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Molecular Analysis and Genome Discovery, Second Edition is a completely revised and updated new edition of this successful book. The text provides a comprehensive overview of recent developments in the fast moving field of molecular based diagnostics of disease markers. Key concepts and applications are provided alongside practical information on current techniques currently being researched and developed. Each chapter offers an up-to-date analysis of the subject encompassing the very latest technology platforms and is an essential reference for researchers in the field looking for an…mehr
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Molecular Analysis and Genome Discovery, Second Edition is a completely revised and updated new edition of this successful book. The text provides a comprehensive overview of recent developments in the fast moving field of molecular based diagnostics of disease markers. Key concepts and applications are provided alongside practical information on current techniques currently being researched and developed. Each chapter offers an up-to-date analysis of the subject encompassing the very latest technology platforms and is an essential reference for researchers in the field looking for an up-to-date overview of the subject. The book will also be an indispensable resource for those working in the biotechnology and pharmaceutical industries. New for this edition: chapters on Genotyping through Mutation Detection; Differential Gene Expression; Haplotyping and Molecular Profiling.
Produktdetails
- Produktdetails
- Verlag: John Wiley & Sons
- Seitenzahl: 320
- Erscheinungstermin: 15. September 2011
- Englisch
- ISBN-13: 9781119977445
- Artikelnr.: 37353029
- Verlag: John Wiley & Sons
- Seitenzahl: 320
- Erscheinungstermin: 15. September 2011
- Englisch
- ISBN-13: 9781119977445
- Artikelnr.: 37353029
Ralph Rapley, Ph.D. Department of Biosciences, University of Hertfordshire, Hatfield, UKElectrical Engineers, Mechanical Engineers, Automation Engineers, Optical Industry, Students in Electrical Engineering, Students in Physics, Robotics Engineers, Automation Industry, Sensor Industry, Automobile Industry, Aircraft and Space Industry, Company Libraries, University Institutes and Libraries, Industry.
Overview of Genotyping Mònica Bayés and Ivo Glynne Gut Centro Nacional de Análisis Genómico C/Baldiri Reixac 4, 08028 Barcelona, Spain DNA Chip Analysis in Genome Discovery Ross N. Nazar and Jane Robb Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 qPCR, theory, reliability & use in molecular analysis Jamie Murphy & Stephen A Bustin Academic Surgical Unit, 3rd Floor Alexandra Wing, Royal London Hospital, Whitechapel, London E1 1BB. DNA Analysis in Droplet-Based Microfluidic Devices Pinar Ozdemir, Yonghao Zhang Department of Mechanical Engineering, University of Strathclyde, Glasgow, G1 1XJ, UK High Resolution Melt Profiling *Steven F. Dobrowolski PhD and Carl T. Wittwer MD, PhD Department of Pathology University of Utah School of Medicine Massively Parallel Sequencing Tracy Tucker1, Marco Marra1,2, Jan M Friedman1,3 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6H 3N1 Canada; BC Cancer Agency Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6 Canada; Child & Family Research Institute, Vancouver, British Columbia, V6H 3N1 Canada; Aptamers for Analysis: nucleic acids ligands in the post genomic era Pedro Nadali, Alessandro Pintoi, Marketa Svobodovai and Ciara K. O' Sullivan*,i,ii i Department d'Enginyeria Quimica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain. ii Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain Use of Nanotechnology for Enhancing of Cancer Biomarker Discovery and Analysis: A Molecular Approach Farid E. Ahmed, Ph.D. GEM Tox Consultants & Labs, Inc., Greenville, NC 27834, USA Chip Based Proteomics Julian Bailes, Andrew Milnthorpe, Sandra Smieszek, Mikhail Soloviev School of Biological Sciences, Royal Holloway, University of London, Egham,, Surrey, TW20 0EX, UK Antibody Microarrays in Proteome Profiling Mohamed Saiel Saeed Alhamdani and Jörg D. Hoheisel Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Mass Spectrometry and Metabolomics William J. Griffiths and Yuqin Wang Institute of Mass Spectrometry, School of Medicine, Room 352 Grove Building, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK.
