InhaltsangabePreface 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 Crossspecies 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 Continuousflow microPCR chips 58 PCR inhibition and carryover contamination 62 PCR in droplets 65 Conclusions 73 References 75 5 HighResolution 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 Pairedend or matepaired reads 123 Targetenrichment 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 Surfaceenhanced Raman scattering (SERS) 182 References 188 9 ChipBased Proteomics 193 Julian Bailes, Andrew Milnthorpe, Sandra Smieszek and Mikhail Soloviev Introduction 193 Labonachip 194 Arrays 196 Chipbased 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 Acknowle

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Overview of Genotyping Mònica Bayes and Ivo Glynne Gut Centro Nacional de Analisis Genomico 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 Institucio Catalana de Recerca i Estudis Avancats, 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.