New High Throughput Technologies for DNA Sequencing and Genomics (eBook)

Cover 1
New High Throughput Technologies for DNA Sequencing and Genomics 4
Copyright Page 5
Contents 6
Contributors 12
Preface 16
Part I: Enabling Technologies 18
Chapter 1. Overview: Developments in DNA Sequencing 20
1. Introduction 21
2. Advanced Sequencing Technologies 26
3. Solid-Phase Array Sequencing Devices 32
4. Future Technologies 39
5. Applied Short-Read Genomic Sequencing 42
6. Summary 52
References 53
Chapter 2. Chip Capillary Electrophoresis and Total Genetic Analysis Systems 62
Abstract 63
1. Introduction 63
2. Chip Design and Fluid Manipulation 65
3. Materials and Fabrication 68
4. Detection 74
5. Surface Modification 82
6. Applications 85
7. DNA Sequencing 91
References 104
Chapter 3. Comparative Sequence Analysis by MALDI-TOF Mass Spectrometry – Utilizing the Known to Discover the New 114
Abstract 114
1. The Concept of Comparative Sequencing 115
2. MALDI-TOF MS-Based Nucleic Acid Analysis 116
3. The Base-Specific Cleavage Assay 117
4. Applications for Comparative Sequencing 120
5. Summary 129
6. Outlook 129
Acknowledgements 132
References 132
Chapter 4. Advances in Dye-Nucleotide Conjugate Chemistry for DNA Sequencing 136
Abstract 136
1. Introduction 136
2. Fluorescent DNA Sequencing 138
3. Energy Transfer Dye Terminators 142
4. Terminal Phosphate-Labeled Nucleotides 161
5. Conclusions 163
References 163
Part II: Sequencing by Synthesis Platforms 168
Chapter 5. The 454 Life Sciences Picoliter Sequencing System 170
Abstract 170
1. Introduction 171
2. The 454 Life Sciences Picoliter Sequencing System 172
3. Applications 187
4. Discussion 199
Acknowledgments 201
References 201
Chapter 6. An Integrated System for DNA Sequencing by Synthesis 204
Abstract 204
1. Introduction 204
2. DNA Sequencing by Synthesis Methodology 206
3. Conclusion 220
Acknowledgments 220
References 220
Part III:Single-Molecule Sequencing 224
Chapter 7. Single-Molecule Fluorescence Microscopy and its Applications to Single-Molecule Sequencing by Cyclic Synthesis 226
Abstract 227
1. Introduction 227
2. Background 229
3. DNA Sequencing by Cyclic Synthesis 236
4. Data Analysis 247
5. Error Sources in Base Calling 251
6. Performance 254
7. Applications 255
8. Conclusions 255
Acknowledgments 256
References 256
Chapter 8. Rapid DNA Sequencing by Direct Nanoscale Reading of Nucleotide Bases on Individual DNA chains 262
Abstract 262
1. Introduction 263
2. DNA Sequencing b Nanoelectrode-Gated Electron-Tunneling Conductance Spectroscopic Molecular Detection 265
3. DNA Sequencing by Massively Parallel Optical Readout of Nanopore Arrays and Design Polymer 273
4. Conclusion 277
Acknowledgments 278
References 278
Chapter 9. A Single Molecule System for Whole Genome Analysis 282
Abstract 283
1. Introduction 283
2. The Optical Mapping System 290
3. The Optical Mapping System: Image Acquisition, Processing, and Analysis 297
4. Applications of Optical Mapping 304
5. Comparison of Optical Mapping and Alternate Methods for Genome Analysis 309
6. Optical Sequencing 311
References 315
Part IV: Sequencing Validations and Analysis 318
Chapter 10. Sequencing Aided by Mutagenesis Facilitates the De Novo Sequencing of Megabase DNA Fragments by Short Read Lengths 320
Abstract 321
1. Introduction 321
2. Principles of SAM Sequencing 324
3. Simulated SAM Sequencing 326
4. Analysis of SAM Sequencing Target Assemblies 329
5. Discussion 336
References 342
Chapter 11. Genome Sequencing and Assembly 344
Abstract 344
1. Introduction 345
2. Approaches to Genome Sequencing 345
3. Problems Inherent with Genome Assemblies 352
4. A Mathematical Model of Shotgun Sequencing 355
5. Genome Assembly Approaches and Programs 356
6. New Generation Sequence Assembly Tools 360
7. Assembly of Genomes by Comparative Means 364
8. Assembly of Sequence Data from Emerging Sequencing Technologies 365
References 367
Chapter 12. Valid Recovery of Nucleic Acid Sequence Information from High Contamination Risk Samples – Ancient DNA and Environmental DNA 374
Abstract 374
1. Introduction 375
2. Features of High Contamination and Artifact Risk Samples 376
3. Amplification and/or Recovery of Nucleic Acids in the Laboratory 380
4. Consideration in Laboratory Set-Up 382
5. Looking to the Future 384
References 385
Subject Index 390