Forensic DNA Applications: An Interdisciplinary Perspective

Cover
Half Title
Title Page
Copyright Page
Table of Contents
Foreword
Preface
Acknowledgments
Editors
Contributors
Part I: General Background and Methodological Concepts
Chapter 1 Basic Genetics and Human Genetic Variation
1.1 Introduction
1.2 Historical Overview of DNA Research
1.2.1 Introduction to Human Genetics
1.2.2 Genome Structure
1.2.3 Chromosomes and Genes
1.2.4 Deoxyribonucleic Acid
1.2.5 Genetic Diversity
1.2.6 Variability of DNA
1.2.7 Structure and Nomenclature of STR Markers
1.2.8 Analysis of Sex Chromosomes
1.2.8.1 Y Chromosome DNA Testing
1.2.8.2 X Chromosome DNA Testing
1.2.9 Mitochondrial DNA
1.2.10 RNA Profiling
1.2.11 Application of New Molecular Markers
1.3 Potential Biological Sources of DNA
1.3.1 Basic Models and Steps of Forensic DNA Analysis
1.3.2 Collecting and Storing Samples
1.3.3 Determination of Biological Evidence
1.3.3.1 Blood
1.3.3.2 Semen
1.3.3.3 Vaginal Body Fluid
1.3.3.4 Saliva
1.3.3.5 Urine
1.3.3.6 Feces
1.4 DNA Isolation
1.5 DNA Quantification
1.5.1 Quantitative RT-PCR Quantification Technology
1.6 Polymerase Chain Reaction
1.7 PCR Methods
1.7.1 Multiplex STR Systems
1.7.2 PowerPlex® Fusion System
1.7.3 GlobalFiler® PCR Amplification Kit
1.7.4 Investigator 24plex QS Kit
1.8 Detection of PCR Products
1.8.1 Analytical Thresholds and Sensitivity for Forensic DNA Analysis
1.8.2 Sequencing
1.9 Massive Parallel Sequencing
1.10 DNA Phenotyping
1.11 Forensic Analysis of Plant DNA
1.12 Forensic Analysis of Animal DNA
References
Chapter 2 Forensic DNA Analysis and Statistics
2.1 Introduction
2.1.1 Genetic and Statistical Principles in Forensic Genetics
2.1.2 Principles of Parentage Testing
2.1.3 Hardy–Weinberg Equilibrium
2.1.4 Linkage Equilibrium
2.2 DNA Evidence in Court
2.3 Forensic Identification
2.3.1 Correction for Substructuring
2.3.2 Individualization and Identification
2.3.3 Parentage Testing
2.3.4 Paternity Index or Combined Paternity Index
2.3.5 Probability of Paternity
2.3.6 Random Man Not Excluded
2.3.7 Motherless Paternity Testing
2.3.8 Effect of Mutations
2.3.9 Maternity Testing
2.3.10 Parentage Testing with Mixed Populations
2.4 Identification of Human Body Remains
2.4.1 Victim Identification Using Parental DNA
2.4.2 Victim Identification Using Child’s DNA
2.4.3 Parentage Testing versus Forensic Identification
References
Chapter 3 Forensic Aspects of mtDNA Analysis
3.1 Mitochondrion and mtGenome Structure
3.2 mtDNA Copy Number
3.3 mtDNA Inheritance
3.4 Massively Parallel Sequencing
3.5 Alignment, Nomenclature, and Databasing of mtDNA Profiles
3.6 mtDNA Heteroplasmy
3.7 Nuclear mtDNA Segments
3.8 Application of mtDNA Analysis to Forensic Cases
3.9 Genetic Variability and Random Match Probabilities
References
