Download or read book DNA Methylation Microarrays written by Sun-Chong Wang and published by CRC Press. This book was released on 2008-04-24 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing an interface between dry-bench bioinformaticians and wet-lab biologists, DNA Methylation Microarrays: Experimental Design and Statistical Analysis presents the statistical methods and tools to analyze high-throughput epigenomic data, in particular, DNA methylation microarray data. Since these microarrays share the same under
Download or read book The Use of Genome Wide DNA Methylation Microarray to Study Both the Common and Rare Diseases written by Kit-San Yeung and published by . This book was released on 2017-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "The Use of Genome-wide DNA Methylation Microarray to Study Both the Common and Rare Diseases" by Kit-san, Yeung, 楊傑燊, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: DNA methylation plays many important roles in human physiology such as imprinting and X chromosome inactivation (XCI), and therefore disruption in DNA methylation can lead to disease development. The objective of this study is to study the role of DNA methylation in both the common and rare disease, using Systemic Lupus Erythematosus (SLE) and chromosome X translocation as the example respectively. The genome-wide DNA methylation analysis was studied by Illumina HumanMethylation450 BeadChip, which is the microarray that allows the detection of more than 480,000 CpG sites across 99% of reference sequence genes. Numerous studies have shown that hypomethylation occurred in specific genes of SLE patients, and genome-wide DNA methylation analysis has never been performed in Chinese before. Since DNA methylation can be ethnicity-specific, we aim to identify the Chinese-specific DNA methylation pattern in SLE patients. Microarray results showed that differential DNA methylation changes were loci-specific, where 36 CpG sites showed loss of DNA methylation while 8 of them showed gain of it, representing 24 genes and 7 genes respectively. In order to replicate the microarray findings, bisulfite pyrosequencing was performed in an additional cohort of 100 patients and 100 controls on four hypomethylated genes, which were selected based on their relevance with immunity. Bisulfite pyrosequencing confirmed the microarray result that hypomethylation occurred in SLE, and were associated with increased in the corresponding gene's mRNA expressions. Gene ontology analysis revealed that hypomethylated genes identified in the microarray study were overrepresented in type I interferon pathway, where type I interferon has long been implicated in SLE pathogenesis. Therefore this study also support the importance of type I interferon in SLE from the epigenetic point of view. X;autosome translocation is a rare condition and the autosome with chromosome X translocated on can be inactivated by XCI, but DNA methylation change is rarely used to investigate the spread of XCI. In this study, we aim to identify genes subjected to XCI in X;15 translocation using the DNA methylation microarray. Results of microarray showed that 586 CpG sites spanning the long arm of chromosome 15 had DNA methylation gain of more than 20%. Since genes subjected to XCI are known to have gain of DNA methylation in their corresponding CpG-island promoters, the analysis was then focused on CpG sites in these regions, and a total of 75 sites representing 24 genes were hypermethylated. Nearly all of these CpG sites are located in region proximal to the breakpoint, from 15q11.2 to 15q21.3 accounting for 35Mb, suggesting that XCI was spread to the proximal region of 15q. Gain of DNA methylation, especially in the CpG-island promoter, can result in functional inactivation of genes, and therefore could explain the worsen phenotype of the patient. In conclusion, we successfully demonstrated the use of genome-wide DNA methylation microarray in different diseases, allowing the identification of genes or pathways important in diseases and opened the door for further investigation of the effect of these differentially methylated genes on disease. DOI: 10.5353/th_b5334844 Subjects: DNA - Methylation Medical genetics
Download or read book Discovery of Problematic Probes in Illumina DNA Methylation Microarrays written by Yi-an Chen and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Microarray Innovations written by Gary Hardiman and published by CRC Press. This book was released on 2009-04-02 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, high-density DNA microarrays have revolutionized biomedical research and drug discovery efforts by the pharmaceutical industry. Their efficacy in identifying and prioritizing drug targets based on their ability to confirm a large number of gene expression measurements in parallel has become a key element in drug discovery. Microarr
