit with notable variability in the estimates. CONCLUSIONS: Accounting for environmental contamination in stochastic modelling of MRSA transmission within a hospital ward provides a richer interpretation of the FRs, and is particularly pertinent in quantitative investigations of hospital cleaning interventions to reduce MRSA acquisition.

Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation.

In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2-12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226-268 µm2h-1, 311-351 µm2h-1 and 0.23-0.39, 0.32-0.61 for the experimental periods of 0-24 h and 24-48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ.

Quantifying uncertainty in parameter estimates for stochastic models of collective cell spreading using approximate Bayesian computation.

Wound healing and tumour growth involve collective cell spreading, which is driven by individual motility and proliferation events within a population of cells. Mathematical models are often used to interpret experimental data and to estimate the parameters so that predictions can be made. Existing methods for parameter estimation typically assume that these parameters are constants and often ignore any uncertainty in the estimated values. We use approximate Bayesian computation (ABC) to estimate the cell diffusivity, D, and the cell proliferation rate, λ, from a discrete model of collective cell spreading, and we quantify the uncertainty associated with these estimates using Bayesian inference. We use a detailed experimental data set describing the collective cell spreading of 3T3 fibroblast cells. The ABC analysis is conducted for different combinations of initial cell densities and experimental times in two separate scenarios: (i) where collective cell spreading is driven by cell motility alone, and (ii) where collective cell spreading is driven by combined cell motility and cell proliferation. We find that D can be estimated precisely, with a small coefficient of variation (CV) of 2-6%. Our results indicate that D appears to depend on the experimental time, which is a feature that has been previously overlooked. Assuming that the values of D are the same in both experimental scenarios, we use the information about D from the first experimental scenario to obtain reasonably precise estimates of λ, with a CV between 4 and 12%. Our estimates of D and λ are consistent with previously reported values; however, our method is based on a straightforward measurement of the position of the leading edge whereas previous approaches have involved expensive cell counting techniques. Additional insights gained using a fully Bayesian approach justify the computational cost, especially since it allows us to accommodate information from different experiments in a principled way.

Model choice problems using approximate Bayesian computation with applications to pathogen transmission data sets.

Analytically or computationally intractable likelihood functions can arise in complex statistical inferential problems making them inaccessible to standard Bayesian inferential methods. Approximate Bayesian computation (ABC) methods address such inferential problems by replacing direct likelihood evaluations with repeated sampling from the model. ABC methods have been predominantly applied to parameter estimation problems and less to model choice problems due to the added difficulty of handling multiple model spaces. The ABC algorithm proposed here addresses model choice problems by extending Fearnhead and Prangle (2012, Journal of the Royal Statistical Society, Series B 74, 1-28) where the posterior mean of the model parameters estimated through regression formed the summary statistics used in the discrepancy measure. An additional stepwise multinomial logistic regression is performed on the model indicator variable in the regression step and the estimated model probabilities are incorporated into the set of summary statistics for model choice purposes. A reversible jump Markov chain Monte Carlo step is also included in the algorithm to increase model diversity for thorough exploration of the model space. This algorithm was applied to a validating example to demonstrate the robustness of the algorithm across a wide range of true model probabilities. Its subsequent use in three pathogen transmission examples of varying complexity illustrates the utility of the algorithm in inferring preference of particular transmission models for the pathogens.

Incorporating adverse event relatedness into dose-finding clinical trial designs.

Dose-finding designs estimate the dose level of a drug based on observed adverse events. Relatedness of the adverse event to the drug has been generally ignored in all proposed design methodologies. These designs assume that the adverse events observed during a trial are definitely related to the drug, which can lead to flawed dose-level estimation. We incorporate adverse event relatedness into the so-called continual reassessment method. Adverse events that have 'doubtful' or 'possible' relationships to the drug are modelled using a two-parameter logistic model with an additive probability mass. Adverse events 'probably' or 'definitely' related to the drug are modelled using a cumulative logistic model. To search for the maximum tolerated dose, we use the maximum estimated toxicity probability of these two adverse event relatedness categories. We conduct a simulation study that illustrates the characteristics of the design under various scenarios. This article demonstrates that adverse event relatedness is important for improved dose estimation. It opens up further research pathways into continual reassessment design methodologies.

