Forensic DNA Evidence Interpretation is the most comprehensive resource for DNA casework available today. Written by leaders in the fields of biology and statistics, the book emphasizes the interpretation of test results and provides the necessary formulae in an easily accessible manner.
The book begins by reviewing all pertinent biology, and then provides information on every aspect of DNA analysis, including modern interpretation methods and issues, and contemporary population genetic models available for estimating DNA frequencies or likelihood ratios. Following a chapter on procedures for validating databases, the text presents overviews and performance assessments of both modern sampling uncertainty methods and current paternity testing techniques. Later chapters discuss the latest methods for mixture analysis, LCN (ultra trace) analysis, and non-autosomal (mito, X, and Y) DNA analysis. The text concludes with procedures for disaster victim identification and information on DNA intelligence databases.
Supported by numerous tables and over 800 references, this authoritative book provides a link among the biological, forensic, and interpretative domains of the DNA profiling field. It is a valuable resource that allows forensic scientists and technicians, molecular biologists, and attorneys to use forensic DNA evidence to its greatest potential.

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edited by John Buckleton, Christopher M. Triggs, Simon J. Walsh

Christopher M. Triggs, John S. Buckleton, Simon J. Walsh

John Buckleton and Christopher M. Triggs

Auerbach Publishers, Incorporated

Chapman & Hall/CRC

CRC Press (Unlimited), Boca Raton, 2005

United States, United States of America

Boca Raton, Florida, 2005

November 29, 2004

1, US, 2004

Great Science Textbooks -- 1

lg79603

producers:
Acrobat Distiller 5.0.5 for Macintosh

{"edition":"1","isbns":["0849330173","9780849330179"],"last_page":552,"publisher":"CRC Press","series":"Forensicnetbase"}

Memory of the World Librarian: Quintus

Includes bibliographical references (p. 479-525) and index.