Download or read book Epigenomics in Health and Disease written by Mario Fraga and published by Academic Press. This book was released on 2015-10-12 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenomics in Health and Disease discusses the next generation sequencing technologies shaping our current knowledge with regards to the role of epigenetics in normal development, aging, and disease. It includes the consequences for diagnostics, prognostics, and disease-based therapies made possible by the study of the complete set of epigenetic modifications to the genetic material of human cells. With coverage pertinent to both basic biology and translational research, the book will be of particular interest for medical and bioscience researchers and students seeking current translational knowledge in epigenesis and epigenomics. Coverage includes the latest findings on epigenome-wide research in disease-based profiling, epidemiological implications, epigenome-wide epigenetic studies, the cancer epigenome, and other pervasive disease categories. Presents critical reviews that provide the means for reviewing and analyzing the epigenome as a whole, also discussing its translational potential Combines basic epigenomic knowledge with methodological and biostatistical topics related to technology and data analysis Includes coverage of relatively new topics, including DNA methylation dynamics during development and differentiation, genome-wide histone post-translational modifications during development and differentiation, and genome-wide DNA methylation changes during aging
Download or read book Epigenetic Mechanisms of Gene Regulation written by Vincenzo E. A. Russo and published by . This book was released on 1996 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many inheritable changes in gene function are not explained by changes in the DNA sequence. Such epigenetic mechanisms are known to influence gene function in most complex organisms and include effects such as transposon function, chromosome imprinting, yeast mating type switching and telomeric silencing. In recent years, epigenetic effects have become a major focus of research activity. This monograph, edited by three well-known biologists from different specialties, is the first to review and synthesize what is known about these effects across all species, particularly from a molecular perspective, and will be of interest to everyone in the fields of molecular biology and genetics.
Download or read book Development of Oligonucleotide Microarray for High Throughput DNA Methylation Analysis written by Xiaopeng Li and published by . This book was released on 2008 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA methylation is a key event regulating gene expression. DNA methylation analysis plays a pivotal role in unlocking association of epigenetic events with cancer. However, simultaneous evaluation of the methylation status of multiple genes is still a technical challenge. Microarray is a promising approach for high-throughput analysis of the methylation status at numerous CpG sites within multiple genes of interest. In this dissertation study, we conducted a systematic study to examine the use of microarray methods for methylation analysis. First, a robust universal microarray was established with more flexible in design and content, and potential cost saving over commercial arrays. In order to produce high quality microarray data, we optimized the attachment chemistry for the modified oligonucleotides, searched for the good combination of fluorescent dyes, and hybridization conditions. To improve the specificity of the microarray, we conducted a study to experimentally search for a set of highly discriminative tag Sequences. Second, SBE-TAGs microarray was successfully adapted from the SNP detection for methylation analysis of multiple genes. SBE-TAGs microarray performed quite well in multiplex methylation analysis of cell lines if a standard calibration curve method was used. 10 CpG sites of 9 tumor suppressor genes (MGMT, GATA4, HLTF, SOCS1, p16, RASSF2, CHFR, TPEF, and Reprimo) were selected for this study. Third, a novel method called CHZMA (Competing-Hybridization- Zipcode-MicroArray) was developed for methylation analysis of tumor tissue samples, which is based on two steps of hybridization to achieve the specific detection of methylation on microarray. On the basis of analysis of seven genes (MGMT, GATA4, HLTF, SOCS1, RASSF2, ER, 3-OST-2), we found that the CHZMA assay can robustly detect methylation of multiple genes in the samples containing as low as 10% of methylated DNA. With the strict control group test and statistical analysis, CHZMA can be a good high-throughput method in place of MSP for methylation analysis of tumor tissue samples. These studies provide reliable and robust tools for methylation analysis, and could be used for cancer prognosis and diagnosis in the future.
