Related books on 'genotyping'
Return to life science book listNumber of products: 343
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by: Yun Li publisher: ProQuest, UMI Dissertation Publishing, published: 2011-09-08 ASIN: 1243701439 EAN: 9781243701435 Searches for the elusive genetic mechanisms underlying complex diseases have long challenged human geneticists. Recently, genome-wide association studies (GWAS) have successfully identified many complex disease susceptibility loci by genotyping a subset of several hundred thousand common genetic variants across many individuals. With the rapid deployment of next-generation sequencing technologies, it is anticipated that future genetic association studies will be able to more comprehensively survey genetic variation, both to identify new loci that were missed in the original round of genome-wide association studies and to finely characterize the contributions of identified loci. GWAS, whether in the current genotyping-based form or in the anticipated sequencing-based form, pose a range of computational and analytical challenges. I first propose and implement a computationally efficient hidden Markov model that can rapidly reconstruct the two chromosomes carried by each individual in a study. To achieve this goal, the methods combine partial genotype or sequence data for each individual with additional information on additional individuals. Comparisons with standard haplotypers in both simulated and real datasets show that the proposed method is at least comparable and more computational efficient. I next extend my method for imputing genotypes at untyped SNP loci. Specifically, I consider how my approach can be used to assess several million common variants that are not directly genotyped in a typical association study but for which data are available in public databases. I describe how the extended method performs in a wide range of simulated and real settings. Finally, I consider how low-depth shot-gun resequencing data on a large number of individuals can be combined to provide accurate estimates of individual sequences. This approach should speed up the advent of large-scale genome resequencing studies and facilitate the identification of rare variants that contribute to disease susceptibility and that cannot be adequately assessed with current genotyping-based GWAS approaches. My methods are flexible enough to accommodate phased haplotype data, genotype data, or re-sequencing data as input and can utilize public resources such as the HapMap consortium and the 1000 Genomes Project that now include data on several million genetic variants typed on hundreds of individuals. |
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by: Norman R. Relkin publisher: New York Academy of Sciences, published: 1996-10 ASIN: 1573310484 EAN: 9781573310482 sales rank: 8920208 |
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publisher: New York Academy of Sciences, published: 1996-06 ASIN: 1573310492 EAN: 9781573310499 sales rank: 10558983 |
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by: Dan-Oscar Antson publisher: Uppsala Universitet, published: 2001-06 ASIN: 9155450571 EAN: 9789155450571 |
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publisher: Springer, published: 2008-10-23 ASIN: 1934115932 EAN: 9781934115930 sales rank: 1739839 Blood samples have consistently proven to be a key source of genetic material for a wide variety of diagnostic or research purposes. In DNA and RNA Profiling in Human Blood: Methods and Protocols, leading international experts contribute both established and recently developed protocols for complex and high-throughput DNA and RNA profiling. Divided into two thorough sections, the volume concentrates on DNA profiling for blood cell antigens through methods on high-throughput multiplex approaches and SNP typing, along with RNA profiling in blood cells addressing certain blood cell types such as platelets, reticulocytes, and megakaryocytes. Written in the highly successful Methods in Molecular Biology™ series format, all of the chapters include brief introductions on the subject, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, as well as the Notes section which highlights tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, DNA and RNA Profiling in Human Blood: Methods and Protocols is an ideal guide to the molecular profiling approaches that have opened up this broad field of research and have shown great promise in the further identifying of disease markers in blood. |
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by: Margaret Anne Taub publisher: ProQuest, UMI Dissertation Publishing, published: 2011-09-09 ASIN: 1243768320 EAN: 9781243768322 The many areas of research of high-throughput computational biology provide endless opportunities for methodological contributions by statisticians. In this thesis, we present results in two main areas, one just emerging and one well-established. In Part I of this thesis, we present new results related to the analysis of high-throughput sequencing data. The last year or so has seen the emergence of many new technologies aimed at enabling the massively parallel sequencing of many molecules of DNA simultaneously. This technological leap forward has enabled scientists to conduct exciting experiments that were impossible