fm
rt3017_fm.pdf 1
Forensic DNA Evidence Interpretation 2
Preface 4
Acknowledgments 6
Editors 8
Contributors 9
Contents 10
RT3017_C001.pdf 12
Contents -1
Chapter 1 Biological Basisfor DNA Evidence 12
1.1 Historical and Biological Background 13
1.1.1 DNA Profiling Technology 15
1.1.1.1 Multilocus (Minisatellite) Testing 16
1.1.1.2 Single-Locus Probes 17
1.1.1.3 STR Analysis 18
1.1.1.3.1 Selection of STR loci for forensic multiplexing. 19
1.1.1.3.2 STR locus nomenclature. 22
1.1.1.3.3 STR allele designation. 22
1.1.1.3.4 STR allelic nomenclature. 24
1.2 Understanding STR Profiles 25
1.2.1 Genetic Anomalies 25
1.2.1.1 Trisomy and Gene Duplication 25
1.2.1.2 Somatic Mutation 25
1.2.2 PCR Artifacts 27
1.2.2.1 Heterozygote Balance 27
1.2.2.2 Allelic Dropout 32
1.2.2.3 Stuttering 32
1.2.2.4 Nonspecific Artifacts 34
1.2.2.5 Pull-Up 34
1.2.2.6 Poor Operator Technique 34
1.2.2.7 Suppression of Amplification Efficiency, Silent or Null Alleles 34
1.2.2.8 Promotion of Amplification Efficiency 36
1.3 Summary 36
RT3017_C002.pdf 37
Contents -1
Chapter 2 A Framework for Interpreting Evidence 37
2.1 The Frequentist Approach 39
2.1.1 Coincidence Probabilities 40
2.1.2 Exclusion Probabilities 41
2.1.3 Natural Frequenciesd 42
2.2 The Logical Approach 44
Box 2.1 A Derivation of Bayes’s Theorem 45
Box 2.2. Conditional Probability 46
2.3 The Full Bayesian Approach 49
Box 2.3 Which Way Up? 51
Box 2.4 53
2.4 A Possible Solution 54
2.5 Comparison of the Different Approaches 55
2.6 Evidence Interpretation in Court 60
2.6.1 The Fallacy of the Transposed Conditional 60
2.6.2 Establishing the Propositions 62
2.6.3 Errors in Analysisl 65
2.6.4 The Absence of Evidence 71
2.7 Summary 73
RT3017_C003.pdf 74
Contents -1
Chapter 3 Population Genetic Models 74
3.1 Introduction 75
3.2 Product Rule 77
3.2.1 Hardy–Weinberg Law 77
3.2.2 Linkage and Linkage Equilibrium 79
3.2.3 Consideration of the Hardy–Weinberg and Linkage Equilibrium Assumptions 81
3.2.3.1 Infinite Population 81
3.2.3.2 No Mutation 81
3.2.3.3 No Migration Into or Away from the Population 83
3.2.3.4 No Selection 83
3.2.3.5 Random Mating 85
3.2.3.6 An Infinite Number of Generations 89
3.2.3.7 Summary 90
3.2.4 How Big Is the Potential Departure If We Use the Product Rule? 90
3.2.5 Populations Separating By Genetic Drift 91
3.3 Simulation Testing 93
3.3.1 Product Rule 93
3.3.2 NRC II Recommendation 4.1 96
3.3.3 The Subpopulation Formulae 97
Box 3.1 Linkage Equilibrium and Conditional Probabilities ( J. S. Buckleton and C. M. Triggs) 100
3.4 Discussion of the Product Rule and the Subpopulation Model 106
3.4.1 Effect of Mutation 108
3.4.2 Admixture 109
3.4.3 Allelic Dropout 111
3.4.4 Arbitrary Limits 112
3.4.5 Same Source? 113
3.4.6 Animal and Plant DNA 118
3.5 A Complex Case Example — DNA Evidence and Orenthal James Simpsonl 119
3.5.1 The Evidence 123
3.5.2 The Trial 127
RT3017_C004.pdf 132
Contents -1
Chapter 4 Relatedness 132
4.1 Introduction 132
Box 4.1 Buckleton’s Buckets 133
4.2 Conditional Probabilities 134
4.2.1 The Method of Balding and Nichols 134
4.2.2 The Method of Weir 138
4.3 Joint Probabilities 145
4.4 The Unifying Formula 148
4.4.1 Full-Siblings 151
4.4.2 Match Probabilities for Half-Siblings 154
4.4.3 Numerical Effect of Linkage for Full-Siblings and Half- Siblings 155
RT3017_C005.pdf 158
Contents -1
Chapter 5 Validating Databases 158
5.1 Introduction 159
5.2 Which Is the Relevant Population? 160
5.3 Population Databases 160