Bayesian experimental design for models with intractable likelihoods.

In this paper we present a methodology for designing experiments for efficiently estimating the parameters of models with computationally intractable likelihoods. The approach combines a commonly used methodology for robust experimental design, based on Markov chain Monte Carlo sampling, with approximate Bayesian computation (ABC) to ensure that no likelihood evaluations are required. The utility function considered for precise parameter estimation is based upon the precision of the ABC posterior distribution, which we form efficiently via the ABC rejection algorithm based on pre-computed model simulations. Our focus is on stochastic models and, in particular, we investigate the methodology for Markov process models of epidemics and macroparasite population evolution. The macroparasite example involves a multivariate process and we assess the loss of information from not observing all variables.

Driving performance impairments due to hypovigilance on monotonous roads.

Drivers' ability to react to unpredictable events deteriorates when exposed to highly predictable and uneventful driving tasks. Highway design reduces the driving task mainly to a lane-keeping manoeuvre. Such a task is monotonous, providing little stimulation and this contributes to crashes due to inattention. Research has shown that driver's hypovigilance can be assessed with EEG measurements and that driving performance is impaired during prolonged monotonous driving tasks. This paper aims to show that two dimensions of monotony - namely road design and road side variability - decrease vigilance and impair driving performance. This is the first study correlating hypovigilance and driver performance in varied monotonous conditions, particularly on a short time scale (a few seconds). We induced vigilance decrement as assessed with an EEG during a monotonous driving simulator experiment. Road monotony was varied through both road design and road side variability. The driver's decrease in vigilance occurred due to both road design and road scenery monotony and almost independently of the driver's sensation seeking level. Such impairment was also correlated to observable measurements from the driver, the car and the environment. During periods of hypovigilance, the driving performance impairment affected lane positioning, time to lane crossing, blink frequency, heart rate variability and non-specific electrodermal response rates. This work lays the foundation for the development of an in-vehicle device preventing hypovigilance crashes on monotonous roads.

Real-time performance modelling of a Sustained Attention to Response Task.

Vigilance declines when exposed to highly predictable and uneventful tasks. Monotonous tasks provide little cognitive and motor stimulation and contribute to human errors. This paper aims to model and detect vigilance decline in real time through participants' reaction times during a monotonous task. A laboratory-based experiment adapting the Sustained Attention to Response Task (SART) is conducted to quantify the effect of monotony on overall performance. Relevant parameters are then used to build a model detecting hypovigilance throughout the experiment. The accuracy of different mathematical models is compared to detect in real time - minute by minute - the lapses in vigilance during the task. It is shown that monotonous tasks can lead to an average decline in performance of 45%. Furthermore, vigilance modelling enables the detection of vigilance decline through reaction times with an accuracy of 72% and a 29% false alarm rate. Bayesian models are identified as a better model to detect lapses in vigilance as compared with neural networks and generalised linear mixed models. This modelling could be used as a framework to detect vigilance decline of any human performing monotonous tasks. STATEMENT OF RELEVANCE: Existing research on monotony is largely entangled with endogenous factors such as sleep deprivation, fatigue and circadian rhythm. This paper uses a Bayesian model to assess the effects of a monotonous task on vigilance in real time. It is shown that the negative effects of monotony on the ability to sustain attention can be mathematically modelled and predicted in real time using surrogate measures, such as reaction times. This allows the modelling of vigilance fluctuations.

Using samples to estimate the sensitivity and specificity of a surveillance process.

Determining sensitivity and specificity of a postoperative infection surveillance process is a difficult undertaking. Because postoperative infections are rare, vast numbers of negative results exist, and it is often not reasonable to assess them all. This study gives a methodological framework for estimating sensitivity and specificity by taking only a small sample of the number of patients who test negative and comparing their findings to the reference or "gold standard" rather than comparing the findings of all patients to the gold standard. It provides a formula for deriving confidence intervals for these estimates and a guide to minimum requirements for sampling results.

Bayesian statistical MUNE method.