with previous technologies, and statisticians are being flooded with new data to analyze. We focus on two analytical problems related to new short-read sequencing technologies, each aimed at a different aspect of the goal of quantifying gene expression using sequencing. First, we present a new method aimed at determining which gene a particular sequence fragment originated from, in order to obtain better unbiased estimates of gene expression. Second, we develop a new empirical Bayes test statistic aimed at measuring differential gene expression between two samples which have been sequenced. Both problems combine fundamental statistical concepts with cutting-edge biology research. Part II of this thesis focuses on genetic analysis of the mouse model organism, a more established area of both biological and statistical inquiry. We present an analysis of the performance of a high-throughput microarray in measuring genotype information in a pooled set of mice, for the purposes of detecting a disease-carrying mutation locus. This problem combines relatively new technological advances with classical theories of linkage analysis. |
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publisher: Humana Press, published: 2010-11-19 ASIN: 1617375713 EAN: 9781617375712 sales rank: 4720730 Expert researchers and physician/clinicians describe in detail the newest and most commonly used technologies today in this rapidly advancing field. The authors provide readily reproducible methods for assessing the functional consequences of a certain polymorphism, evaluate the variety of genotyping platforms currently available, and discuss the management of pharmacogenomic information. Highlights include techniques for making a snapshot of the allele-specific variation in human gene expression, genome wide analysis of allele-specific expression using oligo microarrays, in vivo assays with HaploChIP, SNP genotyping in DNA pools, and PharmGKB, the pharmacogenetics and pharmacogenomics knowledge base. The methodologies for genotyping include denaturing high-performance liquid chromarography, pyrosequencing, kinetic-fluorescence detection, mass spectrometry, and TaqMan assay for insertion/deletions. |
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by: American Water Works Association Researc publisher: Intl Water Assn, published: 2007-10-30 ASIN: 1843399474 EAN: 9781843399476 |
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by: Edited by Jia Zhang and Kai Li publisher: Transworld Research Network, published: 2010-06-01 ASIN: 8178954672 EAN: 9788178954677 Enzymatic processes have been known to mankind for several millenia and even mentioned in the story of Noah in the Bible on the making of wine, but their catalytic roles in life have only been discovered at the end of the 19th century. However during the last fifty years or so, the USES of enzymes not only for solving some of the secrets of life but for the development of commercial goods have made major advances. More recent discoveries on enzymes has revolutionized biomedical research and it is now common knowledge that novel health care and life quality developments could be attributed to the discovery and optimal application of a new variety of enzymes. For instance, the identification of DNA polymerases, restriction endonuclease, reverse transcriptase, ribozyme, and telomerase have greatly changed our understanding of life and led to technological revolution including DNA sequencing, gene cloning, gene therapy, and many other milestones in modern biomedicine. Two main strategies have been developed for the optimal use of enzymes: modification of the enzymatic properties of known enzymes by molecular engineering or other methods, and the direct application of known enzymes combined to other components without modification of their enzymatic properties. This book is not dealing with the discovery of new enzymes. Instead, it is a book focusing on the discovery and development of novel applications to old enzymes. DNA polymerase with proofreading activity has been known for four decades. This book discussed the strategies for transforming the high fidelity of the proofreading polymerase into nucleotide identification switches. New applications of the high fidelity DNA polymerases are not only for mutation assay, but also for the development of the third generation of high speed sequencing technologies. Readers of this book will find how an old enzyme is revitalized in the post-genomic era, such as in the applications of viral load assay and in the rare mutation detection. This book content is based on some of our recent publications. We are in debt to those who encouraged us or collaborated with us in the recent past years. Particularly, we would like to thank Professors P. Sirois from Sherbrooke University, Canada and S.S. Sommer at City of Hope National Medical Center, USA for their support. We also want to acknowledge the help of our colleagues Drs. J.R. Padinas, H.L Gao and J.S. Saldivar, as well as our son Wenbing Li for his proofreading of some book chapters. We would also like to acknowledge the generous editorial assistance of our student Li Xiao. |
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by: Nicole T Vu publisher: Available through the National Technical Information Service, published: 1999 ASIN: B0006R4HQK |