5.3.1 Validating Population Databases 161
5.3.2 Sampling Races or Populations? 162
5.3.3 Source of Samples 163
5.3.4 Self-Declaration 165
5.3.5 Systematic Mistyping or Systematic Nontyping 167
5.3.6 Size of Database 169
Box 5.1 Stratification 163
5.4 Validating the Population Genetic Model 170
5.4.1 Independence Testing 171
5.4.1.1 The Exact Test 171
5.4.1.2 Total Heterozygosity Test 172
5.4.1.3 Variance of Heterozygosity Test 173
5.4.2 Performance of the Tests 173
5.4.2.1 Population Substructure 173
5.4.2.2 Randomly Mating Admixed Populations 175
5.4.3 Misuse of Independence Testing 176
5.4.3.1 Weakness of the Tests 178
5.4.3.2 Assuming That Independence Testing Measures Departure from Independence 179
5.4.3.3 Extrapolation from Single-Locus Tests 180
5.4.3.4 Assuming That Other Weak Tests Support This Weak Test 180
5.4.3.5 Post Hoc Rationalization 181
5.4.3.6 Multitesting 182
5.4.3.7 Effect of Silent Alleles 182
5.4.3.8 Misuse of Genetics 183
Box 5.2 An Example Using the Truncated Product Method for Hardy– Weinberg Tests on Nine Loci 183
Box 5.3 Hypothetical Example Showing the Creation of a 184
5.5 Estimating 185
5.5.1 Historic and Modern Consanguineous Marriage 188
5.5.2 Summary of Published Estimates of 190
5.5.2.1 Caucasian 191
5.5.2.2 Black African, Caribbean 193
5.5.2.3 Asian (Indo-Pakistani) 195
5.5.2.4 Hispanic and Latin American 195
5.5.2.5 Amerinds 196
5.5.2.6 East Asian 196
5.5.3 Dealing with Diverse Populations 196
5.6 Tippett Testing 197
5.7 Descriptive Statistics for Databases 200
5.7.1 Heterozygosity 200
5.7.2 Homozygosity 201
5.7.3 Gene Diversity (Often Termed Hex) 201
5.7.4 Match Probability 202
5.7.5 Power of Discrimination 202
5.7.6 Polymorphism Information Content 203
5.7.7 Probability of Excluding Paternity 203
5.7.8 Average Paternity Index 203
5.7.9 Haplotype Diversity 203
5.7.10 Summary 203
Appendix 5.1 (by James Curran and John Buckleton) 204
RT3017_C006.pdf 206
Contents -1
Chapter 6 Sampling Effects 206
6.1 Introduction 206
6.2 Bounds and a-Level 209
6.3 Methods for Assessing Sampling Uncertainty 210
6.3.1 Method: NRC I 210
6.3.2 Method: Factor of 10 210
6.3.3 Method: Asymptotic Normality of the Logarithm Extended by NRC II to Allow for Population Structure 211
6.3.4 Method: Bootstrap 213
6.3.5 Balding’s Size Bias Correction Corrected in Evett and Weir 214
6.3.5.1 Theoretical Support (following Weir et al. 215
6.3.5.1.1 Support intervals. 215
6.3.5.1.2 Uniform allele prior distribution. 216
6.3.5.1.3 Nonuniform allele prior distribution. 217
6.3.6 Method: Posterior Densityc 219
6.3.6.1 Explanation of the Bayesian Highest Posterior Density 220
6.3.6.1.1 Bayes theorem and Bayesian estimation. 220
6.3.6.1.2 Prior probabilities. 220
6.3.6.1.3 Posterior probabilities. 221
6.3.6.1.4 Highest posterior density intervals. 222
6.4 Minimum Allele Probabilities 223
6.5 Discussion of Appropriateness of Sampling Uncertainty Estimates — Buckleton 223
RT3017_C007.pdf 226
Contents -1
Chapter 7 Mixtures 226
7.1 Introduction 227
7.2 The Frequentist Approach 228
7.2.1 Method 1 — Exclusion Probabilities 228
Box 7.1 Provided by Professor Bruce Weir 229
Box 7.2 Arguments for the Use of the RMNE approach by Laszlo Szabo ( Tasmania Forensic Science Laboratory) 231
7.3 Bayesian Approaches 232
7.3.1 Models Employing Qualitative Approaches 232
7.3.1.1 The General Formula 237
7.3.2 Models Employing Quantitative and Qualitative Data 239
