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E-grāmata: New High Throughput Technologies for DNA Sequencing and Genomics

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  • Formāts: PDF+DRM
  • Sērija : Perspectives in Bioanalysis
  • Izdošanas datums: 22-Sep-2011
  • Izdevniecība: Elsevier Science Ltd
  • Valoda: eng
  • ISBN-13: 9780080471280
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New High Throughput Technologies for DNA Sequencing and GenomicsPalielināt
  • Formāts: PDF+DRM
  • Sērija : Perspectives in Bioanalysis
  • Izdošanas datums: 22-Sep-2011
  • Izdevniecība: Elsevier Science Ltd
  • Valoda: eng
  • ISBN-13: 9780080471280
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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

Papildus informācija

Provides a concise overview of recent developments in DNA sequencing technology and genomics
Contributors xi
Preface xv
ENABLING TECHNOLOGIES
Chapter
1. Overview: Developments in DNA Sequencing
Keith R. Mitchelson, David B. Hawkes, Rustam Turakulov and Artem E. Men
3
1. Introduction
4
1.1. Biotechnological implications of ultra-high-throughput sequencing capability
6
2. Advanced sequencing technologies
9
2.1. Capillary electrophoresis and Sanger sequencing
9
2.2. High-throughput capillary-array sequencing
9
2.3. Signal detection dyes and detectors
10
2.4. Microchip electrophoresis
11
2.5. Capillary electrophoretic sequencing on microcapillary chips
11
2.6. Sequencing by mass spectrometry
14
3. Solid-phase array sequencing devices
15
3.1. Ultra-sensitive detectors and sequencers
15
3.2. Sequencing by synthesis
15
3.3. Single DNA molecule sequencing
19
3.4. Hybridization re-sequencing
22
4. Future technologies
22
4.1. Nanopore membranes
23
4.2. Direct electrical detection of DNA synthesis
25
5. Applied short-read genomic sequencing
25
5.1. Genotyping by re-sequencing
25
5.1.1. Polony genotyping
26
5.1.2. Pyrosequencer genotyping
26
5.1.3. Polymorphism ratio sequencing
26
5.1.4. BEAMing
27
5.2. PaleoGenomics
27
5.3. Neanderthal genomics
28
5.4. MetaGenomics
29
5.5. SAM sequencing of repetitive DNAs
30
5.6. Transcriptome and expressed RNA sequence analysis
31
5.7. MPSS and genome analysis
34
5.8. Optical mapping
34
6. Summary
35
References
36
Chapter
2. Chip Capillary Electrophoresis and Total Genetic Analysis Systems
Qiang Xiong and Jing Cheng
45
Abstract
46
1. Introduction
46
1.1. Various chip-based capillary electrophoresis systems
46
2. Chip design and fluid manipulation
48
2.1. Chip design
48
2.2. Fluid manipulation
50
3. Materials and fabrication
51
3.1. Materials
51
3.2. Fabrication
53
3.2.1. Fabrication procedures for glass materials
53
3.2.2. Fabrication procedures for polymer materials
53
4. Detection
57
4.1. Optical detection
58
4.1.1. Laser-induced fluorescence detection
58
4.1.2. Absorbance detection
60
4.1.3. Chemiluminescence detection
60
4.2. Electrochemical detection
60
4.2.1. Amperometric detection
61
4.2.2. Conductimetric detection
63
4.2.3. Potentiometric detection
63
4.3. Mass spectrometry
63
5. Surface modification
65
5.1. Dynamic coating
65
5.1.1. Dynamic coating for glass/quartz substrates
66
5.1.2. Dynamic coating for PMMA substrates
66
5.1.3. Dynamic coating for PDMS substrates
66
5.2. Permanent coatings
67
5.2.1. Permanent coating for glass/quartz substrates
67
5.2.2. Permanent coating for PMMA substrates
67
5.2.3. Permanent coating for PDMS substrates
67
6. Applications
68
6.1. Nucleic acid analyses
