Comparison of Statistical Methods of Haplotype Reconstruction and Logistic Regression for Association Studies


Book Description

Investigating association between disease and single nucleotide polymorphisms (SNPs) has been an approach for genetic association studies and more recently investigating association between disease and haplotypes has become another accepted method. Haplotypes are physically linked combinations of alleles from a stretch of DNA and can serve to increase power of finding an association due to interactions between inclusive SNPs and the increased area of chromosome that is taken into consideration. Determining haplotypes experimentally or by family studies is a costly and timeinefficient method, so haplotype reconstruction by statistical methods has become an adopted practice. The problem with computational methods is the extra. source of error from ambiguous haplotypes that has to be included in statistical analysis. This paper investigates methods of error management with three different 1ogistic regression packages, two of which are specific to analysis of genetic data. Methods are applied to simulated data and a data set looking for genetic risk factors for non-Hodgkin Lymphoma.




Applied Statistical Genetics with R


Book Description

Statistical genetics has become a core course in many graduate programs in public health and medicine. This book presents fundamental concepts and principles in this emerging field at a level that is accessible to students and researchers with a first course in biostatistics. Extensive examples are provided using publicly available data and the open source, statistical computing environment, R.




Introduction to Markov Chains


Book Description

Besides the investigation of general chains the book contains chapters which are concerned with eigenvalue techniques, conductance, stopping times, the strong Markov property, couplings, strong uniform times, Markov chains on arbitrary finite groups (including a crash-course in harmonic analysis), random generation and counting, Markov random fields, Gibbs fields, the Metropolis sampler, and simulated annealing. With 170 exercises.




Analysis of Complex Disease Association Studies


Book Description

According to the National Institute of Health, a genome-wide association study is defined as any study of genetic variation across the entire human genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight), or the presence or absence of a disease or condition. Whole genome information, when combined with clinical and other phenotype data, offers the potential for increased understanding of basic biological processes affecting human health, improvement in the prediction of disease and patient care, and ultimately the realization of the promise of personalized medicine. In addition, rapid advances in understanding the patterns of human genetic variation and maturing high-throughput, cost-effective methods for genotyping are providing powerful research tools for identifying genetic variants that contribute to health and disease. This burgeoning science merges the principles of statistics and genetics studies to make sense of the vast amounts of information available with the mapping of genomes. In order to make the most of the information available, statistical tools must be tailored and translated for the analytical issues which are original to large-scale association studies. Analysis of Complex Disease Association Studies will provide researchers with advanced biological knowledge who are entering the field of genome-wide association studies with the groundwork to apply statistical analysis tools appropriately and effectively. With the use of consistent examples throughout the work, chapters will provide readers with best practice for getting started (design), analyzing, and interpreting data according to their research interests. Frequently used tests will be highlighted and a critical analysis of the advantages and disadvantage complimented by case studies for each will provide readers with the information they need to make the right choice for their research. Additional tools including links to analysis tools, tutorials, and references will be available electronically to ensure the latest information is available. Easy access to key information including advantages and disadvantage of tests for particular applications, identification of databases, languages and their capabilities, data management risks, frequently used tests Extensive list of references including links to tutorial websites Case studies and Tips and Tricks




Graph Theory and Computing


Book Description

Graph Theory and Computing focuses on the processes, methodologies, problems, and approaches involved in graph theory and computer science. The book first elaborates on alternating chain methods, average height of planted plane trees, and numbering of a graph. Discussions focus on numbered graphs and difference sets, Euclidean models and complete graphs, classes and conditions for graceful graphs, and maximum matching problem. The manuscript then elaborates on the evolution of the path number of a graph, production of graphs by computer, and graph-theoretic programming language. Topics include FORTRAN characteristics of GTPL, design considerations, representation and identification of graphs in a computer, production of simple graphs and star topologies, and production of stars having a given topology. The manuscript examines the entropy of transformed finite-state automata and associated languages; counting hexagonal and triangular polyominoes; and symmetry of cubical and general polyominoes. Graph coloring algorithms, algebraic isomorphism invariants for graphs of automata, and coding of various kinds of unlabeled trees are also discussed. The publication is a valuable source of information for researchers interested in graph theory and computing.




A Statistical Approach to Genetic Epidemiology


Book Description

A Statistical Approach to Genetic Epidemiology After studying statistics and mathematics at the University of Munich and obtaining his doctoral degree from the University of Dortmund, Andreas Ziegler received the Johann-Peter-Süssmilch-Medal of the German Association for Medical Informatics, Biometry and Epidemiology for his post-doctoral work on “Model Free Linkage Analysis of Quantitative Traits” in 1999. In 2004, he was one of the recipients of the Fritz-Linder-Forum-Award from the German Association for Surgery.




The Fundamentals of Modern Statistical Genetics


Book Description

This book covers the statistical models and methods that are used to understand human genetics, following the historical and recent developments of human genetics. Starting with Mendel’s first experiments to genome-wide association studies, the book describes how genetic information can be incorporated into statistical models to discover disease genes. All commonly used approaches in statistical genetics (e.g. aggregation analysis, segregation, linkage analysis, etc), are used, but the focus of the book is modern approaches to association analysis. Numerous examples illustrate key points throughout the text, both of Mendelian and complex genetic disorders. The intended audience is statisticians, biostatisticians, epidemiologists and quantitatively- oriented geneticists and health scientists wanting to learn about statistical methods for genetic analysis, whether to better analyze genetic data, or to pursue research in methodology. A background in intermediate level statistical methods is required. The authors include few mathematical derivations, and the exercises provide problems for students with a broad range of skill levels. No background in genetics is assumed.




Statistical Genetics


Book Description

Statistical Genetics is an advanced textbook focusing on conducting genome-wide linkage and association analysis in order to identify the genes responsible for complex behaviors and diseases. Starting with an introductory section on statistics and quantitative genetics, it covers both established and new methodologies, providing the genetic and statistical theory on which they are based. Each chapter is written by leading researchers, who give the reader the benefit of their experience with worked examples, study design, and sources of error. The text can be used in conjunction with an associated website (www.genemapping.org) that provides supplementary material and links to downloadable software.




Genetic Dissection of Complex Traits


Book Description

The field of genetics is rapidly evolving and new medical breakthroughs are occuring as a result of advances in knowledge of genetics. This series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines. Five sections on the latest advances in complex traits Methods for testing with ethical, legal, and social implications Hot topics include discussions on systems biology approach to drug discovery; using comparative genomics for detecting human disease genes; computationally intensive challenges, and more




Molecular Epidemiology


Book Description

This book will serve as a primer for both laboratory and field scientists who are shaping the emerging field of molecular epidemiology. Molecular epidemiology utilizes the same paradigm as traditional epidemiology but uses biological markers to identify exposure, disease or susceptibility. Schulte and Perera present the epidemiologic methods pertinent to biological markers. The book is also designed to enumerate the considerations necessary for valid field research and provide a resource on the salient and subtle features of biological indicators.