Chapter 4 Y Chromosome in Forensic Science
4.1 Introduction
4.2 Sex Determination
4.3 Paternal Lineage Differentiation and Identification
4.3.1 Y-STR Markers in Forensic Genetics
4.3.2 Forensic Interpretation of Y-STR-Profile Matches
4.4 Paternal Male-Relative Differentiation and Identification
4.5 Paternity Testing, DVI, and Familial Search
4.6 Paternal Geographic Origin Inferences
4.6.1 Paternal Ancestry from Y-STR Haplotypes
4.6.2 Paternal Ancestry from Y-SNP Haplogroups
4.6.3 Y-SNP-Typing Technologies in Forensics
Acknowledgments
References
Chapter 5 Forensic Application of X Chromosome STRs
5.1 Introduction
5.1.1 Changes in Allele Frequencies Over Time
5.1.2 Random Match
5.2 Mutation Rates
5.2.1 Frequency of Zero Mutation Rates
5.3 Exchange and Compatibility of Data
5.4 The Anthropological Genetics of XSTRs
5.4.1 Allele Frequency Differences
5.5 Future Directions
Acknowledgments
Appendix: XSTR World Distribution
References
Chapter 6 Increasing the Efficiency of Typing Challenged Forensic Biological Samples
6.1 Introduction
6.2 Pre-PCR Improvement Strategies
6.3 PCR Improvement Strategies
6.3.1 Polymerases
6.3.2 PCR Enhancers
6.3.3 Reduction of the Size of Amplicons
6.3.4 PCR Cycles
6.3.5 Whole Genome Amplification
6.3.6 DNA Damage Repair
6.4 Post-PCR Approaches
6.4.1 Cleanup of Post-Amplification Products
6.4.2 Increased CE Injection Time
6.5 Conclusion
References
Chapter 7 Mixtures and Probabilistic Genotyping
7.1 Introduction
7.2 Conventional Methods for Mixture Interpretation
7.3 Number of Contributors
7.4 Probabilistic Genotyping
7.4.1 Semicontinuous Modeling
7.4.2 Continuous Modeling
7.5 Validation of Probabilistic Genotyping
7.6 Challenges to the Process
7.7 The Future of Mixtures and Probabilistic Genotyping
References
Chapter 8 Rapid DNA
8.1 Introduction
8.1.1 Overview
8.1.2 How Rapid DNA May Expand Use of DNA Testing
8.1.3 Rapid DNA Instrument: How Rugged?
8.1.4 Rapid DNA: Especially Important to DHS
8.2 Rapid DNA Development
8.2.1 Overview
8.2.2 Legislative and Regulatory Overview
8.2.3 Initial Concepts and Efforts
8.2.4 Department of Homeland Security (DHS)/Small Business Innovation Research (SBIR) Program
8.2.4.1 People Screening (PS)–Integrated Product Team (IPT)
8.2.4.2 PS-IPT/Homeland Security Institute (HSI) Partnership
8.2.5 Federal Funding
8.2.6 HSI Gap Assessment
8.2.6.1 Phase I SBIR technical objectives
8.2.6.2 The Objective of the 2009 DHS S&T SBIR Phase II and III
8.2.6.3 Massachusetts Institute of Technology/Lincoln Laboratory Solicitation
8.2.6.4 Applications and Field Studies
8.3 Advantages and Limitations of Rapid DNA Technology
8.3.1 Technology Strengths
8.3.2 Technology Limitations
8.3.3 Technology Applications
8.4 Transition of Rapid DNA into Operations
8.4.1 Examples of Successful Rapid DNA Applications