7.3.2.1 Quantitative Data — Peak Areas or Heights? 240
7.3.3 The Binary Model 240
7.3.3.1 Application of the Binary Model 242
7.3.3.2 Automation of Mx Estimation: PENDULUM 248
7.3.3.3 Assumptions of the Binary Model 251
7.3.3.4 Allowing for Stutters 251
7.3.3.5 Allowing for Incomplete Representation 252
7.3.3.6 Reliability of the Binary Model. 253
7.3.4 Continuous Methods 262
7.3.4.1 Normal Approximation-Based Methods 262
7.3.4.2 Monte Carlo and Monte Carlo Markov Chain ( MCMC) Methods 263
7.4 Statistical Evaluation of Mixtures 268
7.4.1 The Sampling Formula 268
7.4.1.1 Shortcut Rules 270
7.4.1.2 When Should a Genotype Be Used in the Conditioning? 273
7.4.1.3 The General Formula 274
7.4.1.4 Mixtures and Relatives 277
7.4.2 The Two-Trace Problem and the Factor of 2 278
7.4.2.1 The Issue of Relevance and the Factor of 2 278
7.4.2.2 Propositions 279
7.4.2.3 Locus-by-Locus Approachl 282
7.4.2.4 The Full-Genotype Approach 282
7.4.2.5 Unknown Number of Contributors and Ethnicity 283
RT3017_C008.pdf 284
Contents -1
Chapter 8 Low Copy Number 284
8.1 Introduction 284
8.2 Changes in LCN Profile Morphology 287
8.2.1 Heterozygote Balance 287
8.2.2 Allelic Dropout 288
8.2.3 Stutter 289
8.2.4 Spurious Alleles 289
8.3 Interpretation of LCN Profiles 292
8.3.1 The “Biological” Model 292
8.3.2 A Formative Bayesian Model 293
8.3.2.1 A Coarse Statistical Theoryf 295
8.3.2.2 Dealing with Multiple Spurious Alleles 305
8.3.2.3 Mixture Analysis 306
RT3017_C009.pdf 307
Contents -1
Chapter 9 Nonautosomal Forensic Markers 307
9.1 Introduction 308
9.2 Forensic Mitochondrial DNA Typing 308
9.2.1 Matrilineal Inheritance and Recombination 309
9.2.2 Mutations and Heteroplasmy 311
9.2.3 Nomenclature 313
9.2.3.1 Insertions and Deletions 314
9.2.3.2 Point Heteroplasmy 314
9.2.3.3 Length Heteroplasmy 315
9.2.4 Interpretation — The Logical Approach 315
9.2.4.1 Distribution of Mitochondrial DNA Types in Populations 318
9.2.4.2 Heteroplasmy 320
9.2.4.3 Sampling Uncertainty 320
9.2.4.4 Examples of the Logical Approach in Practice 322
9.2.5 Interpretation — The Frequentist Approach 324
9.2.6 Combining Mitochondrial DNA Estimates with Nuclear DNA Estimates 325
9.3 Forensic Y Chromosome Analysis 325
9.3.1 Introduction 325
9.3.2 Mutation 329
9.3.3 Databases of Y Haplotypes 332
9.3.4 Y chromosome θ, RST, GST, or Values 332
9.3.5 Negative Correlation of Mitochondrial DNA and Y Chromosome Haplotypes 333
9.3.6 Combining Y Chromosome Evidence with Autosomal or Mitochondrial DNA Evidence 333
9.3.7 Y Chromosome Mixtures 335
9.4 Forensic X Chromosome Analysis 337
9.5 A Famous Case Example — The Romanovs 339
RT3017_C010.pdf 349
Contents -1
Chapter 10 Parentage Testing 349
10.1 Introduction 350
10.1.1 Testing Diverse Sample Types 351
10.1.1.1 Termination Products 351
10.1.1.2 Preserved Histology Samples 351
10.1.2 Principles of Mendelian inheritance 352
10.2 Evaluation of Evidence 355
10.2.1 Exclusion Probability 355
10.2.2 Paternity Index 356
10.2.2.1 Use of the Product Rule in the Evaluation of the Paternity Index 357
10.2.3 Probability of Paternity 358
10.2.4 Paternity Trios: Mother, Child, and Alleged Father 359
10.2.4.1 Distribution of PI 363
10.2.5 Paternity Duos: Child and Alleged Father 365
10.2.6 Linked Loci 367
10.2.7 Paternally Imprinted Alleles 369
10.3 Nonautosomal DNA Markers 369
10.3.1 Y Chromosome Analysis 369
10.3.2 X Chromosome Analysis 370
10.3.2.1 Maternity Analysis for X Chromosomes 371
