Next Generation Sequencing (NGS) Technology in DNA Analysis

Next Generation Sequencing (NGS) Technology in DNA Analysis explains and summarizes next generation sequencing (NGS) technological applications in the field of forensic DNA analysis. The book covers the transition from capillary electrophoresis (CE)-based technique to NGS platforms and the fundamentals of NGS technologies, applications, and advances. Sections provide an overview of NGS technology and forensic science, including information on processing biological samples for forensic analysis, sequence analysis, and data analysis software as well as the analysis of NGS data. The book explores the valuable applications of NGS-based forensic DNA analysis and covers the validations and interpretation guidelines of NGS workflows.

With chapter contributions from an international array of experts and the inclusion of practical case studies, this book is a useful reference for academicians and researchers in genetics, biotechnology, bioinformatics, biology, and medicine as well as forensic DNA scientists and practitioners who aim to learn, use, apply, and validate NGS-based technologies.

Cover image
Title page
Table of Contents
Copyright
Dedications
Contributors
Preface
Acknowledgments
Section 1. Useful applications of NGS-based forensic DNA analysis
Chapter 1. Transition of capillary electrophoresis to next generation sequencing for forensic DNA analysis: Need of the hour
Introduction
DNA sequencing platforms
Overview of the methodology
Template preparation
Sequencing and imaging
Data analysis
The impact of NGS on genomics research
Genomic analysis
Targeted genomic resequencing
Metagenomics
The impact of NGS on forensic genetics
Short tandem repeats sequencing
The initial commercial NGS kits for forensic genetics
Current status of next generation sequencing
Recommendations
Concluding remarks
Chapter 2. Using conventional STR technology in analyzing biological transfer evidence
Introduction
Touch DNA (or trace DNA)
Direct and indirect transfer of biological evidence
Effects on transfer and shedder status (assessment of shedder status and implications for secondary DNA transfer)
Touch DNA and wrongful convictions
A new awareness
Chapter 3. Overview of NGS platforms and technological advancements for forensic applications
Introduction
Next-generation sequencing platforms
NGS forensic applications
Forensic NGS commercial systems
NGS advantages and challenges
Chapter 4. Processing of biological samples for forensic NGS analysis
Overview of next-generation sequencing
NGS versus Sanger sequencing: What's the difference?
Next-generation sequencing in forensic science
Overview of the sample preparation process for next-generation sequencing
Sample preparation methods
DNA extraction
DNA quantitation
Library preparation
Library normalization
Chapter 5. Commercial kits commonly used for NGS based forensic DNA analysis
Introduction
Development of next-generation sequencing systems
Use of NGS in forensic sciences
Conclusion
Chapter 6. Applications of nanopore sequencing for forensic analysis
Introduction
Nanopore sequencing
Forensic applications of nanopore sequencing
Opportunities
Challenges
Conclusions
Chapter 7. Microhaplotypes analysis for human identification using next-generation sequencing (NGS)
Introduction to forensic DNA analysis
DNA typing techniques used in forensic DNA analysis
DNA sequencing
Microhaplotypes as a tool for human identification
Next-generation sequencing for microhaplotypes analysis
Validation of NGS-based microhaplotypes analysis
Future directions and opportunities in NGS-based microhaplotypes analysis
Ethical considerations for NGS-based microhaplotypes analysis
Potential applications of NGS-based microhaplotypes analysis
Future directions of NGS-based microhaplotypes analysis
Conclusion
Chapter 8. Tools and techniques of using NGS platforms in forensic population genetic studies
Overview of the concept of population study
Forensic parameters of population genetics
Commonly used markers of population study on NGS platform
Statistical analytical methods of population genetic study
Learning practices of population study based on NGS platform for developing a 40 ancestry informative SNPs (AI-SNPs) multiplex panel for forensic ancestral inference on 17 different continental populations
Summary
Section 2. Useful applications of NGS-based forensic DNA analysis
Chapter 9. Applications of NGS in analysis of autosomal STRs
Introduction
Next-generation sequencing
Application of NGS in autosomal STR analysis
Comparing loci amplified using different kits for NGS applications, including two kits for CE applications
Population studies of autosomal STRs using NGS
Conclusion
Chapter 10. Differentiating monozygotic twins using NGS
Introduction to DNA analysis methods
Mitochondrial genome sequencing
Nuclear genome sequencing
RNA profiling: microRNAs
High-resolution melting to determine DNA methylation
Detecting DNA methylation with pyrosequencing
Genome-wide DNA methylation profiling
Conclusion
Chapter 11. Application of NGS in maternal genome analysis in ancient human remains
Introduction
What stories ancient DNA analysis tell us?
Challenges faced in studying ancient DNA
Next-generation sequencing for maternal genome analysis in ancient samples
Next-generation sequencing based on ancient sample mtDNA in evolutionary studies
Recent developments
Future perspective
Chapter 12. Application of NGS technology for parentage testing and relatedness analysis