68
6.1.1. Sieving matrices
69
6.1.2. DNA fragment sizing
71
6.1.3. Genotyping
71
7. DNA Sequencing
74
7.1. MicroChip DNA sequencing
77
7.2. Total genetic analysis systems
79
7.2.1. Sample preparation on microchips
80
7.2.2. Bioreactions on microchips
80
7.2.3. System integration
82
7.3. DNA sequencing lab-on-a-chip
85
7.3.1. Alternative DNA sequencing technologies
86
References
87
Chapter
3. Comparative Sequence Analysis by MALDI-TOF Mass Spectrometry – Utilizing the Known to Discover the New
Mathias Ehrich, Franz Hillenkamp and Dirk van den Boom
97
Abstract
97
1. The concept of comparative sequencing
98
1.1. Population genotyping
98
2. MALDI-TOF MS-based nucleic acid analysis
99
2.1. Sample preparation
99
3. The base-specific cleavage assay
100
3.1. Methods for base-specific cleavage
102
3.2. MassCLEAVE
103
4. Applications for comparative sequencing
103
4.1. Signature sequence identification/pathogen identification
103
4.2. SNP discovery and mutation detection
105
4.3. Methylation detection
109
5. Summary
112
6. Outlook
112
6.1. Improvements in instrumentation and processing
113
6.2. High-resolution mass spectrometers and isotopically depleted nucleotides
113
6.3. Use of cleavable/non-cleavable nucleotide mixtures
114
Acknowledgements
115
References
115
Chapter
4. Advances in Dye-Nucleotide Conjugate Chemistry for DNA Sequencing
Shiv Kumar and Carl W. Fuller
119
Abstract
119
1. Introduction
119
2. Fluorescent DNA sequencing
121
2.1. Single dye-labeled primers and terminators
121
2.2. Fluorescence resonance energy transfer (FRET) based primers and terminators
124
3. Energy transfer dye terminators
125
3.1. Charged terminators for "direct-load" DNA sequencing
132
3.2. Negatively charged terminators
134
3.3. Lysine-derived charge terminators
136
3.4. Trimethyllysine-derived terminators
140
4. Terminal phosphate-labeled nucleotides
144
5. Conclusions
146
References
146
SEQUENCING BY SYNTHESIS PLATFORMS
Chapter
5. The 454 Life Sciences Picoliter Sequencing System
Marcel Margulies, Thomas P. Jarvie, James R. Knight and Jan Fredrik Simons
153
Abstract
153
1. Introduction
154
2. The 454 life sciences picoliter sequencing system
155
2.1. Sample preparation
155
2.2. Sequencing
158
2.3. Image processing
163
2.4. Sequencing accuracy
165
2.5. Base calling
165
2.6. Sequence alignment
168
3. Applications
170
3.1. De novo sequence assembly
170
3.2. Sequencing results
172
3.3. Comparative genomics
173
3.4. Ultra-deep sequencing of PCR amplicons
174
3.5. Scalability
181
4. Discussion
182
Acknowledgments
184
References
184
Chapter
6. An Integrated System for DNA Sequencing by Synthesis
John R. Edwards, Dae Hyun Kim and Jingyue Ju
187
Abstract
187
1. Introduction
187
2. DNA sequencing by synthesis methodology
189
2.1. DNA attachment chemistries on surfaces
192
2.2. Novel reporter nucleotides
193
2.2.1. Nucleotide reporter groups for SBS
195
2.3. Blocking of 3'-hydroxyl groups
200
3. Conclusion
203
Acknowledgments
203
References
203
SINGLE-MOLECULE SEQUENCING
Chapter
7. Single-Molecule Fluorescence Microscopy and its Applications to Single-Molecule Sequencing by Cyclic Synthesis
Benedict Hebert and Ido Braslaysky
209
Abstract
210
1. Introduction
210
2. Background
212
2.1. Single-molecule detection
212
2.2. Total internal reflection
214
2.3. FRET theory
218
3. DNA sequencing by cyclic synthesis
219
3.1. Motivation
219
3.2. Surface treatment
221
3.3. Polymerase kinetics
222
3.4. Sequencing strategies
224