10.3.3 Mitochondrial DNA Analysis 371
10.4 Use of the Subpopulation Model 371
10.5 Relatedness in Paternity Cases 376
10.5.1 A Relative of the Accused is Suggested as the Alleged Father 377
10.5.2 Deficient Paternity Analysis (The Alleged Father is Unavailable) 378
10.6 Multiple Children 382
10.7 Mutation 384
10.7.1 Paternity Trios with “Apparent Mutation” 392
10.7.1.1 Mother, Child, and Alleged Father — Father Does Not Possess the Paternal Allele 392
10.7.1.2 Mother, Child, and Alleged Father — The Possibility of Silent ( Null) Alleles 394
10.7.2 Mutation and Nonautosomal DNA 396
10.7.2.1 Y Chromosome 396
10.7.2.2 X Chromosome Analysis 397
10.7.2.3 Mitochondrial Maternity Analysis and Mutation 398
10.8 Inconsistencies in the Mendelian Pattern 398
10.8.1 Three-Banded Patterns 399
10.8.1.1 Somatic Mutation 399
10.8.1.2 Trisomy and Translocation 400
10.9 “Exclusions” 401
10.9.1 Mutation and Exclusion Probabilitiesh 401
RT3017_C011.pdf 403
Contents -1
Chapter 11 Disaster Victim Identification, Identification of Missing Persons, and Immigration Cases 403
11.1 Introduction 404
11.2 Mitochondrial or Nuclear DNA? 405
11.2.1 MtDNA 405
11.2.2 Nuclear DNA 405
11.3 Human Remains — Obtaining a Profile from Bodily Remains 406
11.3.1 Category 1: Remains Displaying Relatively Few Signs of Decomposition 407
11.3.2 Category 2: Remains Exhibiting Partial Decomposition 407
11.3.3 Category 3: Remains in an Advanced State of Decomposition 407
11.3.4 Category 4: Remains that are Fully Skeletonized ( Including Mummified or Desiccated Remains) 408
11.3.4.1 Extraction of DNA from Bone, Tooth, Hair, and Nail 408
11.4 Comparisons 409
11.4.1 Surrogate Samples 409
11.4.1.1 Twins 409
11.4.2 Pedigree Analysis 410
11.4.2.1 General Principles 410
11.4.2.2 Parents 411
11.4.2.3 Children 415
11.4.2.4 Siblings 418
11.4.2.5 Distribution of the LR 419
11.4.2.6 Other Combinations of First-Degree Relatives 421
Box 11.1 Evaluation of the Probability of Observing a Set of Genotypes Conditional on a Specified Pedigree 413
11.5 Complicating Factors 436
11.6 Mass Disasters 438
11.6.1 Closed Set Matching 439
11.6.2 The Waco Incident 442
RT3017_C012.pdf 446
Contents -1
Chapter 12 DNA Intelligence Databases 446
12.1 A Brief History 446
12.2 Functional Aspects 447
12.2.1 Administration 449
12.2.2 Performance Management 451
12.3 Legislation 453
12.4 Aspects of Forensic Significance 457
12.5 Social and Ethical Considerations 465
12.6 Interpretation Issues Associated with DNA Databases 467
12.6.1 Adventitious Matches 467
12.6.2 Assessing the Strength of the Evidence from a Match Derived from the Intelligence Database 471
Box 12.1 Triggs and Buckleton 470
12.7 Summary 476
RT3017_gloss.pdf 477
Contents -1
Glossary 477
RT3017_ref.pdf 485
Contents -1
References 485

"Forensic DNA Evidence Interpretation is the most comprehensive resource for DNA casework available today. Written by leaders in the fields of biology and statistics, the book emphasizes the interpretation of test results and provides the necessary formulae in an easily accessible manner." "Supported by numerous tables and over 800 references, this authoritative book provides links connecting the biological, forensic, and interpretative domains of the DNA profiling field. It is a valuable resource that allows forensic scientists and technicians, molecular biologists, and attorneys to use forensic DNA evidence to its greatest potential."--Jacket

2009-07-20