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24 results on '"Verzilli, Claudio"'

2. Methods for the analysis of incomplete longitudinal data

Author

Verzilli, Claudio John and Carpenter, J.

Subjects
614.420285
Abstract

Unplanned missing data commonly arise in longitudinal trials. When the mechanism driving the missing data process is related to the outcome under investigation, traditional methods of analysis may yield seriously biased parameter estimates. Motivated by data from two clinical trials, this thesis explores various approaches to dealing with data incompleteness. In the first part, a Monte Carlo EM algorithm is developed and used to fit so called random-co efficient-based dropout models; these models relate the probability of a patient's dropout in follow-up studies to some subject-specific characteristics such as their deviation from the average rate of progression of the disease over time. The approach is used to model incomplete data from a 5-year study of patients with Parkinson's disease. The validity of the results obtained using these methods however, depends in general on distributional and modelling assumptions about the missing data that are inherently untestable as no data were collected. For this reason, many have advocated the need for a sensitivity analysis aimed at assessing the robustness of the conclusions from an analysis that ignores the missing data mechanism. In the second part of the thesis we address these issues. In particular, we present results from sensitivity analyses based on local influence and sampling-based methods used in conjunction with the random-coefficient-based dropout model described in the first part. Recently, a more formal approach to sensitivity analysis for missing data problems has been proposed whereby traditional point estimates are replaced by intervals encoding our lack of knowledge due to incompleteness of the data. In the third part of the thesis, we extend these methods to longitudinal ordinal data. Also, for cross-sectional discrete data having distribution belonging to the exponential family, we propose using the proportion of possible estimates of a parameter of interest, over all solutions corresponding to all sample completions, as a measure of ignorance. We develop a computationally efficient algorithm to calculate this proportion and illustrate our methods using data from a dental pain trial.

Published
2003
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3. An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

Author

Nelson, Matthew R., Wegmann, Daniel, Ehm, Margaret G., Kessner, Darren, St. Jean, Pamela, Verzilli, Claudio, Shen, Judong, Tang, Zhengzheng, Bacanu, Silviu-Alin, Fraser, Dana, Warren, Liling, Aponte, Jennifer, Zawistowski, Matthew, Liu, Xiao, Zhang, Hao, Zhang, Yong, Li, Jun, Li, Yun, Li Li, Woollard, Peter, Topp, Simon, Hall, Matthew D., Nangle, Keith, Wang, Jun, Abecasis, Gonçalo, Cardon, Lon R., Zöllner, Sebastian, Whittaker, John C., Chissoe, Stephanie L., Novembre, John, and Mooser, Vincent

Published
2012
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4. Gene-centric Association Signals for Lipids and Apolipoproteins Identified via the HumanCVD BeadChip

Author

Talmud, Philippa J., Drenos, Fotios, Shah, Sonia, Shah, Tina, Palmen, Jutta, Verzilli, Claudio, Gaunt, Tom R., Pallas, Jacky, Lovering, Ruth, Li, Kawah, Casas, Juan Pablo, Sofat, Reecha, Kumari, Meena, Rodriguez, Santiago, Johnson, Toby, Newhouse, Stephen J., Dominiczak, Anna, Samani, Nilesh J., Caulfield, Mark, Sever, Peter, Stanton, Alice, Shields, Denis C., Padmanabhan, Sandosh, Melander, Olle, Hastie, Claire, Delles, Christian, Ebrahim, Shah, Marmot, Michael G., Smith, George Davey, Lawlor, Debbie A., Munroe, Patricia B., Day, Ian N., Kivimaki, Mika, Whittaker, John, Humphries, Steve E., and Hingorani, Aroon D.

Published
2009
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8. Bayesian Meta-Analysis of Genetic Association Studies with Different Sets of Markers

Author

Verzilli, Claudio, Shah, Tina, Casas, Juan P., Chapman, Juliet, Sandhu, Manjinder, Debenham, Sally L., Boekholdt, Matthijs S., Khaw, Kay Tee, Wareham, Nicholas J., Judson, Richard, Benjamin, Emelia J., Kathiresan, Sekar, Larson, Martin G., Rong, Jian, Sofat, Reecha, Humphries, Steve E., Smeeth, Liam, Cavalleri, Gianpiero, Whittaker, John C., and Hingorani, Aroon D.

