New High Throughput Technologies for DNA Sequencing and Genomics
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Table of contents
- Cover
- New High Throughput Technologies for DNA Sequencing and Genomicsiii
- Copyright Pageiv
- Contentsv
- Contributorsxi
- Prefacexv
- Part I: Enabling Technologies1
- Chapter 1. Overview: Developments in DNA Sequencing3
- 1. Introduction4
- 2. Advanced Sequencing Technologies9
- 3. Solid-Phase Array Sequencing Devices15
- 4. Future Technologies22
- 5. Applied Short-Read Genomic Sequencing25
- 6. Summary35
- References36
- Chapter 2. Chip Capillary Electrophoresis and Total Genetic Analysis Systems45
- Abstract46
- 1. Introduction46
- 2. Chip Design and Fluid Manipulation48
- 3. Materials and Fabrication51
- 4. Detection57
- 5. Surface Modification65
- 6. Applications68
- 7. DNA Sequencing74
- References87
- Chapter 3. Comparative Sequence Analysis by MALDI-TOF Mass Spectrometry – Utilizing the Known to D97
- Abstract97
- 1. The Concept of Comparative Sequencing98
- 2. MALDI-TOF MS-Based Nucleic Acid Analysis99
- 3. The Base-Specific Cleavage Assay100
- 4. Applications for Comparative Sequencing103
- 5. Summary112
- 6. Outlook112
- Acknowledgements115
- References115
- Chapter 4. Advances in Dye-Nucleotide Conjugate Chemistry for DNA Sequencing119
- Abstract119
- 1. Introduction119
- 2. Fluorescent DNA Sequencing121
- 3. Energy Transfer Dye Terminators125
- 4. Terminal Phosphate-Labeled Nucleotides144
- 5. Conclusions146
- References146
- Part II: Sequencing by Synthesis Platforms151
- Chapter 5. The 454 Life Sciences Picoliter Sequencing System153
- Abstract153
- 1. Introduction154
- 2. The 454 Life Sciences Picoliter Sequencing System155
- 3. Applications170
- 4. Discussion182
- Acknowledgments184
- References184
- Chapter 6. An Integrated System for DNA Sequencing by Synthesis187
- Abstract187
- 1. Introduction187
- 2. DNA Sequencing by Synthesis Methodology189
- 3. Conclusion203
- Acknowledgments203
- References203
- Part III:Single-Molecule Sequencing207
- Chapter 7. Single-Molecule Fluorescence Microscopy and its Applications to Single-Molecule Sequencin209
- Abstract210
- 1. Introduction210
- 2. Background212
- 3. DNA Sequencing by Cyclic Synthesis219
- 4. Data Analysis230
- 5. Error Sources in Base Calling234
- 6. Performance237
- 7. Applications238
- 8. Conclusions238
- Acknowledgments239
- References239
- Chapter 8. Rapid DNA Sequencing by Direct Nanoscale Reading of Nucleotide Bases on Individual DNA ch245
- Abstract245
- 1. Introduction246
- 2. DNA Sequencing b Nanoelectrode-Gated Electron-Tunneling Conductance Spectroscopic Molecular Detec248
- 3. DNA Sequencing by Massively Parallel Optical Readout of Nanopore Arrays and Design Polymer256
- 4. Conclusion260
- Acknowledgments261
- References261
- Chapter 9. A Single Molecule System for Whole Genome Analysis265
- Abstract266
- 1. Introduction266
- 2. The Optical Mapping System273
- 3. The Optical Mapping System: Image Acquisition, Processing, and Analysis280
- 4. Applications of Optical Mapping287
- 5. Comparison of Optical Mapping and Alternate Methods for Genome Analysis292
- 6. Optical Sequencing294
- References298
- Part IV: Sequencing Validations and Analysis301
- Chapter 10. Sequencing Aided by Mutagenesis Facilitates the De Novo Sequencing of Megabase DNA Fragm303
- Abstract304
- 1. Introduction304
- 2. Principles of SAM Sequencing307
- 3. Simulated SAM Sequencing309
- 4. Analysis of SAM Sequencing Target Assemblies312
- 5. Discussion319
- References325
- Chapter 11. Genome Sequencing and Assembly327
- Abstract327
- 1. Introduction328
- 2. Approaches to Genome Sequencing328
- 3. Problems Inherent with Genome Assemblies335
- 4. A Mathematical Model of Shotgun Sequencing338
- 5. Genome Assembly Approaches and Programs339
- 6. New Generation Sequence Assembly Tools343
- 7. Assembly of Genomes by Comparative Means347
- 8. Assembly of Sequence Data from Emerging Sequencing Technologies348
- References350
- Chapter 12. Valid Recovery of Nucleic Acid Sequence Information from High Contamination Risk Samples357
- Abstract357
- 1. Introduction358
- 2. Features of High Contamination and Artifact Risk Samples359
- 3. Amplification and/or Recovery of Nucleic Acids in the Laboratory363
- 4. Consideration in Laboratory Set-Up365
- 5. Looking to the Future367
- References368
- Subject Index373
Since the independent invention of DNA sequencing by Sanger and by Gilbert 30 years ago, it has grown from a small scale technique capable of reading several kilobase-pair of sequence per day into today's multibillion dollar industry. This growth has spurred the development of new sequencing technologies that do not involve either electrophoresis or Sanger sequencing chemistries. Sequencing by Synthesis (SBS) involves multiple parallel micro-sequencing addition events occurring on a surface, where data from each round is detected by imaging.
New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, which looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century.
Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book.
* 'Hot Topic' with DNA sequencing continuing as a major research activity in many areas of life science and medicine.
* Bringing together new developments in DNA sequencing technology
* Reviewing issues relevant to the new applications used
New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, which looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century.
Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book.
* 'Hot Topic' with DNA sequencing continuing as a major research activity in many areas of life science and medicine.
* Bringing together new developments in DNA sequencing technology
* Reviewing issues relevant to the new applications used