8.4.1.1 Law Enforcement Offices
8.4.1.2 Rapid Processing of Casework in the Crime Laboratory
8.4.1.3 Rapidly Identifying Human Remains in Medical Examiner Offices
8.4.1.4 Mass Fatality Planning and Response
8.4.1.5 Combating Family Unit Fraud
8.5 Lights out Rapid DNA for Biometric Uses
8.5.1 Expanding Capabilities: Software Support
8.5.2 Expanding Capabilities: Reachback Support
8.6 Rapid DNA Over the Next 20 Years
Notes
References
Part II: Uses and Applications
Chapter 9 Collection and Preservation of Physical Evidence
9.1 Introduction
9.1.1 Sample Collection from Victim or Suspect
9.1.1.1 Known Oral Swab Standards
9.1.1.2 Liquid Urine and/or Fecal Material
9.1.1.3 Vaginal Materials
9.1.1.4 Nasal Mucous
9.1.1.5 Bite Mark Evidence
9.1.1.6 Skin Tissue
9.1.1.7 Clothing or Personal Items
9.2 Recognition and Identification of Blood Evidence
9.2.1 Presumptive Blood Tests
9.2.2 Confirmatory Blood Tests
9.3 Collection Methods for Blood
9.3.1 Dried Blood Stains
9.3.2 Liquid Blood Samples
9.3.3 Seminal Stains
9.3.4 Stains from Other Physiological Fluids
9.4 Blood Stain Pattern Analysis
9.5 Crime Scene Reconstruction
9.6 Case Examples
9.6.1 Murder in Texas: Artificial Intelligence (AI) Resolves DNA Evidence Recovered from the Crime Scene
9.6.2 Concetta “Penney” Serra Homicide
9.6.3 Brown’s Chicken Murders
References
Chapter 10 Mass Disaster Victim Identification by DNA
10.1 Mass Fatality Incidents
10.2 Postmortem or Morgue Operations
10.3 Antemortem or Family Assistance Center Operations
10.4 DNA-Driven Victim Identifications: Lessons Learned from the World Trade Center Remains Identification Project
10.5 Reconciliation and Conclusions
References
Chapter 11 Bioterrorism and Microbial Forensics
11.1 Definitions
11.2 History of Bioterrorism and Biological Warfare
11.3 Classification of Specific Bioterrorism Agents
11.4 Microbial Forensic Protocols and Practices
11.5 Criteria for Considering an Outbreak Unusual
11.6 Suspicious Infectious Diseases Outbreaks
11.7 Does SARS-CoV-2 Have the Potential to be a Bioterrorism Agent?
11.8 Biosafety and Biosecurity
References
Chapter 12 Forensic Animal DNA Analysis
12.1 Introduction
12.2 Felid Forensic DNA Testing
12.2.1 Case Studies
12.2.2 Development of a Forensic Typing System for Genetic Individualization of Domestic Cat Samples
12.2.3 Validation Studies of Cat Multiplex
12.3 Canine Forensic DNA Testing
12.3.1 Case A Details: Fatal Dog Attack
12.3.2 Case B Details: Homicide
12.4 Bovine Forensic DNA Testing
12.5 Wildlife Forensic DNA Testing
12.5.1 mtDNA in Species Testing
12.5.2 Species Identification Using Loci on Mitochondrial Genome
12.5.3 Mitochondrial Sequence Analysis
12.5.4 Conclusions on Animal Testing
Acknowledgments
References
Chapter 13 Application of DNA-Based Methods in Forensic Entomology
13.1 Introduction