Published
2008
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9. A novel protective prion protein variant that colocalizes with kuru exposure

Author

Mead, Simon, Whitfield, Jerome, Poulter, Mark, Shah, Paresh, Uphill, James, Campbell, Tracy, Al-Dujaily, Huda, Hammerich, Holger, Beck, Jon, Mein, Charles A., Verzilli, Claudio, Whittaker, John, Alpers, Michael P., and Collinge, John

Subjects
Kuru -- Genetic aspects, Kuru -- Demographic aspects, Kuru -- Control, Gene mutations -- Analysis, Genetic polymorphisms -- Research, Papua New Guinea -- Health aspects
Abstract

The study performed genetic and selected clinical and genealogic assessments of persons exposed to kuru, an epidemic prion disease that affected the Fore linguistic group of the Eastern Highlands Province of Papua New Guinea. Findings reveal a novel prion protein gene variant, G127V, which is an acquired prion disease resistance factor selected during the kuru epidemic.

Published
2009

10. Bayesian graphical models for genomewide association studies

Author

Verzilli, Claudio J., Stallard, Nigel, and Whittaker, John C.

Subjects
Genetic research -- Models, Genomes -- Research, Bayesian statistical decision theory, Biological sciences
Abstract

A computationally efficient approach is described to mining genotype-phenotype association that scales to the size of the data sets currently being collected. A discrete graphical model is used as a data-mining tool, searching for single-or multilocus patterns of association around a causative site.

Published
2006

11. Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration

Author

Angelakopoulou, Aspasia, Shah, Tina, Sofat, Reecha, Shah, Sonia, Berry, Diane J., Cooper, Jackie, Palmen, Jutta, Tzoulaki, Ioanna, Wong, Andrew, Jefferis, Barbara J., Maniatis, Nikolas, Drenos, Fotios, Gigante, Bruna, Hardy, Rebecca, Laxton, Ross C., Leander, Karin, Motterle, Anna, Simpson, Iain A., Smeeth, Liam, Thomson, Andy, Verzilli, Claudio, Kuh, Diana, Ireland, Helen, Deanfield, John, Caulfield, Mark, Wallace, Chris, Samani, Nilesh, Munroe, Patricia B., Lathrop, Mark, Fowkes, F. Gerry R., Marmot, Michael, Whincup, Peter H., Whittaker, John C., de Faire, Ulf, Kivimaki, Mika, Kumari, Meena, Hypponen, Elina, Power, Chris, Humphries, Steve E., Talmud, Philippa J., Price, Jackie, Morris, Richard W., Ye, Shu, Casas, Juan P., and Hingorani, Aroon D.

Published
2012
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13. A Comparison of Bayesian and Frequentist Approaches to Incorporating External Information for the Prediction of Prostate Cancer Risk

Author

Newcombe, Paul J., primary, Reck, Brian H., additional, Sun, Jielin, additional, Platek, Greg T., additional, Verzilli, Claudio, additional, Kader, A. Karim, additional, Kim, Seong-Tae, additional, Hsu, Fang-Chi, additional, Zhang, Zheng, additional, Zheng, S. Lilly, additional, Mooser, Vincent E., additional, Condreay, Lynn D., additional, Spraggs, Colin F., additional, Whittaker, John C., additional, Rittmaster, Roger S., additional, and Xu, Jianfeng, additional

Published
2012
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14. Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration

Author

Angelakopoulou, Aspasia, primary, Shah, Tina, additional, Sofat, Reecha, additional, Shah, Sonia, additional, Berry, Diane J., additional, Cooper, Jackie, additional, Palmen, Jutta, additional, Tzoulaki, Ioanna, additional, Wong, Andrew, additional, Jefferis, Barbara J., additional, Maniatis, Nikolas, additional, Drenos, Fotios, additional, Gigante, Bruna, additional, Hardy, Rebecca, additional, Laxton, Ross C., additional, Leander, Karin, additional, Motterle, Anna, additional, Simpson, Iain A., additional, Smeeth, Liam, additional, Thomson, Andy, additional, Verzilli, Claudio, additional, Kuh, Diana, additional, Ireland, Helen, additional, Deanfield, John, additional, Caulfield, Mark, additional, Wallace, Chris, additional, Samani, Nilesh, additional, Munroe, Patricia B., additional, Lathrop, Mark, additional, Fowkes, F. Gerry R., additional, Marmot, Michael, additional, Whincup, Peter H., additional, Whittaker, John C., additional, de Faire, Ulf, additional, Kivimaki, Mika, additional, Kumari, Meena, additional, Hypponen, Elina, additional, Power, Chris, additional, Humphries, Steve E., additional, Talmud, Philippa J., additional, Price, Jackie, additional, Morris, Richard W., additional, Ye, Shu, additional, Casas, Juan P., additional, and Hingorani, Aroon D., additional