Introduction
Parentage testing
Kinship testing
Conclusions
Chapter 13. Forensic relevance of SNP analysis in next-generation sequencing
Introduction
Characterization and origin of SNPs
Conventional SNP genotyping assays
Benefits of next generation sequencing technology over conventional genotyping assays
Forensic application of SNP markers using NGS technology
Limitations of SNP analysis in forensics
Conclusions
Chapter 14. Forensic analysis of hair using NGS technology
Introduction to hair analysis in forensic science
Mitochondrial DNA analysis
Nuclear DNA analysis
Application of NGS for hair analysis
Conclusion
Chapter 15. Forensic DNA phenotyping using next-generation sequencing
Introduction
Progression to next-generation sequencing
Phenotypic-informative SNP in forensics
Externally visible characteristics
Next-generation sequencing in forensics
Chapter 16. Forensic DNA phenotyping in the next-generation sequencing era
Introduction
Forensic DNA Phenotyping
Final remarks
Chapter 17. Forensic applications of epigenetic (DNA methylation) markers through NGS
Introduction
Emerging MPS methods for forensics
Body fluid identification by MPS
Age estimation by MPS
Improvements in the application of epigenetic markers via MPS
Future considerations
Chapter 18. Forensic applications of NGS-based microRNA analysis
Introduction
miRNA and body fluid identification
Discrimination of monozygotic twins
miRNAs and time since death determination
Wound age estimation using miRNA
Organ tissue identification using miRNA
miRNA and drowning
miRNA and sepsis
Other potential future application
Potential limitations
Concluding remarks
Chapter 19. NGS profiling of water and soil microbial DNA in forensic science
NGS approaches for microbial profiling of soil and water
Extraction methods for obtaining microbial DNA from soil and water
Quantitation methods for microbial DNA
NGS methods for microbial DNA analysis
Application of microbial DNA analysis in geolocation in the United States
Ongoing challenges and conclusion
Chapter 20. Applications of NGS in analysis of challenging samples
Introduction
Application of next-generation sequencing technology in forensic science
Panels developed for the forensic samples using the NGS technologies
DNA damage and degradation
Challenging DNA evidence
Previous types of technologies used to analyze challenging DNA
Application of NGS in challenging DNA evidence
Conclusion: The main challenges of NGS in forensic applications
Chapter 21. Detection of human body fluid through mRNA analysis using NGS
Introduction
Body fluid identification
Sequencing approach
Beyond just body fluids
Analysis methods for mRNA data
Future of mRNA body fluid identification
Chapter 22. NGS-based detection and differentiation of forensically relevant body fluids using conventional, molecular, and microbial techniques
Background
Existing technologies for human body fluid detection
Conclusions
List of abbreviations
Chapter 23. Application of next-generation sequencing technology and investigative genetic genealogy to solving cold cases
Introduction
Methods
Results
Discussion and conclusion
Section 3. Challenges in implementing NGS in forensic laboratories
Chapter 24. Troubleshooting and challenges of Next-generation sequencing technology in forensic use
Forensic genetics: timeline of technology evolution
Current limitations and problem solving in forensic genetics
NGS: from diagnostics to forensic applications
NGS in forensics and the issue of privacy: a global overview
Applications of NGS technology in forensic entomology
Chapter 25. Validation of NGS for casework at forensic DNA laboratories
Introduction
NGS kits and platforms for generating DNA profiles
Milestones for NGS in forensic casework
Validation of NGS-based DNA analysis methods
Funding for forensic laboratories to adopt and validate NGS technology
Chapter 26. Challenges in using genetic genealogy in forensics
Introduction
How forensic DNA profiling differs from forensic genetic genealogy
How investigative genetic genealogy works
Challenges in using genetic genealogy
Way forward
Conclusions
Chapter 27. The role of artificial intelligence and machine learning in NGS
What is next-generation sequencing?
Next-generation sequencing for forensics
What is artificial intelligence? Why is it useful for forensics?
What is machine learning?
How do artificial intelligence and machine learning help with NGS?
Challenges of utilizing AI and ML in NGS
Conclusion
Chapter 28. Ethical issues of forensic application of NGS technology
Introduction to forensic DNA analysis
Ethics and forensic DNA typing
How does forensic genetic genealogy differ from familial DNA searches?
Misuse of tools indicated for forensic use?
Personal genomics companies and consumer data in the forensic setting
Forensic NGS and genetic genealogy
Next-generation sequencing and environmental impact
Next-generation sequencing education needs
Conclusion
Chapter 29. Ethical, legal, and social challenges of next-generation sequencing technologies (NGS) in forensic criminal identification
Introduction
Gaps in legislation and regulation
Access to databases that hold full-genome data
Data protection
Algorithms, privacy, and discrimination
Societal trends framing NGS technologies
Conclusion
Index

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Next Generation Sequencing (NGS) Technology in DNA Analysis

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Hirak Ranjan Dash

Kelly M. Elkins

Noora Rashid Al-Snan