Genomics The Science and Technology Behind the Human Genome Project

, by Cantor, Charles R.; Smith, Cassandra L.

Write a Review

Note: Supplemental materials are not guaranteed with Rental or Used book purchases.

ISBN: 9780471599081 | 0471599085
Cover: Hardcover
Copyright: 3/12/1999

Buy New

Print on Demand: 2-4 Weeks. This item cannot be cancelled or returned.

$277.39
eBook

Available Instantly

Online: 1825 Days

Downloadable: Lifetime Access

*To support the delivery of the digital material to you, a digital delivery fee of $3.99 will be charged on each digital item.

$252.00*

Summary

Author Biography

Supplemental Materials

Informed predictions for the future of DNA sequencing

Preface

xiii

(2)

Introduction

1 DNA Chemistry and Biology

(28)

Basic Properties of DNA

(1)

Covalent Structure

(1)

Double Helical Structure

(4)

Methylated Bases

(2)

Plasticity in DNA Structure

(1)

DNA Synthesis

(7)

DNA as a Flexible Set of Chemical Reagents

(4)

Basic DNA Biology

(6)

Genome Sizes

(2)

Number of Genes

(1)

Sources and Additional Readings

(2)

2 A Genome Overview at the Level of Chromosomes

(35)

Basic Properties of Chromosomes

(1)

Bacterial Chromosomes

(3)

Chromosomes of Eukaryotic Organisms

(1)

Centromeres

(2)

Telomeres

(1)

Dynamic Behavior of Telomeres

(1)

Chromatin and the Higher-Order Structure of Chromosomes

(3)

Chromosomes in the Cell Cycle

(1)

Genome Organization

(3)

Chromosome Purification

(8)

Chromosome Number

(3)

Unusual Characteristics of Sex Chromosomes and Mitochondria

(5)

Synteny

(4)

Sources and Additional Readings

(1)

3 Analysis of DNA Sequences by Hybridization

(34)

Basic Requirements for Selectivity and Sensitivity

(2)

Detection of Specific DNA Sequences

(1)

Equilibria between DNA Double and Single Strands

(4)

Thermodynamics of the Melting of Short Duplexes

(3)

Thermodynamics of Imperfectly Paired Duplexes

(3)

Kinetics of the Melting of Short Duplexes

(2)

Kinetics of Melting of Long DNA

(1)

Kinetics of Double-Strand Formation

(5)

Complexity

(1)

Hybridization on Filters

(4)

Sensitive Detection

(7)

Sources and Additional Readings

(1)

4 Polymerase Chain Reaction and Other Methods for In Vitro DNA Amplification

(33)

Why Amplify DNA?

(1)

Basic Principles of the Polymerase Chain Reaction (PCR)

(5)

Noise in PCR: Contamination

103

(1)

PCR Noise: Mispriming

104

(2)

Misincorporation

106

(1)

Long PCR

106

(1)

Incorporating Extra Functionalities

107

(1)

Single-Sided PCR

107

(5)

Reducing Complexity with PCR

112

(2)

Additional Variants of the Basic PCR Reaction

114

(2)

Total Genome Amplification Methods

116

(3)

Application of PCR to Detect Molecules Other Than DNA

119

(3)

DNA Amplification without Thermal Cycling and Other Alternatives to PCR

122

(5)

Future of PCR

127

(1)

Sources and Additional Readings

128

(3)

5 Principles of DNA Electrophoresis

131

(34)

Physical Fractionation of DNA

131

(1)

Separation of DNA in the Ultracentrifuge

131

(1)

Electrophoretic Size Separations of DNA

132

(1)

Electrophoresis without Gels

133

(2)

Motions of DNA Molecules in Gels

135

(1)

Complex Effects of Gel Structure and Behavior

136

(2)

Biased Reptation Model of DNA Behavior in Gels

138

(2)

Pulsed Field Gel Electrophoresis (PFG)

140

(6)

Macroscopic Behavior of DNA in PFG

146

(2)

Inadequacy of Reptation Models for PFG

148

(7)

DNA Trapping Electrophoresis

155

(2)

Secondary Pulsed Field Gel Electrophoresis (SPFG)

157

(1)

Entry of DNAs into Gels

158

(6)

Sources and Additional Readings

164

(1)

6 Genetic Analysis

165

(43)

Why We Need Genetics

165

(1)

Basic Strategy for Genetic Analysis in the Human: Linkage Mapping

165

(5)

A Glossary of Genetic Terms

170

(4)

Relationship between the Physical and the Genetic Maps

174

(4)

Power of Mouse Genetics

178

(1)

