Advancements in Forensic DNA Analysis

This textbook for undergraduate and postgraduate students discusses advancements in forensic DNA analysis since early texts were published. It presents conventional and latest serological and molecular biological methods for body fluid identification. This book also describes the applications and advantages of next-generation sequencing (NGS) compared to conventional methods in forensic DNA analysis. It also defines the growing importance, techniques, and applications for the analysis of non-human DNA in forensic sciences. Further, the book examines the role of DNA databases in forensic interpretation and criminal investigations. Towards the end, this textbook reviews the application of forensic DNA technology in analyzing real-time casework samples and presents the guidelines, ethical issues, and other challenges of forensic DNA analysis. This textbook is an essential resource for students and practitioners interested in gaining knowledge of up-to-date forensic techniques and their applications in forensic DNA analysis. Preface Contents About the Editors 1: Current Status and Advancements of Forensic DNA Analysis 1.1 Introduction to Forensic DNA Analysis 1.2 An Overview of DNA Typing Targets and Approaches 1.3 An Overview of the DNA Typing Process with Advancements 1.4 An Overview of the Advancements in Chemistry and Technology 1.5 Addition of Genetic Genealogy to Solve Unsolved Cases 1.6 Conclusion References 2: Use of Advanced Molecular Techniques for Human Body Fluids Detection 2.1 Introduction to Forensic Body Fluids Analysis 2.2 mRNA Expression 2.3 microRNA Expression 2.4 snRNA, snoRNA, and piRNA Expression 2.5 Methylated DNA Analysis 2.6 MPS DNA Analysis 2.7 Microbiome Analysis for Body Fluids and Sites 2.8 Conclusion and Future of Body Fluids Analysis References 3: Technological Advancements in DNA Extraction and Quantification of Forensic Samples 3.1 Introduction 3.2 DNA Extraction 3.2.1 Organic DNA Extraction System 3.2.2 Automated DNA Extraction System 3.2.2.1 EZ1&2 DNA Investigator Kit, Qiagen 3.2.2.2 Maxwell FSC DNA IQ Casework Kit, Promega 3.2.2.3 PrepFiler Express Forensic DNA Extraction Kit, Thermo Fisher Scientific 3.3 Comparison Between Different Extraction Platforms 3.4 Quality Control of the Extracted DNA 3.5 DNA Quantification 3.6 DNA Quantification Instrumentation 3.7 Conclusion References 4: Advanced Emerging Techniques for Forensic DNA Analysis: STRs, SNPs, and mtDNA Analysis 4.1 Introduction 4.2 STR Techniques and Its Advancements 4.2.1 Characteristics and Advantages of STR Markers 4.2.2 Nomenclature of STR Markers 4.3 Types of STR Markers 4.4 STR Loci Used for Forensic DNA Analysis and Core STRs 4.4.1 Autosomal STR Markers 4.4.1.1 Parameters Used to Assess the Usability of an STR Marker 4.4.1.1.1 Allele Number and Total Possible Genotypes 4.4.1.1.2 Match Probability 4.4.1.1.3 Power of Discrimination 4.4.1.1.4 Power of Exclusion 4.4.1.1.5 Polymorphic Information Content 4.4.1.1.6 Typical Paternity Index 4.4.1.1.7 Genetic Diversity 4.4.1.1.8 Heterozygosity 4.4.2 Y-Chromosome STRs 4.4.2.1 Applications of Y-STR Analysis 4.4.2.1.1 Analysis of DNA with High M:F Ratio 4.4.2.1.2 AMELY Deletion Cases 4.4.2.1.3 Exclusion of Male Suspects 4.4.2.1.4 Identification of Paternal Lineage 4.4.2.1.5 Cases Involving Multiple Male Contributors 4.4.2.1.6 Investigative Leads for Unknown Male Perpetrators 4.4.2.2 Interpretation of Y-STR Profile 4.4.2.3 RM-YSTRs 4.4.3 X-STRs 4.4.3.1 Commercially Available New Generation Kits 4.4.3.1.1 Autosomal STR Kits 4.4.3.1.2 Y-Chromosome STR Kits 4.4.3.1.3 X-Chromosome STR Kits 4.5 Mitochondria DNA Analysis and Its Advancements 4.5.1 Structural Characteristics of mtDNA 4.5.2 Reference Sequence of Human mtDNA 4.5.3 Unique Inheritance Pattern of mtDNA 4.5.4 Heteroplasmy in mtDNA Sequences 4.5.5 Analysis of mtDNA and Haplotype Group Assignment 4.6 Single Nucleotide Polymorphism (SNPs) in Forensic DNA Analysis 4.6.1 Characteristics of SNP