Molecular Analysis and Genome Discovery 2e

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.

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