Weakness of Human Genetics

178

(2)

Linkage Analysis Ignoring Recombination

180

(3)

Linkage Analysis with Recombination

183

(2)

Interval Mapping

185

(3)

Finding Genes by Genetic Mapping

188

(2)

Moving from Weak Linkage Closer to a Gene

190

(1)

Linkage Disequilibrium

191

(2)

Complications in Linkage Disequilibrium and Genetic Maps in General

193

(1)

Distortions in the Genetic Map

194

(1)

Current State of the Human Genetic Map

195

(2)

Genetics in the Pseudoautosomal Region

197

(4)

Why Genetics Needs DNA Analysis

201

(3)

Detection of Homozygous Regions

204

(2)

Sources and Additional Readings

206

(2)

7 Cytogenetics and Pseudogenetics

208

(26)

Why Genetics Is Insufficient

208

(1)

Somatic Cell Genetics

208

(2)

Subchromosomal Mapping Panels

210

(2)

Radiation Hybrids

212

(3)

Single-Sperm PCR

215

(3)

In Situ Hybridization

218

(6)

High-Resolution FISH

224

(5)

Chromosome Painting

229

(1)

Chromosome Microdissection

230

(2)

Sources and Additional Readings

232

(2)

8 Physical Mapping

234

(51)

Why High Resolution Physical Maps Are Needed

234

(1)

Restriction Maps

235

(4)

Ordered Libraries

239

(2)

Restriction Nuclease Genomic Digests

241

(4)

HTF Islands

245

(1)

Ordering Restriction Fragments

246

(2)

Identifying the DNA Fragments Generated by a Rare-Cutting Restriction Enzyme

248

(4)

Mapping in Cases Where Fragment Lengths Can Be Measured Directly

252

(1)

Generation of Larger DNA Fragment Sizes

253

(1)

Linking Clones

254

(3)

Jumping Libraries

257

(2)

Partial Digestion

259

(3)

Exploiting DNA Polymorphisms to Assist Mapping

262

(2)

Placing Small Fragments on Maps

264

(1)

Reaching the Ends of the Physical Map: Cloning Telomeres

265

(4)

Optical Mapping

269

(1)

Bottom-Up Library Ordering

269

(6)

Measurements of Progress in Building Ordered Libraries

275

(2)

Survey of Restriction Map and Ordered Library Construction

277

(7)

Sources and Additional Readings

284

(1)

9 Enhanced Methods for Physical Mapping

285

(40)

Why Better Mapping Methods Are Needed

285

(1)

Larger Yeast Artificial Chromosomes (YACs)

285

(3)

How Far Can YACs Go?

288

(2)

Vector Obsolescence

290

(1)

Hybrid Mapping Strategies: Cross-connections between Libraries

291

(5)

Screening by PCR versus Hybridization

296

(2)

Tiered Sets of Samples

298

(2)

Simple Pooling Strategies for Finding a Clone of Interest

300

(1)

Sequence-Specific Tags

301

(2)

Pooling in Mapping Strategies

303

(2)

Probe Pooling in S. pombe Mapping

305

(6)

False Positives with Simple Pooling Schemes

311

(1)

More General Pooling Schemes

312

(4)

Alternate Array Configurations

316

(2)

Inner Product Mapping

318

(2)

Sliced PFG Fractionations as Natural Pools of Samples

320

(1)

Restriction Landmark Genome Scanning

320

(2)

Prognosis for the Future of Genome Mapping

322

(1)

Sources and Additional Readings

323

(2)

10 DNA Sequencing: Current Tactics

325

(36)

Why Determine DNA Sequence

325

(1)

Design of DNA Sequencing Projects

326

(1)

Ladder Sequencing Tactics

327

(3)

Issues in Ladder Sequencing

330

(4)

Current Fluorescent DNA Sequencing

334

(2)

Variations in Contemporary DNA Sequencing Tactics

336

(5)

Errors in DNA Sequencing

341

(4)

Automated DNA Sequencing Chemistry

345

(3)

Future Improvements in Ladder Sequencing

348

(1)

Approaches to DNA Sequencing by Mass Spectrometry

349

(9)

Rate-Limiting Steps in Current DNA Sequencing

358

(1)

Sources and Additional Readings

359

(2)

11 Strategies for Large-Scale DNA Sequencing

361

(33)

Why Strategies Are Needed

361

(1)

Shotgun DNA Sequencing

361

(2)

Directed Sequencing with Walking Primers

363

(2)

Priming with Mixtures of Short Oligonucleotides

365

(3)

Ordered Subdivision of DNA Targets

368

(1)

Transposon-Mediated DNA Sequencing

368

(2)

Delta Restriction Cloning

370

(1)

Nested Deletions

371

(2)

Primer Jumping

373

(2)

Primer Multiplexing

375

(1)

Multiplex Genomic Walking

376

(1)

Global Strategies

377

(2)

Sequence-Ready Libraries

379

(1)

Sequencing cDNA Libraries

380

(1)

Dealing with Uneven cDNA Distribution

381

(3)

Large-Scale cDNA Sequencing

384

(5)

What Is Meant by a Complete Genome Sequence?