Preface ix Contributors xi 1 Overview of Genotyping 1 Monica Bayes and Ivo
Glynne Gut Introduction 1 Methods for interrogating SNPs 3 Commercial
platforms for SNP genotyping 7 Practical recommendations 11 SNP databases
14 Methylation analysis 15 Copy number variation analysis 16 Second
generation sequencing technologies 17 Conclusions 18 References 19 2 DNA
Chip Analysis in Genome Discovery 24 Ross N. Nazar and Jane Robb
Introduction 24 Interrogating a genome 25 Cross-species hybridization 28
Comparative genomic hybridization and microarray-based genotyping 31
Barcodes, DNA microarrays and organism identification 34 Concluding remarks
36 References 37 3 qPCR, Theory, Reliability and Use in Molecular Analysis
43 Jamie Murphy and Stephen A. Bustin Sample preparation 44 RNA quality 45
Reagents 46 Assay design 47 Transparency of published data 51 Further
considerations 52 Conclusion 52 References 52 4 DNA Analysis in
Droplet-Based Microfluidic Devices 56 Pinar Ozdemir and Yonghao Zhang
Introduction 56 Continuous-flow microPCR chips 58 PCR inhibition and
carryover contamination 62 PCR in droplets 65 Conclusions 73 References 75
5 High-Resolution Melt Profiling 81 Steven F. Dobrowolski and Carl T.
Wittwer Introduction 81 Basic concepts of melt profiling 82 HRMP and
polymerase chain reaction 84 DNA specimens and HRMP 89 Determining a
temperature window for melting 90 Dyes and platforms for melt profiling 92
Scanning PCR products for sequence variation 93 Genotyping with
high-resolution melt profiling 102 Other applications of HRMP 108 Final
notes 109 References 110 6 Massively Parallel Sequencing 114 Tracy Tucker,
Marco Marra and Jan M. Friedman Sanger sequencing 114 Massively parallel
sequencing 114 Commercially available massively parallel sequencers 115
Future technologies 122 Paired-end or mate-paired reads 123
Target-enrichment strategies for MPS 124 Applications of MPS 125 Summary
131 References 132 7 Aptamers for Analysis: Nucleic Acids Ligands in the
Post-Genomic Era 135 Pedro Nadal, Alessandro Pinto, Marketa Svobodova and
Ciara K. O'Sullivan Introduction 135 SELEX 136 Aptamers in analysis 147
Imaging with aptamers 157 Conclusions, outlooks and perspectives 160
References 161 8 Use of Nanotechnology for Enhancing of Cancer Biomarker
Discovery and Analysis: A Molecular Approach 175 Farid E. Ahmed
Introduction 175 Proteomics and nanotechnology 176 Nanoscale multicomponent
separation 176 Nanoscale protein detection strategies 178 Surface-enhanced
Raman scattering (SERS) 182 References 188 9 Chip-Based Proteomics 193
Julian Bailes, Andrew Milnthorpe, Sandra Smieszek and Mikhail Soloviev
Introduction 193 Lab-on-a-chip 194 Arrays 196 Chip-based mass spectrometry
203 Surface plasmon resonance (SPR) and quartz crystal microbalance (QCM)
chip instruments 205 Microfluidics 207 Conclusion 209 References 211 10
Antibody Microarrays in Proteome Profiling 219 Mohamed Saiel Saeed
Alhamdani and Jorg D. Hoheisel Introduction 219 Technical aspects 220
Antibody array applications 226 Summary 229 Acknowledgements 229 References
229 11 Biomarker Detection and Molecular Profiling by Multiplex Microbead
Suspension Array Based Immunoproteomics 244 V. V. Krishhan, Imran H. Khan
and Paul A. Luciw Introduction 244 Principles of microbead-based
multiplexing 245 Experimental aspects of the multiplex microbead assay 247
Multiplex microbead assay design and comparison with other methods 250
Applications of the multiplex microbead assay system for biomedical
research and clinical studies 252 Selected investigational fields for
multiplex analysis and examples of applications 255 Challenges and current
limitations 255 Summary and future directions 259 Acknowledgements 261
References 261 12 Mass Spectrometry in Metabolomics 271 William J.