3.4.1. Cyclic synthesis using FRET
224
3.4.2. Real-time imaging
226
3.4.3. Non-FRET imaging
227
3.4.4. Cleavable linkers
227
3.4.5. Cleavable terminators
229
3.4.6. Multi-color versus one-color imaging
229
4. Data analysis
230
4.1. Spatial correlations
230
4.2. Data collection – base calling
231
4.2.1. Intensity traces
232
4.2.2. Single-image data collection
233
4.3. Aligning the sequences
234
5. Error sources in base calling
234
6. Performance
237
7. Applications
238
8. Conclusions
238
Acknowledgments
239
References
239
Chapter
8. Rapid DNA Sequencing by Direct Nanoscale Reading of Nucleotide Bases on Individual DNA chains
James Weifu Lee and Amit Meller
245
Abstract
245
1. Introduction
246
2. DNA sequencing by nanoclectrode-gated electron-tunneling conductance spectroscopic molecular detection
248
2.1. The concept and its origin
248
2.2. Potential speed of the envisioned nanoelectrode-gated DNA-sequencing system
251
2.3. Unique features of the nanoclectrode-gated molecular-detection concept
252
2.4. Theoretical analysis for the nanoclectrode-gated electronic detection
253
2.5. Preliminary experimental work toward proof-of-principle demonstration
254
2.6. Possible application of design polymers to enhance nanoelectrode-gated electron-tunneling DNA sequence detection
255
3. DNA sequencing by massively parallel optical readout of nanopore arrays and design polymer
256
3.1. The concept and its development
256
3.2. Biochemical conversion of DNA to design polymers format
257
3.3. Features of the nanopore-guided optical readout platform
258
3.4. Research effort toward proof-of-principle demonstration
260
4. Conclusion
260
Acknowledgments
261
References
261
Chapter
9. A Single Molecule System for Whole Genome Analysis
Shiguo Zhou, Jill Herschleb and David C. Schwartz
265
Abstract
266
1. Introduction
266
1.1. Presentation of long, restriction enzyme-digested DNA molecules
267
1.2. Image acquisition, processing, and machine vision: moving from images to data files
269
1.3. Data management, system network, map construction and analysis tools
269
1.3.1. Summary
271
1.4. The history of optical mapping
271
2. The optical mapping system
273
2.1. DNA preparation methods for optical mapping
273
2.1.1. Limitations and constraints of dealing with large DNA molecules: shearing and PFGE sample preparation
274
2.1.2. Extraction of DNA from PFGE inserts
274
2.1.3. Direct DNA extraction via heat lysis
274
2.2. Optical mapping surface preparation
275
2.2.1. Surface cleaning
275
2.2.2. Silane derivitization
276
2.3. Microfluidic device fabrication
276
2.4. DNA mounting, overlay, digestion, and staining
277
2.4.1. Mounting/overlay
278
2.4.2. Digestion and staining
279
3. The optical mapping system: image acquisition, processing, and analysis
280
3.1. A single molecule scanning system – "Genome Zephyr"
280
3.2. Constructing single molecule restriction maps from fluorescence micrographs
282
3.2.1. FlatOverMerge
282
3.2.2. PathFinder
283
3.3. Data storage, file management and visualization
284
3.4. Optical map assembly and alignment
285
3.4.1. De novo map assembly
285
3.4.2. Map Aligner: pairwise alignment of single DNA molecule optical maps against a reference map
286
3.4.3. Cluster computing
286
4. Applications of optical mapping
287
4.1. Use of optical maps to dissect complex genome structures and facilitate sequence assembly
287
4.2. Use of optical maps for microbial comparative genomics
287