Marker 4.6.2 SNP Classes 4.6.2.1 Identity Informative SNPs (iiSNPs) 4.6.2.2 Lineage-Informative SNPs (liSNPs) 4.6.2.3 Ancestry-Informative SNPs (aiSNPs) 4.6.2.4 Phenotype-Informative SNPs (piSNPs) 4.6.2.5 Pharmacogenetic SNPs 4.6.2.6 Advantages of SNP Markers 4.6.2.7 Disadvantages of SNP Markers References 5: Fast, High-Sensitive, and High-Resolution DNA Techniques 5.1 Introduction 5.2 Sensitivity of the Advanced Techniques 5.3 Cell Selection and Cell Picking Methods 5.3.1 Laser Capture Microdissection Technique 5.3.2 Other Techniques 5.4 Tolerance to PCR Inhibitors 5.5 DNA Profiling in Degraded Samples 5.6 Number of STR Markers in the New Generation Multiplex Systems 5.7 Fast Amplification Conditions 5.8 Faster and Reliable DNA Quantification Techniques 5.9 DNA Separation Techniques 5.10 NGS 5.11 Use of Automation in Forensic DNA Analysis 5.12 RAPID DNA Analysis 5.12.1 ANDE System 5.12.1.1 DNAscan and ANDE 4C System 5.12.1.2 ANDE 6C System 5.12.2 Applied Biosystems Systems 5.12.2.1 RapidHIT System 5.12.2.2 RapidHIT ID System 5.13 Conclusion References 6: Advancements in Non-human Forensic DNA Analysis 6.1 Introduction 6.2 Animals 6.3 Insects 6.4 Plants 6.5 Pathogens 6.6 Microbiome Analysis 6.7 Conclusion References 7: Applications of NGS Technology in Forensic DNA Analysis 7.1 Introduction to Technology in Forensic DNA Typing 7.2 DNA Extraction Technology 7.2.1 Maxprep, Maxwell 16, Maxwell FSC, and Maxwell 48 Instruments by Promega 7.2.2 Biorobot EZ1, EZ1 Advanced, and EZ2 Connect Instruments by Qiagen 7.3 Capillary Electrophoresis Technology for DNA Typing 7.3.1 Applied Biosystems 3500 7.3.2 Promega Spectrum SE 7.4 Liquid Handling Technology for NGS Library Prep 7.4.1 PrepStation by Verogen 7.4.2 Ion Chef by Life Technologies 7.5 NGS Technology for DNA Typing 7.5.1 Illumina iSeq 7.5.2 Illumina MiniSeq 7.5.3 Illumina MiSeq 7.5.4 Verogen MiSeq FGx 7.5.5 Thermo Fisher Ion S5 7.5.6 ThermoFisher Ion Torrent PGM 7.5.7 ThermoFisher Ion GeneStudio S5 7.5.8 Illumina NextSeq 7.5.9 Illumina HiSeq 7.5.10 Illumina NovaSeq 7.5.11 Summary of CE and NGS DNA Typing Instruments 7.6 Software Tools for CE and NGS Data Analysis 7.7 Conclusion References 8: Statistical Interpretation of Forensic DNA Evidence 8.1 Introduction 8.2 Two Fallacies 8.3 Choosing a Population-Specific Database 8.4 Allele Frequency 8.5 Genotype Frequency 8.6 Random Match Probability 8.7 Paternity Index 8.7.1 Calculation of PI in Paternity Trio 8.7.2 Calculation of PI in Paternity Duo 8.7.3 Sibship Index 8.8 Avuncular Index 8.9 Calculation of PI in Atypical Cases 8.10 Haplotype Frequency 8.11 Interpretation of Mixed Profile References 9: Role of Forensic DNA Databases in Criminal Identification 9.1 Introduction 9.2 Custody of the Databases 9.3 DNA Database Composition 9.4 National DNA Databases 9.5 Solving Cold Cases 9.6 DNA Mixture Profiles 9.7 Health-Related Information 9.8 Indirect Matching 9.9 Cases Solved by Indirect Matching 9.10 Conclusion References 10: Guidelines, Ethical Issues, and Other Challenges of Forensic DNA Analysis 10.1 Introduction 10.2 Debate of Forensic DNA Analysis in the Past 10.3 The Legal Model 10.4 The Scientific Model 10.5 The Libertarian Model 10.6 Forensic DNA Analysis 10.7 Evolution of DNA Techniques 10.8 Guidelines for DNA Analysis 10.9 Post Publication Policies and Conscientious Objection References 11: Application of Forensic DNA Technology in Analyzing Real-Time Casework Samples 11.1 Introduction 11.2 Sources of DNA 11.3 Collection Methods 11.4 DNA Extraction 11.5 Application of DNA Analysis 11.6 Anti-Terrorism Cases 11.7 Anti-Narcotics Cases 11.8 Sexual Assault Cases References 12: Future Directions of Forensic DNA Analysis 12.1 Introduction 12.2 Faster Results 12.3 High Sensitivity and High Information 12.4 Analysis of Challenging Samples 12.5 Investigative Genetic Genealogy 12.6 Microbial Forensics 12.7 CRISPR-Cas9 Technique and Its Challenge 12.8 Triparental Child, Transplantations, and IVF 12.9 Preventive Forensics References