The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem

<p>Abstract</p> <p>Background</p> <p>This paper discusses the problem of automated annotation. It is a continuation of the previous work on the A⁴-algorithm (Adaptive algorithm of automated annotation) developed by Leontovich and others.</p> <p>Results</p> <p>A number of new statistics for the automated annotation of biological sequences is introduced. All these statistics are based on the likelihood ratio criterion.</p> <p>Conclusion</p> <p>Some of the statistics yield a prediction quality that is significantly higher (up to 1.5 times higher) in comparison with the results obtained with the A⁴-procedure.</p

Adjusting for sex and anti-CCP levels in linkage analysis of rheumatoid arthritis

We incorporate population effects of sex and antibodies directed against cyclic citrullinated peptides (anti-CCP) into the linkage analysis of rheumatoid arthritis (RA) with microsatellites data provided by the North American Rheumatoid Arthritis Consortium in Genetic Analysis Workshop 15

Analysis of time-to-event for observational studies: Guidance to the use of intensity models

This paper provides guidance for researchers with some mathematical background on the conduct of time-to-event analysis in observational studies based on intensity (hazard) models. Discussions of basic concepts like time axis, event definition and censoring are given. Hazard models are introduced, with special emphasis on the Cox proportional hazards regression model. We provide check lists that may be useful both when fitting the model and assessing its goodness of fit and when interpreting the results. Special attention is paid to how to avoid problems with immortal time bias by introducing time-dependent covariates. We discuss prediction based on hazard models and difficulties when attempting to draw proper causal conclusions from such models. Finally, we present a series of examples where the methods and check lists are exemplified. Computational details and implementation using the freely available R software are documented in Supplementary Material. The paper was prepared as part of the STRATOS initiative.Comment: 28 pages, 12 figures. For associated Supplementary material, see http://publicifsv.sund.ku.dk/~pka/STRATOSTG8

Integration of gene ontology pathways with North American Rheumatoid Arthritis Consortium genome-wide association data via linear modeling

We describe an empirical Bayesian linear model for integration of functional gene annotation data with genome-wide association data. Using case-control study data from the North American Rheumatoid Arthritis Consortium and gene annotation data from the Gene Ontology, we illustrate how the method can be used to prioritize candidate genes for further investigation

Dynamic predicting by landmarking as an alternative for multi-state modeling: an application to acute lymphoid leukemia data

This paper considers the problem of obtaining a dynamic prediction for 5-year failure free survival after bone marrow transplantation in ALL patients using data from the EBMT, the European Group for Blood and Marrow Transplantation. The paper compares the new landmark methodology as developed by the first author and the established multi-state modeling as described in a recent Tutorial in Biostatistics in Statistics in Medicine by the second author and colleagues. As expected the two approaches give similar results. The landmark methodology does not need complex modeling and leads to easy prediction rules. On the other hand, it does not give the insight in the biological processes as obtained for the multi-state model

Multivariate random effects meta-analysis of diagnostic tests with multiple thresholds

Background. Bivariate random effects meta-analysis of diagnostic tests is becoming a well established approach when studies present one two-by-two table or one pair of sensitivity and specificity. When studies present multiple thresholds for test positivity, usually meta-analysts reduce the data to a two-by-two table or take one threshold value at a time and apply the well developed meta-analytic approaches. However, this approach does not fully exploi

Travel-Related Venous Thrombosis: Results from a Large Population-Based Case Control Study (MEGA Study)

BACKGROUND: Recent studies have indicated an increased risk of venous thrombosis after air travel. Nevertheless, questions on the magnitude of risk, the underlying mechanism, and modifying factors remain unanswered. METHODS AND FINDINGS: We studied the effect of various modes and duration of travel on the risk of venous thrombosis in a large ongoing case-control study on risk factors for venous thrombosis in an unselected population (MEGA study). We also assessed the combined effect of travel and prothrombotic mutations, body mass index, height, and oral contraceptive use. Since March 1999, consecutive patients younger than 70 y with a first venous thrombosis have been invited to participate in the study, with their partners serving as matched control individuals. Information has been collected on acquired and genetic risk factors for venous thrombosis. Of 1,906 patients, 233 had traveled for more than 4 h in the 8 wk preceding the event. Traveling in general was found to increase the risk of venous thrombosis 2-fold (odds ratio [OR] 2.1; 95% confidence interval [CI] 1.5–3.0). The risk of flying was similar to the risks of traveling by car, bus, or train. The risk was highest in the first week after traveling. Travel by car, bus, or train led to a high relative risk of thrombosis in individuals with factor V Leiden (OR 8.1; 95% CI 2.7–24.7), in those who had a body mass index of more than 30 kg/m(2) (OR 9.9; 95% CI 3.6–27.6), in those who were more than 1.90 m tall (OR 4.7; 95% CI 1.4–15.4), and in those who used oral contraceptives (estimated OR > 20). For air travel these synergistic findings were more apparent, while people shorter than 1.60 m had an increased risk of thrombosis after air travel (OR 4.9; 95% CI 0.9–25.6) as well. CONCLUSIONS: The risk of venous thrombosis after travel is moderately increased for all modes of travel. Subgroups exist in which the risk is highly increased

TCT-47 Two-Year Clinical Outcome of the TWENTE Trial, a Randomized Controlled Trial Comparing Second-Generation Zotarolimus-Eluting Resolute Stents Versus Everolimus-Eluting Xience V Stents in Real-World Patients

Background: In the prospective, randomized TWENTE trial, the zotarolimus-eluting Resolute stent was at 1 year follow-up non-inferior to the everolimus-eluting Xience V stent for the primary endpoint target vessel failure. This composite endpoint consisted of cardiac death, clinically indicated target vessel revascularization, or target vessel-related myocardial infarction (MI). So far, few long-term data of prospective head-to-head comparisons between both DES have been reported. Methods: Patients requiring percutaneous coronary interventions (PCI) with DES implantation at Thoraxcentrum Twente in Enschede were randomization between Resolute (Medtronic Vascular, Santa Rosa, CA, USA) and Xience V (Abbott Vascular, Santa Clara, CA, USA) in a 1:1 fashion. Inclusion of all coronary or bypass graft lesions and all clinical settings was permitted except for primary PCI (i.e. acute ST-elevation myocardial infarction (STEMI) was an exclusion criterion). Both external monitoring and clinical event adjudication were performed by an independent external contract research organization (Cardialysis, Rotterdam, the Netherlands). Two year clinical follow-up was performed as indicated in the study protocol. Results: A total of 1,391 patients were enrolled in the TWENTE trial between June 2008 and August 2010. The study population comprised 21.6% diabetics with a vast majority of complex lesions and “off-label” indications for drug-eluting stents (77.4%). Patients presented with either stable angina (48.5%) or unstable angina/Non-STEMI (51.5%). Demographics, baseline angiographic and procedural data, and 2-year clinical follow-up data will be presented. This includes the primary endpoint of the study: Target vessel failure (TVF) at 2 year follow-up. Secondary endpoints include the individual components of the primary endpoint and the incidence of very late stent thrombosis. In addition, results of subgroup analyses will be reported. Conclusions: Results of pre-specified analyses of 2-year clinical outcome of the TWENTE trial will be presented at TCT 2012