We have developed a new method of motor unit number estimation (MUNE) for assessing diseases such as amyotrophic lateral sclerosis (ALS). We used data from the whole stimulus-response curve and then performed a Bayesian statistical analysis. The Bayesian method uses mathematical equations that express the basic elements of motor unit activation after electrical stimulation and allows for the sources of variability and uncertainty in this formulation. The Bayesian MUNE method was used to determine the most probable number of motor units in 8 normal subjects, 49 ALS subjects, and 3 subjects with progressive lower motor neuron (LMN) weakness. In normals the number of motor units was calculated to be 75-85 in hand and 40-58 in foot muscles. In ALS subjects the number of motor units per muscle was less than in normal subjects. In 17 ALS subjects and 3 subjects with LMN weakness the median, ulnar, or peroneal nerve was studied on repeated occasions over an average of 189 days (range 63-1,071) and the number of motor units progressively declined, with a half-life ranging from 62-834 days. The results of our MUNE technique were reproducible on replicate studies. A Bayesian statistical MUNE method is a new approach that can be used to study ALS patients serially for assessment and treatment trials.

Motor unit number estimation--a Bayesian approach.

All muscle contractions are dependent on the functioning of motor units. In diseases such as amyotrophic lateral sclerosis (ALS), progressive loss of motor units leads to gradual paralysis. A major difficulty in the search for a treatment for these diseases has been the lack of a reliable measure of disease progression. One possible measure would be an estimate of the number of surviving motor units. Despite over 30 years of motor unit number estimation (MUNE), all proposed methods have been met with practical and theoretical objections. Our aim is to develop a method of MUNE that overcomes these objections. We record the compound muscle action potential (CMAP) from a selected muscle in response to a graded electrical stimulation applied to the nerve. As the stimulus increases, the threshold of each motor unit is exceeded, and the size of the CMAP increases until a maximum response is obtained. However, the threshold potential required to excite an axon is not a precise value but fluctuates over a small range leading to probabilistic activation of motor units in response to a given stimulus. When the threshold ranges of motor units overlap, there may be alternation where the number of motor units that fire in response to the stimulus is variable. This means that increments in the value of the CMAP correspond to the firing of different combinations of motor units. At a fixed stimulus, variability in the CMAP, measured as variance, can be used to conduct MUNE using the "statistical" or the "Poisson" method. However, this method relies on the assumptions that the numbers of motor units that are firing probabilistically have the Poisson distribution and that all single motor unit action potentials (MUAP) have a fixed and identical size. These assumptions are not necessarily correct. We propose to develop a Bayesian statistical methodology to analyze electrophysiological data to provide an estimate of motor unit numbers. Our method of MUNE incorporates the variability of the threshold, the variability between and within single MUAPs, and baseline variability. Our model not only gives the most probable number of motor units but also provides information about both the population of units and individual units. We use Markov chain Monte Carlo to obtain information about the characteristics of individual motor units and about the population of motor units and the Bayesian information criterion for MUNE. We test our method of MUNE on three subjects. Our method provides a reproducible estimate for a patient with stable but severe ALS. In a serial study, we demonstrate a decline in the number of motor unit numbers with a patient with rapidly advancing disease. Finally, with our last patient, we show that our method has the capacity to estimate a larger number of motor units.

Use of stochastic epidemic modeling to quantify transmission rates of colonization with methicillin-resistant Staphylococcus aureus in an intensive care unit.

OBJECTIVE: To consider statistical methods for estimating transmission rates for colonization of patients with methicillin-resistant Staphylococcus aureus (MRSA) in an intensive care unit (ICU) from three different sources: background contamination, non-isolated patients, and isolated patients. METHODS: We developed statistical methods that allowed for the analysis of interval-censored, routine surveillance data and extended the general epidemic model for the flow of patients through the ICU. RESULTS: Within this ICU, the rate of transmission to susceptible patients from a background source of MRSA (0.0092 case per day; 95% confidence interval [CI95], 0.0062-0.0126) is approximately double the rate of transmission from a non-isolated patient (0.0052 case per day; CI95, 0.0013-0.0096) and six times the rate of transmission from an isolated patient (0.0015 case per day; CI95, 0.0001-0.0043). We used the methodology to investigate whether transmission rates vary with workload. CONCLUSION: Our methodology has general application to infection by and transmission of pathogens in a hospital setting and is appropriate for quantifying the effect of infection control interventions.