Genomic alterations have been linked to the development and progression of cancer. The technique of comparative genomic hybridization (CGH) yields data consisting of fluorescence intensity ratios of test and reference DNA samples. The intensity ratios provide information about the number of copies in DNA. Practical issues such as the contamination of tumor cells in tissue specimens and normalization errors necessitate the use of statistics for learning about the genomic alterations from array CGH data. As increasing amounts of array CGH data become available, there is a growing need for automated algorithms for characterizing genomic profiles. Specifically, there is a need for algorithms that can identify gains and losses in the number of copies based on statistical considerations, rather than merely detect trends in the data.We adopt a Bayesian approach, relying on the hidden Markov model to account for the inherent dependence in the intensity ratios. Posterior inferences are made about gains and losses in copy number. Localized amplifications (associated with oncogene mutations) and deletions (associated with mutations of tumor suppressors) are identified using posterior probabilities. Global trends such as extended regions of altered copy number are detected. Because the posterior distribution is analytically intractable, we implement a Metropolis-within-Gibbs algorithm for efficient simulation-based inference. Publicly available data on pancreatic adenocarcinoma, glioblastoma multiforme, and breast cancer are analyzed, and comparisons are made with some widely used algorithms to illustrate the reliability and success of the technique.

The effects of hydrostatic pressure on conjugated polymers, in particular polyphenyls (see Figure for monomer unit) have been studied using photoluminescence, absorption, photo‐induced absorption, and Raman spectroscopy. The effect of pressure on the singlet and triplet excitons and polarons allows an understanding of localized and delocalized electronic states. Changes in the intensity ratios of Raman bands that correspond to vibrations of a perpendicular and a coplanar array of phenyl rings in the chain, and comparison with calculated intensities, demonstrate the influence of pressure on the polymer's conformation.

Summary. The paper is motivated by cure detection among the prostate cancer patients in the National Institutes of Health surveillance epidemiology and end results programme, wherein the main end point (e.g. deaths from prostate cancer) and the censoring causes (e.g. deaths from heart diseases) may be dependent. Although many researchers have studied the mixture survival model to analyse survival data with non-negligible cure fractions, none has studied the mixture cure model in the presence of dependent censoring. To account for such dependence, we propose a more general cure model that allows for dependent censoring. We derive the cure models from the perspective of competing risks and model the dependence between the censoring time and the survival time by using a class of Archimedean copula models. Within this framework, we consider the parameter estimation, the cure detection and the two-sample comparison of latency distributions in the presence of dependent censoring when a proportion of patients is deemed cured. Large sample results by using martingale theory are obtained. We examine the finite sample performance of the proposed methods via simulation and apply them to analyse the surveillance epidemiology and end results prostate cancer data.

This paper proposes a nonparametric Bayesian framework called VariScan for simultaneous clustering, variable selection, and prediction in high-throughput regression settings. Poisson-Dirichlet processes are utilized to detect lower-dimensional latent clusters of covariates. An adaptive nonlinear prediction model is constructed for the response, achieving a balance between model parsimony and flexibility. Contrary to conventional belief, cluster detection is shown to be aposteriori consistent for a general class of models as the number of covariates and subjects grows. Simulation studies and data analyses demonstrate that VariScan often outperforms several well-known statistical methods.