4.3. Use of optical maps for microbial identification and infectious disease diagnosis
288
4.4. Discovering structural alterations in mammalian genomes
291
5. Comparison of optical mapping and alternate methods for genome analysis
292
5.1. Microarray-based methods
292
5.2. Pulsed-field gel electrophoresis
294
5.3. Cytogenetics
294
5.4. Paired-end sequencing
294
6. Optical sequencing
294
References
298
SEQUENCING VALIDATIONS AND ANALYSIS
Chapter
10. Sequencing Aided by Mutagenesis Facilitates the De Novo Sequencing of Megabase DNA Fragments by Short Read Lengths
Jonathan M. Keith, David B. Hawkes, Jacinta C. Carter, Duncan A.E. Cochran, Peter Adams, Darryn E. Bryant and Keith R. Mitchelson
303
Abstract
304
1. Introduction
304
1.1. Single molecule sequencing
305
1.2. PicoTiterPlate (Pyro)Sequencer 20
305
1.3. Non-repeat DNA sequencing
306
1.4. Limitations to the assembly of short-read data
307
2. Principles of SAM sequencing
307
2.1. Mutation by nucleotide analogues
309
2.2. Integration of SAM sequencing with SBS sequencing
309
3. Simulated SAM Sequencing
309
3.1. Representative sequence motifs
311
3.2. Initial data extraction
311
3.3. SAM assembly of simulated data
312
4. Analysis of SAM sequencing target assemblies
312
4.1. Assembly of contigs using 150 bp long reads
312
4.2. AT-rich insect genomic region
313
4.3. Human H LA region
313
4.4. Human sub-centromeric repeats and BRCA1 regions
314
4.5. Assembly with 100 bp long reads
315
4.6. Modeling with 25 bp long reads
317
4.7. Simulated SAM sequencing of the M. genitalium genome
317
5. Discussion
319
5.1. Assembly of human genomic DNA using SAM methodologies
319
5.2. Accuracy of the assemblies are relatively independent of target length
319
5.3. Can SAM sequencing aid SBS array short-read sequencing?
321
5.4. Costs and coverage for SAM sequencing
321
5.5. The advantages of SAM sequencing
323
5.6. Overcoming the biochemical limitations of SBS
324
References
325
Chapter
11. Genome Sequencing and Assembly
Annette McGrath
327
Abstract
327
1. Introduction
328
2. Approaches to genome sequencing
328
2.1. Whole genome shotgun sequencing
328
2.2. Clone-by-clone approach
331
2.3. Sequencing more complex genomes
333
2.4. Assembly of whole genome shotgun sequence
333
3. Problems inherent with genome assemblies
335
3.1. Repetitive DNA
335
3.2. Data quality
337
3.3. Cloning artifacts
338
4. A mathematical model of shotgun sequencing
338
5. Genome assembly approaches and programs
339
5.1. The shortest common superstring model
339
5.2. Case-study: Phrap
341
5.3. Overlap—layout consensus
342
6. New generation sequence assembly tools
343
6.1. Case Study: Arachne
344
6.2. Filling gaps in supercontigs
346
6.3. Alternative approaches
346
7. Assembly of genomes by comparative means
347
8. Assembly of sequence data from emerging sequencing technologies
348
References
350
Chapter
12. Valid Recovery of Nucleic Acid Sequence Information from High Contamination Risk Samples –Ancient DNA and Environmental DNA
George A. Kowalchuk, Jeremy J. Austin, Paul S. Gooding and John R. Stephen
357
Abstract
357
1. Introduction
358
2. Features of high contamination and artifact risk samples
359
2.1. Sources of nucleic acids and sampling
360
2.2. Nucleic acid extraction
361
3. Amplification and/or recovery of nucleic acids in the laboratory
363
4. Consideration in laboratory set-up
365
4.1. Controls necessary to ensure validity
366
5. Looking to the future
367
Subject Index 373


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