Download or read book Nutritional Epigenomics written by and published by Academic Press. This book was released on 2019-07-20 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nutritional Epigenomics offers a comprehensive overview of nutritional epigenomics as a mode of study, along with nutrition’s role in the epigenomic regulation of disease, health and developmental processes. Here, an expert team of international contributors introduces readers to nutritional epigenomic regulators of gene expression, our diet’s role in epigenomic regulation of disease and disease inheritance, caloric restriction and exercise as they relate to recent epigenomic findings, and the influence of nutritional epigenomics over circadian rhythms, aging and longevity, and fetal health and development, among other processes. Disease specific chapters address metabolic disease (obesity and diabetes), cancer, and neurodegeneration, among other disorders. Diet-gut microbiome interactions in the epigenomic regulation of disease are also discussed, as is the role of micronutrients and milk miRNAs in epigenetic regulation. Finally, chapter authors examine ongoing discussions of race and ethnicity in the social-epigenomic regulation of health and disease. Empowers the reader to employ nutritional epigenomics approaches in their own research Discusses the latest topics in nutritional epigenomics in the regulation of aging, circadian rhythm, inheritance and fetal development, as well as metabolism and disease Offers a full grounding in epigenetic reprogramming and nutritional intervention in the treatment and prevention of disease, as informed by population-based studies
Download or read book Central Nervous System Tumours written by Thomas James Deeley and published by . This book was released on 1974 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Microarrays Part A Array Platforms and Wet Bench Protocols written by and published by Elsevier. This book was released on 2011-08-19 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern DNA microarray technologies have evolved over the past 25 years to the point where it is now possible to take many million measurements from a single experiment. These two volumes, Parts A & B in the Methods in Enzymology series provide methods that will shepard any molecular biologist through the process of planning, performing, and publishing microarray results. Part A starts with an overview of a number of microarray platforms, both commercial and academically produced and includes wet bench protocols for performing traditional expression analysis and derivative techniques such as detection of transcription factor occupancy and chromatin status. Wet-bench protocols and troubleshooting techniques continue into Part B. These techniques are well rooted in traditional molecular biology and while they require traditional care, a researcher that can reproducibly generate beautiful Northern or Southern blots should have no difficulty generating beautiful array hybridizations. Data management is a more recent problem for most biologists. The bulk of Part B provides a range of techniques for data handling. This includes critical issues, from normalization within and between arrays, to uploading your results to the public repositories for array data, and how to integrate data from multiple sources. There are chapters in Part B for both the debutant and the expert bioinformatician. Provides an overview of platforms Includes experimental design and wet bench protocols Presents statistical and data analysis methods, array databases, data visualization and meta-analysis
Download or read book Statistical Analysis of Microarray Based DNA Methylation Data written by Fabian Model and published by . This book was released on 2007 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Use of Genome wide DNA Methylation Microarray to Study Both the Common and Rare Diseases written by 楊傑燊 and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Microarrays written by Ulrike Nuber and published by Garland Science. This book was released on 2007-02-08 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Microarrays introduces all up-to-date microarray platforms and their various applications. It is written for scientists who are entering the field of DNA microarrays as well as those already familiar with the technology, but interested in new applications and methods.
Download or read book DNA Methylation written by Jörg Tost and published by Humana Press. This book was released on 2010-12-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past few years, DNA methylation technologies and our knowledge of DNA methylation patterns have been advancing at a breathtaking pace. Due to this fact, DNA Methylation: Methods and Protocols, Second Edition completely revises, updates, and expands upon the popular first edition with the most current novel techniques, easier to use and more refined by the tested experience of leading experts. This revision reflects contemporary study of the subject: the analysis of gene-specific DNA methylation patterns has been complemented by genome-wide approaches, and epigenomics takes a central place. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters in this volume present brief introductions to the topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes which highlight tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, DNA Methylation: Methods and Protocols, Second Edition is the perfect resource for scientists who wish to further our understanding of the molecular processes that determine the genomic DNA methylation landscape and for those who aim to identify and implement DNA methylation-based biomarkers for clinical and diagnostic applications.