13.2 Methods of Insect DNA Analysis
13.3 Analysis of Human DNA Extracted from Insects
13.3.1 Case Study 1: A Caddisfly Casing in Service of Criminalistics
13.3.2 Case Study 2: Identity of Maggots Found on Outside and Inside of Body Bag
13.3.3 Case Study 3: Human and Insect mtDNA Analysis from Maggots
13.3.3.1 Insect mtDNA
13.3.3.2 Human mtDNA
13.3.4 Case Study 4: Genotyping of Human DNA Recovered from Mosquitoes Found at a Crime Scene
References
Chapter 14 Forensic Botany Plants as Evidence in Criminal Cases and as Agents of Bioterrorism
14.1 Introduction
14.2 Evidence Collection
14.3 Overview of Techniques
14.3.1 Microscopy
14.3.2 Species Identification
14.3.3 DNA Individualization
14.3.3.1 Amplified Fragment Length Polymorphism
14.3.3.2 Short Tandem Repeat
14.3.3.3 Random Amplified Fragment Polymorphism (RAPD)
14.3.3.4 Single-Nucleotide Polymorphism (SNP)
14.4 Examples of Plants with Bioterrorist Potential
14.5 Summary
References
Part III: Recent Developments and Future Directions in Human Forensic Molecular Biology
Chapter 15 Forensic Body Fluid and Tissue Identification
15.1 A Shift of Focus: From Individualization to Contextualization
15.2 Forensic Identification of Body Fluids and Organ Tissues
15.2.1 The “Big Five” and Then Some
15.2.1.1 Peripheral Blood
15.2.1.2 Vaginal Secretion
15.2.1.3 Menstrual Blood
15.2.1.4 Semen
15.2.1.5 Saliva
15.2.1.6 Other Body Fluids
15.2.1.7 Organ Tissues
15.3 Classical Tests for Forensic Body Fluid Identification
15.4 RNA-Based Approaches to Forensic Body Fluid and Tissue Identification
15.4.1 Messenger RNA
15.4.2 Micro-RNA (miRNA)
15.4.3 Other RNA species
15.4.3.1 Piwi-Interacting RNA (piRNA)
15.4.3.2 Circular RNA (circRNA)
15.4.4 Methods of Forensic RNA Analysis
15.4.4.1 Multiplex PCR and CE
15.4.4.2 Quantitative Reverse Transcription PCR (qRT-PCR)
15.4.4.3 Massively Parallel Sequencing (MPS)
15.4.4.4 Other Methods
15.5 DNA-Based Approaches to Forensic Body Fluid and Tissue Identification
15.5.1 Forensic Epigenetics: Methylation Analysis
15.5.1.1 Methods of Forensic Methylation Analysis
15.5.2 Copy-Number Variations
15.6 Other Approaches for Forensic Body Fluid and Tissue Identification
15.6.1 Raman Spectrometry
15.6.2 Fourier Transform Infrared Spectrometry
15.6.3 Microbiome Characterization
15.6.4 Protein Analysis and Proteomics
15.7 Outlook
Reference
Chapter 16 Evolving Technologies in Forensic DNA Analysis
16.1 Introduction
16.2 NGS/MPS
16.2.1 Introduction to NGS Technology
16.3 NGS, Mixtures, and Mitochondrial DNA
16.3.1 Mitochondrial DNA and Mixtures
16.3.2 Software Deconvolution of mtDNA Mixtures
16.4 NGS and STRs
16.5 Rapid DNA
16.6 Conclusions
Acknowledgments
References
Chapter 17 Prediction of Physical Characteristics, such as Eye, Hair, and Skin Color, Based Solely on DNA
