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9780471599081

Genomics The Science and Technology Behind the Human Genome Project

by ;
  • ISBN13:

    9780471599081

  • ISBN10:

    0471599085

  • Edition: 1st
  • Format: Hardcover
  • Copyright: 1999-03-12
  • Publisher: Wiley-Interscience
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Summary

Informed predictions for the future of DNA sequencing

Author Biography

CHARLES R. CANTOR, formerly principal scientist of the DOE Human Genome Project, is the Chief Scientific Officer of Sequenom, Inc., in San Diego. Dr. Cantor is on leave from Boston University, where he is Professor of Biomedical Engineering and Director of the Center for Advanced Biotechnology.<br> DRA L. SMITH is Deputy Director of the Center for Advanced Biotechnology and Professor of Biomedical Engineering, Biology, and Pharmacology at Boston University.

Table of Contents

Preface xiii(2)
Introduction xv
1 DNA Chemistry and Biology
1(28)
Basic Properties of DNA
1(1)
Covalent Structure
1(1)
Double Helical Structure
1(4)
Methylated Bases
5(2)
Plasticity in DNA Structure
7(1)
DNA Synthesis
8(7)
DNA as a Flexible Set of Chemical Reagents
15(4)
Basic DNA Biology
19(6)
Genome Sizes
25(2)
Number of Genes
27(1)
Sources and Additional Readings
27(2)
2 A Genome Overview at the Level of Chromosomes
29(35)
Basic Properties of Chromosomes
29(1)
Bacterial Chromosomes
29(3)
Chromosomes of Eukaryotic Organisms
32(1)
Centromeres
32(2)
Telomeres
34(1)
Dynamic Behavior of Telomeres
35(1)
Chromatin and the Higher-Order Structure of Chromosomes
36(3)
Chromosomes in the Cell Cycle
39(1)
Genome Organization
40(3)
Chromosome Purification
43(8)
Chromosome Number
51(3)
Unusual Characteristics of Sex Chromosomes and Mitochondria
54(5)
Synteny
59(4)
Sources and Additional Readings
63(1)
3 Analysis of DNA Sequences by Hybridization
64(34)
Basic Requirements for Selectivity and Sensitivity
64(2)
Detection of Specific DNA Sequences
66(1)
Equilibria between DNA Double and Single Strands
67(4)
Thermodynamics of the Melting of Short Duplexes
71(3)
Thermodynamics of Imperfectly Paired Duplexes
74(3)
Kinetics of the Melting of Short Duplexes
77(2)
Kinetics of Melting of Long DNA
79(1)
Kinetics of Double-Strand Formation
80(5)
Complexity
85(1)
Hybridization on Filters
86(4)
Sensitive Detection
90(7)
Sources and Additional Readings
97(1)
4 Polymerase Chain Reaction and Other Methods for In Vitro DNA Amplification
98(33)
Why Amplify DNA?
98(1)
Basic Principles of the Polymerase Chain Reaction (PCR)
98(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

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