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