17.1 Introduction
17.2 Complex Traits: Pigmentation
17.2.1 Eye Color Genetics
17.2.2 Hair Color Genetics
17.2.3 Skin Color Genetics
17.3 Developing Genetic Prediction Systems for Eye, Hair, and Skin Color
17.3.1 Genetic Prediction Systems for Eye Color
17.3.2 Genetic Prediction Systems for Hair Color
17.3.3 Genetic Prediction Systems for Skin Color
17.4 Future for Pigmentation Prediction and Forensic DNA Phenotyping
Acknowledgments
References
Chapter 18 Molecular Autopsy
18.1 Molecular Autopsy
18.1.1 Molecular Autopsy: Definition(s)
18.2 Molecular Genetics
18.2.1 Genetics and Genomics in Sudden Natural Death
18.2.1.1 Introduction
18.2.1.2 Positive Autopsy
18.2.1.3 Negative Autopsy
18.3 Postmortem Pharmacogenetics
18.3.1 Pharmacogenetics and Medicolegal Death Investigation
18.3.2 Development of Pharmacogenetic Concept to Pharmacogenomics
18.3.3 Adverse Drug Reactions
18.3.4 Investigation of Death and Toxicology
18.3.4.1 Postmortem Pharmacogenetics and CoD Investigation
18.4 Investigation of Death Due to Neglect or Abuse
18.5 Conclusion
References
Chapter 19 Genetic Genealogy in the Genomic Era
19.1 Introduction
19.2 DNA Testing for Genealogy
19.3 Haploid Chromosome Testing
19.3.1 Y Chromosome Testing
19.3.1.1 Discovering Paternal Lineages
19.3.1.2 Future of Y Chromosome Testing
19.3.2 mtDNA Testing
19.3.2.1 Discovering Maternal Lineages
19.3.2.2 mtDNA Testing Options
19.3.3 Future of Haploid Testing
19.4 Autosomal Testing
19.4.1 Why Assay the Autosomes?
19.4.2 Meiosis: A Genealogical Double-Edged Sword
19.4.3 Genetic Genealogy with Autosomal DNA
19.4.4 Ancestral Origin Estimation
19.4.5 Relative Identification
19.4.6 Conclusions
19.5 Discussion
Acknowledgments
References
Part IV: Law, Ethics, and Policy
Chapter 20 DNA as Evidence in the Courtroom
20.1 The American Experience
20.1.1 Introduction
20.1.2 Standards for Admissibility
20.1.3 Contemporary Issues in the Courtroom
20.1.4 Elements for Statutory DNA Testing
20.2 The European Experience
20.2.1 Introduction
20.2.2 Jurisprudence of the European Court of Human Rights
20.2.3 Croatian Constitutional Court Decision (2012)
20.2.4 Implications of S and Marper in the UK
20.2.5 Standards for DNA Retention and Use in Criminal Proceedings
20.3 The Croatian Experience
20.3.1 Introduction
20.3.2 European Law and Application of DNA Analysis in Criminal Procedure
20.3.3 Application of DNA Analysis in Croatian Criminal Procedure
References
Chapter 21 Some Ethical Issues in Forensic Genetics
21.1 Introduction
21.2 General Concepts in Bioethics
21.2.1 Justice
21.2.2 Privacy and Confidentiality
21.2.3 Autonomy and Informed Consent
21.2.4 Utility
21.3 Ethical Issues in Acquiring DNA Samples
21.3.1 Crime Scene Samples, and Shed or Abandoned DNA
21.3.2 Sampling with Consent
21.3.3 Acquiring DNA Samples from Medical Providers or Researchers
21.4 Law Enforcement DNA Databanks
21.5 Phenotypes and Racial Identifications from Genotypes
21.6 Identification of Remains
21.7 Ethics of Forensic Laboratory Reporting and Expert Testimony
Acknowledgments
References
Chapter 22 DNA in Immigration and Human Trafficking
22.1 Introduction
22.2 Relationship Testing in Immigration
22.2.1 Relationship Testing
22.2.2 Immigration Fraud and DNA
22.2.3 Rapid DNA Analysis
22.3 DNA Identification in Human Trade
22.3.1 Human Trade
22.3.2 Relationship Testing Strategies to Detect or Investigate Human Trafficking
22.3.3 DNA-PROKIDS
22.3.4 Dallas PDI
22.4 Ethical, Legal, and Social Considerations with DNA Identification
22.4.1 Defining “Family” in Immigration Procedures
22.4.2 Privacy of Genetic Information
22.4.3 Abuse of Power
22.4.4 Incidental Findings
22.4.5 Managing International Interoperable DNA Databases
22.4.6 Cultural Perspectives on Genetic Information
22.5 Summary
Acknowledgments
References
Chapter 23 DNA Databases
23.1 Introduction
23.2 Recommendations for Forensic DNA Databases
23.2.1 Legislation
23.2.2 Contents of a DNA Database
23.2.3 Data Protection
23.2.4 Quality Management
23.2.5 Resources
23.3 Volume of Databases Worldwide
23.3.1 National Databases
23.3.2 Interpol DNA Database
23.3.3 Database Efficiency
23.4 Sharing DNA Data across Borders
23.5 Ethical Aspects of Forensic DNA Databases
23.5.1 European Court of Human Rights Decision in UK Cases and North Macedonia Case
23.5.2 United States Supreme Court in Maryland v. King, 569 U.S. 435 (2013)
23.6 Quo Vadis Forensic DNA Database
23.6.1 Mitochondrial DNA
23.6.2 Y-Chromosomal STR Markers
23.6.3 Missing Persons
References
Index