Griffiths and Yuqin Wang Introduction 271 Sample collection and preparation
272 Data acquisition 274 Data analysis 279 Applications 283 Conclusion 294
Acknowledgement 294 References 295 Index 299
Glynne Gut Introduction 1 Methods for interrogating SNPs 3 Commercial
platforms for SNP genotyping 7 Practical recommendations 11 SNP databases
14 Methylation analysis 15 Copy number variation analysis 16 Second
generation sequencing technologies 17 Conclusions 18 References 19 2 DNA
Chip Analysis in Genome Discovery 24 Ross N. Nazar and Jane Robb
Introduction 24 Interrogating a genome 25 Cross-species hybridization 28
Comparative genomic hybridization and microarray-based genotyping 31
Barcodes, DNA microarrays and organism identification 34 Concluding remarks
36 References 37 3 qPCR, Theory, Reliability and Use in Molecular Analysis
43 Jamie Murphy and Stephen A. Bustin Sample preparation 44 RNA quality 45
Reagents 46 Assay design 47 Transparency of published data 51 Further
considerations 52 Conclusion 52 References 52 4 DNA Analysis in
Droplet-Based Microfluidic Devices 56 Pinar Ozdemir and Yonghao Zhang
Introduction 56 Continuous-flow microPCR chips 58 PCR inhibition and
carryover contamination 62 PCR in droplets 65 Conclusions 73 References 75
5 High-Resolution Melt Profiling 81 Steven F. Dobrowolski and Carl T.
Wittwer Introduction 81 Basic concepts of melt profiling 82 HRMP and
polymerase chain reaction 84 DNA specimens and HRMP 89 Determining a
temperature window for melting 90 Dyes and platforms for melt profiling 92
Scanning PCR products for sequence variation 93 Genotyping with
high-resolution melt profiling 102 Other applications of HRMP 108 Final
notes 109 References 110 6 Massively Parallel Sequencing 114 Tracy Tucker,
Marco Marra and Jan M. Friedman Sanger sequencing 114 Massively parallel
sequencing 114 Commercially available massively parallel sequencers 115
Future technologies 122 Paired-end or mate-paired reads 123
Target-enrichment strategies for MPS 124 Applications of MPS 125 Summary
131 References 132 7 Aptamers for Analysis: Nucleic Acids Ligands in the
Post-Genomic Era 135 Pedro Nadal, Alessandro Pinto, Marketa Svobodova and
Ciara K. O'Sullivan Introduction 135 SELEX 136 Aptamers in analysis 147
Imaging with aptamers 157 Conclusions, outlooks and perspectives 160
References 161 8 Use of Nanotechnology for Enhancing of Cancer Biomarker
Discovery and Analysis: A Molecular Approach 175 Farid E. Ahmed
Introduction 175 Proteomics and nanotechnology 176 Nanoscale multicomponent
separation 176 Nanoscale protein detection strategies 178 Surface-enhanced
Raman scattering (SERS) 182 References 188 9 Chip-Based Proteomics 193
Julian Bailes, Andrew Milnthorpe, Sandra Smieszek and Mikhail Soloviev
Introduction 193 Lab-on-a-chip 194 Arrays 196 Chip-based mass spectrometry
203 Surface plasmon resonance (SPR) and quartz crystal microbalance (QCM)
chip instruments 205 Microfluidics 207 Conclusion 209 References 211 10
Antibody Microarrays in Proteome Profiling 219 Mohamed Saiel Saeed
Alhamdani and Jorg D. Hoheisel Introduction 219 Technical aspects 220
Antibody array applications 226 Summary 229 Acknowledgements 229 References
229 11 Biomarker Detection and Molecular Profiling by Multiplex Microbead
Suspension Array Based Immunoproteomics 244 V. V. Krishhan, Imran H. Khan
and Paul A. Luciw Introduction 244 Principles of microbead-based
multiplexing 245 Experimental aspects of the multiplex microbead assay 247
Multiplex microbead assay design and comparison with other methods 250
Applications of the multiplex microbead assay system for biomedical
research and clinical studies 252 Selected investigational fields for
multiplex analysis and examples of applications 255 Challenges and current
limitations 255 Summary and future directions 259 Acknowledgements 261
References 261 12 Mass Spectrometry in Metabolomics 271 William J.
