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Molecular Analysis and Genome Discovery, 2nd Edition

Molecular Analysis and Genome Discovery, 2nd Edition

Ralph Rapley (Editor), Stuart Harbron (Editor)

ISBN: 978-1-119-97844-2

Sep 2011

320 pages



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.
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


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

“It will be of immense value to students, biotechnologists, and scientists in the pharmaceutical industry. This update absolutely justifies replacement of the first edition.”  (Doody’s, 24 August 2012)