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Next-generation genome sequencing : towards personalized medicine / edited by Michal Janitz. — Weinheim : Wiley-VCH ; Chichester : John Wiley [distributor], c2008. – (58.1483/N567) |
Contents
Contents
Part One Sanger DNA Sequencing
1 Sanger DNA Sequencing 3
1.1 The Basics of Sanger Sequencing 3
1.2 Into the Human Genome Project (HGP) and Beyond 6
1.3 Limitations and Future Opportunities 7
1.4 Bioinformatics Holds the Key 8
1.5 Where to Next? 9
References 10
Part Two Next-Generation Sequencing: Toward Personalized Medicine 13
2 Illumina Genome Analyzer II System 15
2.1 Library Preparation 15
2.2 Cluster Creation 17
2.3 Sequencing 19
2.4 Paired End Reads 19
2.5 Data Analysis 20
2.6 Applications 21
3 Applied Biosystems SOLIDTM System: Ligation-Based Sequencing
3.1 Introduction 29
3.2 Overview of the SOLIDTM System 29
3.3 SOLIDTM System Applications 35
3.4 Conclusions 40
References 41
4 The Next-Generation Genome Sequencing: 454/Roche GS FLX
4.1 Introduction 43
4.2 Technology Overview 44
4.3 Software and Bioinformatics 47
4.4 Research Applications 49
References 51
5 Polony Sequencing: History， Technology， and Applications 57
5.1 Introduction 57
5.2 History of Polony Sequencing 57
5.3 Polony Sequencing 62
5.4 Applications 69
5.5 Conclusions 75
References 76
Part Three The Bottleneck: Sequence Data Analysis 77
6 Next-Generation Sequence Data Analysis 79
6.1 Why Next-Generation Sequence Analysis is Different?
6.2 Strategies for Sequence Searching 80
6.3 What is a "Hit，" and Why it Matters for NGS? 82
6.4 Scoring: Why it is Different for NGS? 83
6.5 Strategies for NGS Sequence Analysis 84
6.6 Subsequent Data Analysis 86
References 87
7 DNASTAR's Next-Generation Software 89
7.1 Personalized Genomics and Personalized Medicine 89
7.2 Next-Generation DNA Sequencing as the Means to Personalized Genomics 89
7.3 Strengths of Various Platforms 90
7.4 The Computational Challenge 90
7.5 DNASTAR's Next-Generation Software Solution
7.6 Conclusions 94
References 94
Part Four Emerging Sequencing Technologies 95
8 Real-Time DNA Sequencing 97
8.1 Whole Genome Analysis 97
8.2 Personalized Medicine and Pharmacogenomics 97
8.3 Biodefense， Forensics， DNA Testing， and Basic Research 98
8.4 Simple and Elegant: Real-Time DNA Sequencing 98
References 101
9 Direct Sequencing by TEM of Z-Substituted DNA Molecules 103
9.1 Introduction 103
9.2 Logic of Approach 104
9.3 Identification of Optimal Modified Nucleotides for TEM Visual Resolution of DNA Sequences Independent of Polymerization 106
9.4 TEM Substrates and Visualization 107
9.5 Incorporation of Z-Tagged Nucleotides by Polymerases 108
9.6 Current and New Sequencing Technology 109
9.7 Accuracy 111
9.8 Advantages of ZSG's Proposed DNA Sequencing Technology 111
9.9 Advantages of Significantly Longer Read Lengths 112
10 A Single DNA Molecule Barcoding Method with Applications in DNA Mapping and Molecular Haplotyping 117
10.1 Introduction 117
10.2 Critical Techniques in the Single DNA Molecule Barcoding Method 118
10.3 Single DNA Molecule Mapping 120
10.4 Molecular Haplotyping 124
10.5 Discussion 129
References 131
11 Optical Sequencing: Acquisition from Mapped Single-Molecule Templates 133
11.1 Introduction 133
11.2 The Optical Sequencing Cycle 135
11.3 Future of Optical Sequencing 148
References 149
12 Microchip-Based Sanger Sequencing of DNA 153
12.1 Integrated Microfluidic Devices for Genomic Analysis 154
12.2 Improved Polymer Networks for Sanger Sequencing on Microfluidic Devices 156
12.3 Conclusions 160
References 160
Part Five Next-Generation Sequencing: Truly Integrated Genome Analysis 165
13 Multiplex Sequencing of" Paired End Ditags for Transcriptome and Genome Analysis
13.1 Introduction 167
13.2 The Development of Paired End Ditag Analysis 168
13.3 GIS-PET for Transcriptome Analysis 170
13.4 ChIP-PET for Whole Genome Mapping of Transcription Factor Binding Sites and Epigenetic Modifications 173
13.5 ChIA-PET for Whole Genome Identification of Long-Range Interactions 175
13.6 Perspective 179
References 180
14 Paleogenomics Using the 454 Sequencing Platform 183
14.1 Introduction 183
14.2 The DNA Degradation Challenge 184
14.3 The Effects of DNA Degradation on Paleogenomics 185
14.4 Degradation and Sequencing Accuracy 185
14.5 Sample Contamination 189
14.6 Solutions to DNA Damage 191
14.7 Solutions to Contamination 192
14.8 What Groundwork Remains， and What Does the Future Hold? 195
References 196
15 ChIP-seq: Mapping of Protein-DNA Interactions 201
15.1 Introduction 201
15.2 History 202
15.3 ChIP-seq Method 202
15.4 Sanger Dideoxy-Based Tag Sequencing 203
15.5 Hybridization-Based Tag Sequencing 205
15.6 Application of Sequencing by Synthesis 206
15.7 Medical Applications of ChIP-seq 209
15.8 Challenges 209
15.9 Future Uses of ChIP-seq 211
References 213
16 MicroRNA Discovery and Expression Profiling using Next-Generation Sequencing
16.1 Background on miRNAs 217
16.2 miRNA Identification 218
16.3 Experimental Approach 219
16.4 Validation 225
16.5 Outlook 226
References 226
17 DeepSAGE: Tag-Based Transcriptome Analysis Beyond Microarrays 229
17.1 Introduction 229
17.2 DeepSAGE 231
17.3 Data Analysis 235
17.4 Comparing Tag-Based Transcriptome Profiles 235
17.5 Future Perspectives 238
References 239
18 The New Genomics and Personal Genome Information: Ethical Issues 245
18.1 The New Genomics and Personal Genome Information: Ethical Issues 245
18.2 The New Genomics: What Makes it Special? 245
18.3 Innovation in Ethics: Why do We Need it? 246
18.4 A Proviso: Global Genomics and Local Ethics 247
18.5 Medical Ethics and Hippocratic Confidentiality 247
18.6 Principles of Biomedical Ethics 248
18.7 Clinical Research and Informed Consent 248
18.8 Large-Scale Research Ethics: New Concepts 249
18.9 Personal Genomes 250
18.10 The Personal Genome Project: Consenting to Disclosure 251
References 252
Index 255