Download or read book Cytogenomics written by Thomas Liehr and published by Academic Press. This book was released on 2021-05-25 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cytogenomics demonstrates that chromosomes are crucial in understanding the human genome and that new high-throughput approaches are central to advancing cytogenetics in the 21st century. After an introduction to (molecular) cytogenetics, being the basic of all cytogenomic research, this book highlights the strengths and newfound advantages of cytogenomic research methods and technologies, enabling researchers to jump-start their own projects and more effectively gather and interpret chromosomal data. Methods discussed include banding and molecular cytogenetics, molecular combing, molecular karyotyping, next-generation sequencing, epigenetic study approaches, optical mapping/karyomapping, and CRISPR-cas9 applications for cytogenomics. The book’s second half demonstrates recent applications of cytogenomic techniques, such as characterizing 3D chromosome structure across different tissue types and insights into multilayer organization of chromosomes, role of repetitive elements and noncoding RNAs in human genome, studies in topologically associated domains, interchromosomal interactions, and chromoanagenesis. This book is an important reference source for researchers, students, basic and translational scientists, and clinicians in the areas of human genetics, genomics, reproductive medicine, gynecology, obstetrics, internal medicine, oncology, bioinformatics, medical genetics, and prenatal testing, as well as genetic counselors, clinical laboratory geneticists, bioethicists, and fertility specialists. Offers applied approaches empowering a new generation of cytogenomic research using a balanced combination of classical and advanced technologies Provides a framework for interpreting chromosome structure and how this affects the functioning of the genome in health and disease Features chapter contributions from international leaders in the field
Download or read book Epigenetic Epidemiology written by Karin B. Michels and published by Springer Science & Business Media. This book was released on 2012-01-02 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: The exploding field of epigenetics is challenging the dogma of traditional Mendelian inheritance. Epigenetics plays an important role in shaping who we are and contributes to our prospects of health and disease. While early epigenetic research focused on plant and animal models and in vitro experiments, population-based epidemiologic studies increasingly incorporate epigenetic components. The relevance of epigenetic marks, such as DNA methylation, genomic imprinting, and histone modification for disease causation has yet to be fully explored.This book covers the basic concepts of epigenetic epidemiology, discusses challenges in study design, analysis, and interpretation, epigenetic laboratory techniques, the influence of age and environmental factors on shaping the epigenome, the role of epigenetics in the developmental origins hypothesis, and provides the state of the art on the epigenetic epidemiology of various health conditions including childhood syndromes, cancer, infectious diseases, inflammation and rheumatoid arthritis, asthma, autism and other neurodevelopmental disorders, psychiatric disorders, diabetes, obesity and metabolic disorders, and atherosclerosis. With contributions from: Peter Jones, Jean-Pierre Issa, Gavin Kelsey, Robert Waterland, and many other experts in epigenetics!
Download or read book DNA Microarrays Part B Databases and Statistics written by and published by Elsevier. This book was released on 2006-08-28 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern DNA microarray technologies have evolved over the past 25 years to the point where it is now possible to take many million measurements from a single experiment. These two volumes, Parts A & B in the Methods in Enzymology series provide methods that will shepard any molecular biologist through the process of planning, performing, and publishing microarray results. Part A starts with an overview of a number of microarray platforms, both commercial and academically produced and includes wet bench protocols for performing traditional expression analysis and derivative techniques such as detection of transcription factor occupancy and chromatin status. Wet-bench protocols and troubleshooting techniques continue into Part B. These techniques are well rooted in traditional molecular biology and while they require traditional care, a researcher that can reproducibly generate beautiful Northern or Southern blots should have no difficulty generating beautiful array hybridizations. Data management is a more recent problem for most biologists. The bulk of Part B provides a range of techniques for data handling. This includes critical issues, from normalization within and between arrays, to uploading your results to the public repositories for array data, and how to integrate data from multiple sources. There are chapters in Part B for both the debutant and the expert bioinformatician. Provides an overview of platforms Includes experimental design and wet bench protocols Presents statistical and data analysis methods, array databases, data visualization and meta analysis