389

(1)

Sequencing the Fifth Base

390

(2)

Sources and Additional Readings

392

(2)

12 Future DNA Sequencing without Length Fractionation

394

(39)

Why Try to Avoid Length Fractionations?

394

(1)

Single-Molecule Sequencing

394

(3)

Sequencing by High-Resolution Microscopy

397

(3)

Stepwise Enzymatic Sequencing

400

(3)

DNA Sequencing by Hybridization (SBH)

403

(1)

Branch Point Ambiguities

404

(2)

SBH Using Oligonucleotide Chips

406

(4)

Sequencing by Hybridization to Sample Chips

410

(2)

Early Experiences with SBH

412

(3)

Data Acquisition and Analysis

415

(2)

Obstacles to Successful SBH

417

(3)

SBH in Comparative DNA Sequencing

420

(1)

Oligonucleotide Stacking Hybridization

421

(3)

Other Approaches for Enhancing SBH

424

(1)

Positional Sequencing by Hybridization (PSBH)

425

(5)

Combination of SBH with Other Sequencing Methods

430

(1)

Sources and Additional Readings

431

(2)

13 Finding Genes and Mutations

433

(37)

Detection of Altered DNA Sequences

433

(1)

Finding Genes

434

(14)

Diagnostics at the DNA Level

448

(7)

Analysis of DNA Sequence Differences

455

(1)

Heteroduplex Detection

456

(6)

Diagnosis of Infectious Disease

462

(1)

Detection of New Mutations

463

(4)

Sources and Additional Readings

467

(3)

14 Sequence-Specific Manipulation of DNA

470

(56)

Exploiting the Specificity of Base-Base Recognition

470

(1)

Structure of Triple-Stranded DNA

470

(6)

Triplex-Mediated DNA Cleavage

476

(4)

Sequence-Specific DNA Capture

480

(1)

Triplex-Mediated DNA Capture

480

(6)

Affinity Capture Electrophoresis

486

(3)

Use of Backbone Analogues in Sequence-Specific DNA Manipulation

489

(3)

Sequence-Specific Cloning Procedures

492

(7)

Identification or Cloning of Sequences Based on Differences in Expression Level

499

(1)

Coincidence Cloning

500

(6)

Human Interspersed Repeated DNA Sequences

506

(3)

Distribution of Repeats Along Chromosomes

509

(1)

PCR Based on Repeating Sequences

510

(6)

Repeat Expansion Detection

516

(1)

Aptamer Selection Strategies

517

(3)

Oligonucleotides as Drugs

520

(3)

Sources and Additional Readings

523

(3)

15 Results and Implications of Large-Scale DNA Sequencing

526

(43)

Costing the Genome Project

526

(4)

Finding Genes

530

(2)

More Robust Methods for Finding Genes by DNA Sequence Analysis

532

(3)

Neural Net Analysis of DNA Sequences

535

(5)

Survey of Past Large-Scale DNA Sequencing Projects

540

(5)

Finding Errors in DNA Sequences

545

(2)

Searching for the Biological Function of DNA Sequences

547

(1)

Searching for the Biological Function of Genes

548

(3)

Methods for Comparing Sequences

551

(6)

Dynamic Programming

557

(3)

Gaining Additional Power in Sequence Comparisons

560

(1)

Domains and Motifs

561

(2)

Interpreting Noncoding Sequence

563

(1)

Diversity of DNA Sequences

564

(1)

Sources and Additional Readings

565

(4)

Appendix: Databases

569

(6)

Index

575

Please wait while the item is added to your bag...

FREE SHIPPING

Rent More, Save More! Use code: BBRENTAL

5% off 1 book, 7% off 2 books, 10% off 3+ books

Genomics The Science and Technology Behind the Human Genome Project

Summary

Author Biography

Table of Contents

Supplemental Materials

FREE SHIPPING

Rent More, Save More! Use code: BBRENTAL

5% off 1 book, 7% off 2 books, 10% off 3+ books

Genomics The Science and Technology Behind the Human Genome Project

Summary

Author Biography

Table of Contents

Supplemental Materials

Digital License