Published
2011
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16. Defining the True Sensitivity of Culture for the Diagnosis of Melioidosis Using Bayesian Latent Class Models

Author

Limmathurotsakul, Direk, primary, Jamsen, Kris, additional, Arayawichanont, Arkhom, additional, Simpson, Julie A., additional, White, Lisa J., additional, Lee, Sue J., additional, Wuthiekanun, Vanaporn, additional, Chantratita, Narisara, additional, Cheng, Allen, additional, Day, Nicholas P. J., additional, Verzilli, Claudio, additional, and Peacock, Sharon J., additional

Published
2010
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24. Are further genetic factors associated with the risk of developing variant Creutzfeldt–Jakob disease?

Author

Kretzschmar, Hans, Illig, Thomas, Mead, Simon, Poulter, Mark, Uphill, James, Beck, John, Whitfield, Jerome, Webb, Thomas E F, Campbell, Tracy, Adamson, Gary, Deriziotis, Pelagia, Tabrizi, Sarah J, Hummerich, Holger, Verzilli, Claudio, Alpers, Michael P, Whittaker, John C, and Collinge, John

Subjects
*AGE factors in disease, *ALLELES, *CHROMOSOMES, *COMPARATIVE studies, *CREUTZFELDT-Jakob disease, *DNA, *GENETIC polymorphisms, *GENETICS, *RESEARCH methodology, *MEDICAL cooperation, *MEMBRANE proteins, *PRION diseases, *PRIONS, *PUBLIC health surveillance, *QUALITY control, *RESEARCH, *RESEARCH funding, *STATISTICS, *DATA analysis, *EVALUATION research, *SEQUENCE analysis, *GENOTYPES
Abstract

Background: Human and animal prion diseases are under genetic control, but apart from PRNP (the gene that encodes the prion protein), we understand little about human susceptibility to bovine spongiform encephalopathy (BSE) prions, the causal agent of variant Creutzfeldt-Jakob disease (vCJD).Methods: We did a genome-wide association study of the risk of vCJD and tested for replication of our findings in samples from many categories of human prion disease (929 samples) and control samples from the UK and Papua New Guinea (4254 samples), including controls in the UK who were genotyped by the Wellcome Trust Case Control Consortium. We also did follow-up analyses of the genetic control of the clinical phenotype of prion disease and analysed candidate gene expression in a mouse cellular model of prion infection.Findings: The PRNP locus was strongly associated with risk across several markers and all categories of prion disease (best single SNP [single nucleotide polymorphism] association in vCJD p=2.5 x 10(-17); best haplotypic association in vCJD p=1 x 10(-24)). Although the main contribution to disease risk was conferred by PRNP polymorphic codon 129, another nearby SNP conferred increased risk of vCJD. In addition to PRNP, one technically validated SNP association upstream of RARB (the gene that encodes retinoic acid receptor beta) had nominal genome-wide significance (p=1.9 x 10(-7)). A similar association was found in a small sample of patients with iatrogenic CJD (p=0.030) but not in patients with sporadic CJD (sCJD) or kuru. In cultured cells, retinoic acid regulates the expression of the prion protein. We found an association with acquired prion disease, including vCJD (p=5.6 x 10(-5)), kuru incubation time (p=0.017), and resistance to kuru (p=2.5 x 10(-4)), in a region upstream of STMN2 (the gene that encodes SCG10). The risk genotype was not associated with sCJD but conferred an earlier age of onset. Furthermore, expression of Stmn2 was reduced 30-fold post-infection in a mouse cellular model of prion disease.Interpretation: The polymorphic codon 129 of PRNP was the main genetic risk factor for vCJD; however, additional candidate loci have been identified, which justifies functional analyses of these biological pathways in prion disease. [ABSTRACT FROM AUTHOR]

Published
2009
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