Griffiths and Yuqin Wang Introduction 271 Sample collection and preparation
272 Data acquisition 274 Data analysis 279 Applications 283 Conclusion 294
Acknowledgement 294 References 295 Index 299
Overview of Genotyping Mònica Bayés and Ivo Glynne Gut Centro Nacional de Análisis Genómico C/Baldiri Reixac 4, 08028 Barcelona, Spain DNA Chip Analysis in Genome Discovery Ross N. Nazar and Jane Robb Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 qPCR, theory, reliability & use in molecular analysis Jamie Murphy & Stephen A Bustin Academic Surgical Unit, 3rd Floor Alexandra Wing, Royal London Hospital, Whitechapel, London E1 1BB. DNA Analysis in Droplet-Based Microfluidic Devices Pinar Ozdemir, Yonghao Zhang Department of Mechanical Engineering, University of Strathclyde, Glasgow, G1 1XJ, UK High Resolution Melt Profiling *Steven F. Dobrowolski PhD and Carl T. Wittwer MD, PhD Department of Pathology University of Utah School of Medicine Massively Parallel Sequencing Tracy Tucker1, Marco Marra1,2, Jan M Friedman1,3 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6H 3N1 Canada; BC Cancer Agency Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6 Canada; Child & Family Research Institute, Vancouver, British Columbia, V6H 3N1 Canada; Aptamers for Analysis: nucleic acids ligands in the post genomic era Pedro Nadali, Alessandro Pintoi, Marketa Svobodovai and Ciara K. O' Sullivan*,i,ii i Department d'Enginyeria Quimica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain. ii Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain Use of Nanotechnology for Enhancing of Cancer Biomarker Discovery and Analysis: A Molecular Approach Farid E. Ahmed, Ph.D. GEM Tox Consultants & Labs, Inc., Greenville, NC 27834, USA Chip Based Proteomics Julian Bailes, Andrew Milnthorpe, Sandra Smieszek, Mikhail Soloviev School of Biological Sciences, Royal Holloway, University of London, Egham,, Surrey, TW20 0EX, UK Antibody Microarrays in Proteome Profiling Mohamed Saiel Saeed Alhamdani and Jörg D. Hoheisel Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Mass Spectrometry and Metabolomics William J. Griffiths and Yuqin Wang Institute of Mass Spectrometry, School of Medicine, Room 352 Grove Building, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK.
