Foreword

ix

Preface

xi

Preface to First Edition

xiii

1

Introduction to Forensic Genetics

1

Forensic Genetics

1

A Brief History of Forensic Genetics

2

References

6

2

DNA Structure and the Genome

11

DNA Structure

11

Organization of DNA into Chromosomes

11

The Structure of the Human Genome

13

Genetic Diversity of Modern Humans

15

The Genome and Forensic Genetics

16

Tandem Repeats

16

Single Nucleotide Polymorphisms

18

References

19

3

Biological Material - Collection, Characterization and Storage

21

Sources of Biological Evidence

21

Collection and Handling of Material at the Crime Scene

23

Identification and Characterization of Biological Evidence

23

Evidence Collection

29

Sexual and Physical Assault

31

Storage of Biological Material

32

References

32

4

DNA Extraction and Quantification

37

DNA Extraction

37

General Principles of DNA Extraction

37

DNA Extraction from Challenging Samples

41

Quantification of DNA

45

DNA IQ System

48

References

49

5

Polymerase Chain Reaction

53

The Evolution of PCR-Based Profiling in Forensic Genetics

53

DNA Replication: the Basis of the PCR

54

The Components of PCR

54

Taq DNA Polymerase

54

The PCR Process

56

PCR Inhibition

58

Sensitivity and Contamination

60

The PCR Laboratory

60

Further Reading

62

References

62

6

The Analysis of Short Tandem Repeats

67

Structure of STR Loci

67

The Development of STR Multiplexes

67

Detection of STR Polymorphisms

70

Interpretation of STR Profiles

72

Further Reading

77

References

77

7

Assessment of STR Profiles

81

Stutter Peaks

81

Split Peaks (±N)

81

Pull-Up

83

Template DNA

84

Overloaded Profiles

84

Low Template DNA Typing

84

Peak Balance

86

Mixtures

86

Degraded DNA

88

PCR Inhibition

90

References

91

8

Statistical Interpretation of STR Profiles

95

Population Genetics

95

Deviation from the Hardy-Weinberg Equilibrium

96

Statistical Tests to Determine Deviation from the Hardy-Weinberg Equilibrium

97

Estimating the Frequencies of STR Profiles

98

Corrections to Allele Frequency Databases

98

Which Population Frequency Database should be Used?

103

Conclusions

104

Further Reading

104

References

104

9

Evaluation and Presentation of DNA Evidence

107

Hierarchies of Propositions

107

Likelihood Ratios

109

Two Fallacies

113

Comparison of Three Approaches

114

Further Reading

115

References

1J5

10

Databases of DNA Profiles

117

The UK National DNA Database

117

International Situation

124

Further Reading

128

References

128

11

Kinship Testing

131

Parentage Testing

131

Punnett Square

132

Identification of Human Remains

139

Further Reading

140

References

140

12

Single Nucleotide Polymorphisms

145

SNPs - Occurrence and Structure

145

Detection of SNPs

146

SNP Detection for Forensic Applications

148

Forensic Applications of SNPs

149

SNPs Compared with STR Loci

150

References

152

13

Lineage Markers

155

Mitochondria

155

Applications of mtDNA Profiling

157

Haplotypes and Haplogroups

159

The Y Chromosome

161

Forensic Applications of Y Chromosome Polymorphisms

162

Further Reading

165

References

165

14

Non-Human DNA Typing

171

Non-Human Sample Types

171

Species Identification

173

Linkage to an Individual Using STR Loci

174

Linkage to an Individual Using Mitochondrial Loci

175

Microbial DNA Testing

176

Concluding Comments

176

Further Reading

176

References

176

Appendix A

Forensic Parameters

181

Appendix B

Useful Web Links

183

Glossary

185

Abbreviations

189

Index

193