Genomics The Science and Technology Behind the Human Genome Project

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

• ISBN13: 9780471599081
• ISBN10: 0471599085
• Edition: 1st
• Format: Hardcover
• Copyright: 1999-03-12
• Publisher: Wiley-Interscience

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