Next Generation Sequencing (NGS) Technology in DNA Analysis

✍ Scribed by Hirak Ranjan Dash, Kelly M. Elkins, Noora Rashid Al-Snan

• Publisher: Elsevier
• Year: 2024
• Tongue: English
• Leaves: 614
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Cover
Next Generation Sequencing (NGS) TECHNOLOGYIN DNA ANALYSIS
Next Generation Sequencing (NGS) TECHNOLOGYIN DNA ANALYSIS
Copyright
Dedications
Contents
Contributors
Preface
Acknowledgments
1 - Useful applications of NGS-based forensic DNA analysis
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
References
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
References
Further reading
3 - Overview of NGS platforms and technological advancements for forensic applications
Introduction
Next-generation sequencing platforms
Second-generation sequencing
Third-generation sequencing
NGS forensic applications
Short tandem repeats and single nucleotide polymorphism analysis
Forensic phenotyping and ancestry studies
Epigenetic analysis
RNA analysis
Microbial forensics
Mitochondrial DNA sequencing
Animal and plant DNA analysis
Forensic NGS commercial systems
NGS advantages and challenges
References
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
References
5 - Commercial kits commonly used for NGS based forensic DNA analysis
Introduction
Development of next-generation sequencing systems
Second-generation NGS systems
Third-generation sequencing systems
Use of NGS in forensic sciences
Commercial NGS kits used for forensic analysis
Illumina-Verogen partnership
ForenSeq DNA Signature Prep Kit
ForenSeq Kintelligence Kit
ForenSeq MainstAY Kit
ForenSeq mtDNA Control Region Kit
ForenSeq mtDNA Whole Genome Kit
Thermo fisher scientific
Ion AmpliSeq DNA Phenotyping Panel
Ion AmpliSeq Pheno Trivium Panel
Precision ID mtDNA control region panel
Precision ID mtDNA whole genome panel
Precision ID ancestry panel
Precision ID identity panel
Precision ID Globalfiler NGS panel v2
Ion AmpliSeq HID Y-SNP research panel v1
Ion AmpliSeq MH-74 plex research panel
Ion AmpliSeq VISAGE-basic tool research panel
Conclusion
References
6 - Applications of nanopore sequencing for forensic analysis
Introduction
Nanopore sequencing
Forensic applications of nanopore sequencing
Short tandem repeat genotyping
Single nucleotide polymorphism genotyping
Mitochondrial DNA genotyping
Nonhuman forensics
Species identification
Microbial analysis
Opportunities
Messenger RNA analysis
Epigenetics and epigenomics
Challenges
Conclusions
References
7 - Microhaplotypes analysis for human identification using next-generation sequencing (NGS)
Introduction to forensic DNA analysis
DNA typing techniques used in forensic DNA analysis
Advantages of capillary electrophoresis in forensic DNA analysis
Limitations of capillary electrophoresis in forensic DNA analysis
DNA sequencing
Microhaplotypes as a tool for human identification
Definition of microhaplotypes
Types of compound genetic markers in microhaplotypes
Criminal investigations
Ancestry inference
Disaster victim identification
Challenges and limitations of microhaplotypes
Advantages of microhaplotypes over other DNA typing techniques
Applications of microhaplotypes in forensic DNA analysis
Next-generation sequencing for microhaplotypes analysis
Workflow of NGS-based microhaplotypes analysis
Sample preparation
Library preparation for NGS-based microhaplotypes analysis
Sequencing
Alignment
Data analysis for NGS-based microhaplotypes analysis
Validation of NGS-based microhaplotypes analysis
Quality control
Read alignment
SNP calling
Haplotype reconstruction
Statistical inference
Challenges and limitations related to data analysis
Future directions and opportunities in NGS-based microhaplotypes analysis
The promises of microhaplotypes and advantages over traditional markers
Challenges of NGS-based microhaplotypes technique
Low coverage depth and variability
Read errors and artifacts
Data management and analysis
Improvements to NGS-based microhaplotypes analysis
Enhancing coverage depth and consistency
Reducing read errors and artifacts
Developing and optimizing computational tools
Future directions in microhaplotype analysis
Ethical considerations for NGS-based microhaplotypes analysis
Risks of NGS-based microhaplotypes analysis
Obligations of scientists, researchers, and policymakers
Guidelines for the responsible use of NGS-based microhaplotypes analysis
Potential applications of NGS-based microhaplotypes analysis
Future directions of NGS-based microhaplotypes analysis
NGS-based microhaplotype analysis: state-of-the-art
Opportunities for future research in NGS-based microhaplotype analysis
Conclusion
References
8 - Tools and techniques of using NGS platforms in forensic population genetic studies
Overview of the concept of population study
The concept of population study
Genetic theories of population study
Forensic applications of population study
Forensic parameters of population genetics
Population applicability of candidate molecular genetic markers
Hardy-Weinberg equilibrium test
Linkage and linkage disequilibrium
Genetic markers located on sex chromosomes
Polymorphism parameters of genetic markers
Allele frequency and genotype frequency
Haplotype frequency
Heterozygote (He) and the polymorphism information content
Forensic application analysis based on population genetics
Individual identification
Parentage testing
Inference of ancestry informative
Commonly used markers of population study on NGS platform
Short tandem repeat
Single nucleotide polymorphism
Mitochondrial DNA
Microhaplotype
Compound marker
Statistical analytical methods of population genetic study
Genetic differentiation index (FST)
F test
Multidimensional scaling
Principal component analysis
Phylogenetic tree
Structure analysis
Learning practices of population study based on NGS platform for developing a 40 ancestry informative SNPs (AI-SNPs) multip ...
