Advanced Topics in Forensic DNA Typing: Methodology (eBook)

Front Cover 1
Advanced Topics in Forensic DNA Typing: Methodology 4
Copyright Page 5
Contents 8
Foreword 10
Introduction 12
Acknowledgments 16
About the Author 18
Chapter 1. Sample Collection, Storage, and Characterization 20
Steps in DNA Testing Process 20
Sample Collection 22
Sample Storage and Transport of DNA Evidence 28
Sample Characterization 29
Contamination Concerns 37
Reading List and Internet Resources 38
Chapter 2. DNA Extraction Methods 48
Purpose of DNA Extraction 48
Early Techniques used for DNA Extraction 50
Solid-Phase DNA Extraction Methods 53
Differential Extraction 56
Direct PCR to Bypass DNA Extraction 59
Reading List and Internet Resources 59
Chapter 3. DNA Quantitation 68
Purpose of DNA Quantitation 68
DNA Quantitation Methods 70
Real-Time Quantitative PCR (QPCR) 74
DNA Quantitation as a Gatekeeper 83
Reading List and Internet Resources 84
Chapter 4. PCR Amplification: Capabilities and Cautions 88
PCR Background and Basics 88
PCR Components & Controls
Multiplex PCR 100
PCR Inhibition 102
Modifications to Improve PCR 104
Stochastic Effects 106
Precautions Against Contamination 107
New Capabilities with Improvements in PCR 109
Reading List and Internet Resources 110
Chapter 5. Short Tandem Repeat (STR) Loci and Kits 118
Genetic Markers and Repeated DNA Sequences 118
Core and Common STR Markers 122
Commercial STR Kits 127
Information on 23 Core and Commonly Used STR Loci 133
STR Allele Nomenclature 141
Null (Silent) Alleles 145
STR Typing 146
Gender Identification with Amelogenin 148
STRBase: an Internet Resource 151
Reading List and Internet Resources 151
Chapter 6. Capillary Electrophoresis: Principles and Instrumentation 160
Requirements for STR Typing 160
Principles and Components of Capillary Electrophoresis 161
Electrokinetic Injection 163
DNA Separation 165
Fluorescence Detection 170
Instrumentation 178
Reading List and Internet Resources 181
Chapter 7. Quality Assurance and Validation 186
Importance of Quality Assurance 186
Levels of QA/QC 191
Levels of Validation 195
Other Aids to Quality Assurance 213
Reading List and Internet Resources 220
Chapter 8. DNA Databases: Uses and Issues 232
Value of DNA Databases 232
National DNA Databases around the World 237
The U.S. National DNA Database 240
DNA Database Laws in the United States 256
Issues and Concerns with DNA Databases 258
When There are No Hits after a Database Search 273
Concerns of DNA Database Critics 280
Reading List and Internet Resources 283
Chapter 9. Missing Persons and Disaster Victim Identification Efforts 290
Missing Persons Investigations 290
Disaster Victim Identification (DVI) 292
Issues Faced During Disaster Victim Identification Efforts 293
Reading List and Internet Resources 308
Chapter 10. Degraded DNA 312
Degraded DNA 312
Attempts with DNA Repair following DNA Damage 323
Reading List and Internet Resources 323
Chapter 11. Low-Level DNA Testing: Issues, Concerns, and Solutions 330
Introduction to Issues and Historical Overview 330
Assorted Topics 351
Reading List and Internet Resources 360
Chapter 12. Single Nucleotide Polymorphisms and Applications 366
Single Nucleotide Polymorphisms (SNPs) 366
SNP Analysis Techniques 370
Applications 374
Ethical Considerations 379
Insertion-Deletion Polymorphisms 380
Summary and Final Thoughts 380
Reading List and Internet Resources 382
Chapter 13. Y-Chromosome DNA Testing 390
Lineage Markers 390
Applications of ChrY Testing 390
ChrY Structure 393
Y-STR Markers 395
Y-STR Haplotype Databases 401
Interpretation of Y-STR Results 404
Y-STR Use in Forensic Casework 409
Y-SNPs and Haplogroups 413
ChrY Historical and Genealogical Studies 415
Summary 415
Reading List and Internet Resources 416
Chapter 14. Mitochondrial DNA Analysis 424
Characteristics of mtDNA 424
Mitochondrial DNA Sequencing in Forensic Casework 432
Interpretation of mtDNA Results 444
Issues Impacting Interpretation 448
Laboratories Performing mtDNA Testing 452
Screening Assays for mtDNA Typing 454
Population Databases 457
Reading List and Internet Resources 464
Chapter 15. X-Chromosome Analysis 476
ChrX Inheritance and Application 477
Applications of ChrX Testing 477
X-STR Markers Commonly Used 479
X-STR locus HumARA no longer used 481
X-STR Kits and Multiplex Assays 481
Population Data Collection and Other Studies 482
Reading List and Internet Resources 485
Chapter 16. Non-human DNA 492
Domestic Animal DNA Testing 494
Species Identification 499
Wildlife DNA Testing 500
Plant & Pollen DNA Testing
Identification through Human Parasites 504
Microbial Forensics 504
Challenges with Presenting Non-Human DNA in Court 505
Reading List and Internet Resources 506
Chapter 17. New Technologies and Automation 516
Rapid DNA Analysis 516
Mass Spectrometry 519
Pyrosequencing 520
Next-Generation DNA Sequencing 521
Laboratory Automation 521
Summary and Final Thoughts 527
Reading List and Internet Resources 528
Chapter 18. Legal Aspects of DNA Testing and the Scientific Expert in Court 534
Including input from interviews with Dr. Robin Cotton, Ted Hunt, Brad Bannon, the Orange County (CA) District Attorney’s DNA Unit, and Dr. Charlotte Word 534
Science and Law: Different Perspectives 536
Legal Terms, Concepts, and Important Court Cases 539
The Courtroom Scene 540
The Scientific Expert Witness 546
Admissibility of Evidence 551
Types of DNA Cases and Opposing Counsel Tactics 555
Jury Comprehension of DNA Evidence 560
Facing the “CSI Effect” 561
Final Thoughts 562
Reading List and Internet Resources 562
Appendix 1 Reported Sizes and Sequences of STR Alleles 568
CSF1PO 570
FGA 571
TH01 575
TPOX 576
VWA 577
D3S1358 579
D5S818 581
D7S820 582
D8S1179 (listed as D6S502 in early papers) 584
D13S317 586
D16S539 587
D18S51 588
D21S11 591
D2S1338 595
D19S433 597
Penta D 599
Penta E 601
D1S1656 603
D2S441 604
D10S1248 605
D12S391 606
D22S1045 608
SE33 609
Appendix 2 Familial DNA Searches: Potential, Pitfalls, and Privacy Concerns 622
Pitfalls of False Positives and False Negatives 624
Low Success Rates 625
Lineage Markers to Improve Success Rates 626
Supposed “Genetic Surveillance” of Families 626
Appendix 3 List of Suppliers for DNA Instruments, Reagents, Services 630
Appendix 4 Interviews Supporting Legal Aspects of DNA Testing 638
Interview with Dr. Robin Cotton on Being an Expert Witness 638
Interview with Dr. Charlotte Word on Admissibility Hearings 652
Interview with Ted Hunt, J.D., on a Prosecutor’s Perspective 656
Interview with the Orange County (California) District Attorney’s DNA Unit 663
Interview with Bradley Bannon, J.D., on a Defense Attorney’s Perspective 669
Subject Index 678