- Email: [email protected]
Genotyping 101
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A holistic guide to asthma Asthma: Mechanisms and Protocols Edited by K. Fan Chung and I. Adcock, Humana Press, 2000. Hardback (341 pages) ISBN 089603626X
Asthma – representing one of the most common chronic diseases in the Western world – is characterized by airway inflammation. There is little knowledge about the molecular events predisposing individuals to asthma or about crucial processes of asthma inflammation. It is known that a specific clinical phenotype of asthma is the result of a complex interaction between environmental and genetic factors, which lead to cell activation and to the release of soluble inflammatory mediators. Asthma: Mechanisms and Protocols is promoted as the first laboratory manual for asthma research and provides helpful laboratory methods for collecting and culturing lung cells (epithelial cells, fibroblasts, as well as eosinophils and alveolar macrophages). Moreover, the book represents an overview of the different methodological approaches to study the molecular and cellular events in asthma. It provides up-to-date methodologies used to study the phenotype and the function of immunocompetent and bronchial structural cells in the pathophysiology of asthma. Cellular events such as cell activation, adhesion and proliferation are thoroughly explained, and their role in the pathogenesis of asthma appropriately emphasized. Other events involved in the downregulation of the inflammatory phenomenon in asthma, such as apoptosis, are also described. All these phenomena are appropriately linked to each other and the reader is delivered a clear picture of the scenario related to asthma inflammation. This guide also describes methodologies used to detect, both at a genetic and at a protein level, soluble mediators that play a crucial role in the pathophysiology of asthma. The importance of detecting these mediators is related to the ability to monitor the activity and the severity of the disease by using the mentioned methodologies. The final section of the book is dedicated to the analysis of the laboratory methodologies for assessing the cellular and molecular response to anti-asthma treatments. Leading experts describe methods for genotyping β2-adrenoceptor and glucocorticoid receptor http://tmm.trends.com
TRENDS in Molecular Medicine Vol.7 No.6 June 2001
polymorphisms. Great opportunities exist in the new millennium for the development of new drugs, and for increasing the responsiveness to current anti-asthma drugs. The efficacy, selectivity and safety of both strategies are likely to improve our understanding of disease mechanisms and the genetic basis for efficacy and safety among individuals. The present book provides a detailed and comprehensive approach to the methodologies used to assess all these issues. Asthma: Mechanisms and Protocols offers much to readers who want to understand the complexity of asthma pathogenesis and provides a complete and up-to-date collection of standardized cellular, biochemical, molecular and genetic methods for a better understanding of the effects of the drugs for the treatment of asthma. Maurizio Vignola* Mark Gjomarkaj E. Pace Institute of Respiratory Pathophysiology, Italian National Research Council, Palermo, Italy. *e-mail: [email protected]
Genotyping 101 SNP and Microsatellite Genotyping: Markers for Genetic Analysis Edited by A. Hajeer et al. Eaton Publishing, 2000. Hardback (152 pages) ISBN 1881299384
The post-genome era is upon us, and increasingly, attention is being focused on examining variation within genomes. Tracing common sequence variants such as microsatellites has been key to the understanding of many human genetic diseases with simple Mendelian inheritance. More recent approaches seek to dissect the molecular basis of common, multifactorial diseases, which many people feel will require the use of a very dense set of single nucleotide repeat (SNP) markers typed on many thousands of patients. Largely because of these ever-increasing needs for efficient genotyping methods, diverse methods for scoring SNPs have recently been reported. SNP and Microsatellite Genotyping: Markers for Genetic Analysis presents a survey of some of the modern methods for scoring SNPs and microsatellites, as well as methods for data analysis in human genetic studies.
The book is aimed at the basic research scientist working in human genetics. Although many of the methods might be of interest to clinicians using SNPs as diagnostic tools, the focus is clearly on the research lab setting. Each of the seven chapters is contributed by separate authors with expertise in the given field, and the editors have taken care to limit repetition between chapters. Researchers who are new to the field will find the introductory remarks in each chapter helpful as background information. Some chapters provide quite detailed experimental protocols that could easily be followed by novice users, and others provide only skeletal outlines of a procedure. The index is comprehensive and contains listings for most topics of interest. Most human genome-wide linkage and association studies currently use panels of microsatellite markers. This book has chapters devoted to methods for discovery of microsatellites, high-throughput scoring of microsatellites and software for analysis of human linkage data. The chapter on data analysis is particularly helpful and clearly illustrates some of the more difficult concepts of human genetic analysis. The chapter on SNP discovery focuses on conformational methods such as single strand conformation polymorphism (SSCP) and heteroduplex analysis, but does not mention relatively new but commonly used methods such as denaturing high performance liquid chromatography (HPLC). The chapter on SNP genotyping is somewhat brief, mentioning only three methods in detail, but it does list and provide references for other technologies. Two chapters address methods to increase the efficiency of wholegenome association studies including DNA pooling to reduce the number of patient samples required and new array-based SNP genotyping technologies. This book will find a captive audience in the researcher just entering the field of human genetics and genotyping. Although Hajeer et al. is less comprehensive and generally contains fewer protocol specifics than other books on the market, it will serve as a useful introductory survey of the methods required for modern human genetic analysis and as a complement to a detailed laboratory manual. Michael C. Ellis Exelixis, Inc. 170 Harbor Way, PO Box 511, South San Francisco, CA 94083-0511, USA. e-mail: [email protected]