Preface ix Contributors xi 1 Overview of Genotyping 1 Monica Bayes and Ivo
Glynne Gut Introduction 1 Methods for interrogating SNPs 3 Commercial
platforms for SNP genotyping 7 Practical recommendations 11 SNP databases
14 Methylation analysis 15 Copy number variation analysis 16 Second
generation sequencing technologies 17 Conclusions 18 References 19 2 DNA
Chip Analysis in Genome Discovery 24 Ross N. Nazar and Jane Robb
Introduction 24 Interrogating a genome 25 Cross-species hybridization 28
Comparative genomic hybridization and microarray-based genotyping 31
Barcodes, DNA microarrays and organism identification 34 Concluding remarks
36 References 37 3 qPCR, Theory, Reliability and Use in Molecular Analysis
43 Jamie Murphy and Stephen A. Bustin Sample preparation 44 RNA quality 45
Reagents 46 Assay design 47 Transparency of published data 51 Further
considerations 52 Conclusion 52 References 52 4 DNA Analysis in
Droplet-Based Microfluidic Devices 56 Pinar Ozdemir and Yonghao Zhang
Introduction 56 Continuous-flow microPCR chips 58 PCR inhibition and
carryover contamination 62 PCR in droplets 65 Conclusions 73 References 75
5 High-Resolution Melt Profiling 81 Steven F. Dobrowolski and Carl T.
Wittwer Introduction 81 Basic concepts of melt profiling 82 HRMP and
polymerase chain reaction 84 DNA specimens and HRMP 89 Determining a
temperature window for melting 90 Dyes and platforms for melt profiling 92
Scanning PCR products for sequence variation 93 Genotyping with
high-resolution melt profiling 102 Other applications of HRMP 108 Final
notes 109 References 110 6 Massively Parallel Sequencing 114 Tracy Tucker,
Marco Marra and Jan M. Friedman Sanger sequencing 114 Massively parallel
sequencing 114 Commercially available massively parallel sequencers 115
Future technologies 122 Paired-end or mate-paired reads 123
Target-enrichment strategies for MPS 124 Applications of MPS 125 Summary
131 References 132 7 Aptamers for Analysis: Nucleic Acids Ligands in the
Post-Genomic Era 135 Pedro Nadal, Alessandro Pinto, Marketa Svobodova and
Ciara K. O'Sullivan Introduction 135 SELEX 136 Aptamers in analysis 147
Imaging with aptamers 157 Conclusions, outlooks and perspectives 160
References 161 8 Use of Nanotechnology for Enhancing of Cancer Biomarker
Discovery and Analysis: A Molecular Approach 175 Farid E. Ahmed
Introduction 175 Proteomics and nanotechnology 176 Nanoscale multicomponent
separation 176 Nanoscale protein detection strategies 178 Surface-enhanced
Raman scattering (SERS) 182 References 188 9 Chip-Based Proteomics 193
Julian Bailes, Andrew Milnthorpe, Sandra Smieszek and Mikhail Soloviev
Introduction 193 Lab-on-a-chip 194 Arrays 196 Chip-based mass spectrometry
203 Surface plasmon resonance (SPR) and quartz crystal microbalance (QCM)
chip instruments 205 Microfluidics 207 Conclusion 209 References 211 10
Antibody Microarrays in Proteome Profiling 219 Mohamed Saiel Saeed
Alhamdani and Jorg D. Hoheisel Introduction 219 Technical aspects 220
Antibody array applications 226 Summary 229 Acknowledgements 229 References
229 11 Biomarker Detection and Molecular Profiling by Multiplex Microbead
Suspension Array Based Immunoproteomics 244 V. V. Krishhan, Imran H. Khan
and Paul A. Luciw Introduction 244 Principles of microbead-based
multiplexing 245 Experimental aspects of the multiplex microbead assay 247
Multiplex microbead assay design and comparison with other methods 250
Applications of the multiplex microbead assay system for biomedical
research and clinical studies 252 Selected investigational fields for
multiplex analysis and examples of applications 255 Challenges and current
limitations 255 Summary and future directions 259 Acknowledgements 261
References 261 12 Mass Spectrometry in Metabolomics 271 William J.
