An Introduction to Forensic Genetics

Dr Will Goodwin, Senior Lecturer in Forensic Genetics, Faculty of Science and Technology, University of Central Lancashire. Dr Sibte Hadi, Senior Lecturer in Forensic Genetics, Faculty of Science and Technology, University of Central Lancashire. Dr Adrian M. T. Linacre, Department of Pure and Applied Chemistry, University of Strathclyde.

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 115

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