Forum
A holistic guide to asthma Asthma: Mechanisms and Protocols Edited by K. Fan Chung and I. Adcock, Humana Press, 2000. Hardback (341 pages) ISBN 089603626X
Asthma – representing one of the most common chronic diseases in the Western world – is characterized by airway inflammation. There is little knowledge about the molecular events predisposing individuals to asthma or about crucial processes of asthma inflammation. It is known that a specific clinical phenotype of asthma is the result of a complex interaction between environmental and genetic factors, which lead to cell activation and to the release of soluble inflammatory mediators. Asthma: Mechanisms and Protocols is promoted as the first laboratory manual for asthma research and provides helpful laboratory methods for collecting and culturing lung cells (epithelial cells, fibroblasts, as well as eosinophils and alveolar macrophages). Moreover, the book represents an overview of the different methodological approaches to study the molecular and cellular events in asthma. It provides up-to-date methodologies used to study the phenotype and the function of immunocompetent and bronchial structural cells in the pathophysiology of asthma. Cellular events such as cell activation, adhesion and proliferation are thoroughly explained, and their role in the pathogenesis of asthma appropriately emphasized. Other events involved in the downregulation of the inflammatory phenomenon in asthma, such as apoptosis, are also described. All these phenomena are appropriately linked to each other and the reader is delivered a clear picture of the scenario related to asthma inflammation. This guide also describes methodologies used to detect, both at a genetic and at a protein level, soluble mediators that play a crucial role in the pathophysiology of asthma. The importance of detecting these mediators is related to the ability to monitor the activity and the severity of the disease by using the mentioned methodologies. The final section of the book is dedicated to the analysis of the laboratory methodologies for assessing the cellular and molecular response to anti-asthma treatments. Leading experts describe methods for genotyping β2-adrenoceptor and glucocorticoid receptor http://tmm.trends.com
TRENDS in Molecular Medicine Vol.7 No.6 June 2001
polymorphisms. Great opportunities exist in the new millennium for the development of new drugs, and for increasing the responsiveness to current anti-asthma drugs. The efficacy, selectivity and safety of both strategies are likely to improve our understanding of disease mechanisms and the genetic basis for efficacy and safety among individuals. The present book provides a detailed and comprehensive approach to the methodologies used to assess all these issues. Asthma: Mechanisms and Protocols offers much to readers who want to understand the complexity of asthma pathogenesis and provides a complete and up-to-date collection of standardized cellular, biochemical, molecular and genetic methods for a better understanding of the effects of the drugs for the treatment of asthma. Maurizio Vignola* Mark Gjomarkaj E. Pace Institute of Respiratory Pathophysiology, Italian National Research Council, Palermo, Italy. *e-mail: [email protected]
Genotyping 101 SNP and Microsatellite Genotyping: Markers for Genetic Analysis Edited by A. Hajeer et al. Eaton Publishing, 2000. Hardback (152 pages) ISBN 1881299384
The post-genome era is upon us, and increasingly, attention is being focused on examining variation within genomes. Tracing common sequence variants such as microsatellites has been key to the understanding of many human genetic diseases with simple Mendelian inheritance. More recent approaches seek to dissect the molecular basis of common, multifactorial diseases, which many people feel will require the use of a very dense set of single nucleotide repeat (SNP) markers typed on many thousands of patients. Largely because of these ever-increasing needs for efficient genotyping methods, diverse methods for scoring SNPs have recently been reported. SNP and Microsatellite Genotyping: Markers for Genetic Analysis presents a survey of some of the modern methods for scoring SNPs and microsatellites, as well as methods for data analysis in human genetic studies.
The book is aimed at the basic research scientist working in human genetics. Although many of the methods might be of interest to clinicians using SNPs as diagnostic tools, the focus is clearly on the research lab setting. Each of the seven chapters is contributed by separate authors with expertise in the given field, and the editors have taken care to limit repetition between chapters. Researchers who are new to the field will find the introductory remarks in each chapter helpful as background information. Some chapters provide quite detailed experimental protocols that could easily be followed by novice users, and others provide only skeletal outlines of a procedure. The index is comprehensive and contains listings for most topics of interest. Most human genome-wide linkage and association studies currently use panels of microsatellite markers. This book has chapters devoted to methods for discovery of microsatellites, high-throughput scoring of microsatellites and software for analysis of human linkage data. The chapter on data analysis is particularly helpful and clearly illustrates some of the more difficult concepts of human genetic analysis. The chapter on SNP discovery focuses on conformational methods such as single strand conformation polymorphism (SSCP) and heteroduplex analysis, but does not mention relatively new but commonly used methods such as denaturing high performance liquid chromatography (HPLC). The chapter on SNP genotyping is somewhat brief, mentioning only three methods in detail, but it does list and provide references for other technologies. Two chapters address methods to increase the efficiency of wholegenome association studies including DNA pooling to reduce the number of patient samples required and new array-based SNP genotyping technologies. This book will find a captive audience in the researcher just entering the field of human genetics and genotyping. Although Hajeer et al. is less comprehensive and generally contains fewer protocol specifics than other books on the market, it will serve as a useful introductory survey of the methods required for modern human genetic analysis and as a complement to a detailed laboratory manual. Michael C. Ellis Exelixis, Inc. 170 Harbor Way, PO Box 511, South San Francisco, CA 94083-0511, USA. e-mail: [email protected]