Griffiths and Yuqin Wang Introduction 271 Sample collection and preparation
272 Data acquisition 274 Data analysis 279 Applications 283 Conclusion 294
Acknowledgement 294 References 295 Index 299
Glynne Gut Introduction 1 Methods for interrogating SNPs 3 Commercial
platforms for SNP genotyping 7 Practical recommendations 11 SNP databases
14 Methylation analysis 15 Copy number variation analysis 16 Second
generation sequencing technologies 17 Conclusions 18 References 19 2 DNA
Chip Analysis in Genome Discovery 24 Ross N. Nazar and Jane Robb
Introduction 24 Interrogating a genome 25 Cross-species hybridization 28
Comparative genomic hybridization and microarray-based genotyping 31
Barcodes, DNA microarrays and organism identification 34 Concluding remarks
36 References 37 3 qPCR, Theory, Reliability and Use in Molecular Analysis
43 Jamie Murphy and Stephen A. Bustin Sample preparation 44 RNA quality 45
Reagents 46 Assay design 47 Transparency of published data 51 Further
considerations 52 Conclusion 52 References 52 4 DNA Analysis in
Droplet-Based Microfluidic Devices 56 Pinar Ozdemir and Yonghao Zhang
Introduction 56 Continuous-flow microPCR chips 58 PCR inhibition and
carryover contamination 62 PCR in droplets 65 Conclusions 73 References 75
5 High-Resolution Melt Profiling 81 Steven F. Dobrowolski and Carl T.
Wittwer Introduction 81 Basic concepts of melt profiling 82 HRMP and
polymerase chain reaction 84 DNA specimens and HRMP 89 Determining a
temperature window for melting 90 Dyes and platforms for melt profiling 92
Scanning PCR products for sequence variation 93 Genotyping with
high-resolution melt profiling 102 Other applications of HRMP 108 Final
notes 109 References 110 6 Massively Parallel Sequencing 114 Tracy Tucker,
Marco Marra and Jan M. Friedman Sanger sequencing 114 Massively parallel
sequencing 114 Commercially available massively parallel sequencers 115
Future technologies 122 Paired-end or mate-paired reads 123
Target-enrichment strategies for MPS 124 Applications of MPS 125 Summary
131 References 132 7 Aptamers for Analysis: Nucleic Acids Ligands in the
Post-Genomic Era 135 Pedro Nadal, Alessandro Pinto, Marketa Svobodova and
Ciara K. O'Sullivan Introduction 135 SELEX 136 Aptamers in analysis 147
Imaging with aptamers 157 Conclusions, outlooks and perspectives 160
References 161 8 Use of Nanotechnology for Enhancing of Cancer Biomarker
Discovery and Analysis: A Molecular Approach 175 Farid E. Ahmed
Introduction 175 Proteomics and nanotechnology 176 Nanoscale multicomponent
separation 176 Nanoscale protein detection strategies 178 Surface-enhanced
Raman scattering (SERS) 182 References 188 9 Chip-Based Proteomics 193
Julian Bailes, Andrew Milnthorpe, Sandra Smieszek and Mikhail Soloviev
Introduction 193 Lab-on-a-chip 194 Arrays 196 Chip-based mass spectrometry
203 Surface plasmon resonance (SPR) and quartz crystal microbalance (QCM)
chip instruments 205 Microfluidics 207 Conclusion 209 References 211 10
Antibody Microarrays in Proteome Profiling 219 Mohamed Saiel Saeed
Alhamdani and Jorg D. Hoheisel Introduction 219 Technical aspects 220
Antibody array applications 226 Summary 229 Acknowledgements 229 References
229 11 Biomarker Detection and Molecular Profiling by Multiplex Microbead
Suspension Array Based Immunoproteomics 244 V. V. Krishhan, Imran H. Khan
and Paul A. Luciw Introduction 244 Principles of microbead-based
multiplexing 245 Experimental aspects of the multiplex microbead assay 247
Multiplex microbead assay design and comparison with other methods 250
Applications of the multiplex microbead assay system for biomedical
research and clinical studies 252 Selected investigational fields for
multiplex analysis and examples of applications 255 Challenges and current
limitations 255 Summary and future directions 259 Acknowledgements 261
References 261 12 Mass Spectrometry in Metabolomics 271 William J.
Griffiths and Yuqin Wang Introduction 271 Sample collection and preparation
272 Data acquisition 274 Data analysis 279 Applications 283 Conclusion 294
Acknowledgement 294 References 295 Index 299