Assessing the contributions of the 40 AI-SNPs for ancestral information inference
Gene frequency statistics of 40 AI-SNP loci in the 17 populations from three continents
Investigation of the genetic relationships among the 17 populations from three continents using 40 AI-SNPs
Population differentiation measures of the 17 continental populations
PCA analyses of the 17 continental populations based on 40 AI-SNPs
Phylogenetic analyses of the 17 continental populations based on 40 AI-SNPs
Structure analysis of the 17 continental populations with 40 AI-SNPs
Ancestral inference using the selected 40 AI-SNPs
Summary
References
2 - Useful applications of NGS-based forensic DNA analysis
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
References
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
Acknowledgments
References
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
Contamination
Chemical modifications and degradation of ancient DNA
Next-generation sequencing for maternal genome analysis in ancient samples
Facility for ancient sample processing
Sample preparation and DNA extraction from ancient samples
Library preparation for next-generation sequencing
Mitochondrial DNA capturing and sequencing
Next-generation sequencing data analysis
Next-generation sequencing based on ancient sample mtDNA in evolutionary studies
Mitochondrial DNA from coat hair of mammoth
Mitochondrial DNA of Paleo-Eskimo
The genetic history of Neanderthals (the divergence between extant humans and Neanderthals)
mtDNA analysis of a Hominin from South Siberia
mtDNA analysis of ancient mummies
Recent developments
Future perspective
References
12 - Application of NGS technology for parentage testing and relatedness analysis
Introduction
Parentage and kinship testing through history
Principles of parentage and kinship analysis
Samples used for parentage and kinship analysis
DNA markers used for parentage and kinship analysis
Short tandem repeat markers
Single nucleotide polymorphism markers
Insertion-deletion polymorphism markers
Microhaplotype markers
Genotyping technology
Capillary electrophoresis
Next-generation sequencing
Commercially available NGS kits for parentage and kinship testing
Parentage testing
Postnatal parentage testing
The use of MPS in detecting uniparental disomy in parentage testing
Noninvasive prenatal paternity testing
Kinship testing
Conclusions
References
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
Overview
Current next-generation sequencing platforms
NGS versus traditional capillary electrophoresis-based assays
Advantages of NGS for STR and SNP genotyping
Forensic application of SNP markers using NGS technology
Analysis of highly degraded and mixed samples
Low-copy DNA detection with NGS approach
Individual identification
Human ancestry and migration history
Facial phenotyping
Paternal lineage and kinship analysis
Limitations of SNP analysis in forensics
Conclusions
References
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
References
15 - Forensic DNA phenotyping using next-generation sequencing
Introduction
Progression to next-generation sequencing
Phenotypic-informative SNP in forensics
Externally visible characteristics
Eye color
Hair color
Skin color
Face feature
Next-generation sequencing in forensics
References
16 - Forensic DNA phenotyping in the next-generation sequencing era
Introduction
Forensic DNA Phenotyping
An SNP-based tool
For prediction of complex traits
Human pigmentation as a starting point
Considerations regarding the applicability of NGS to forensic DNA phenotyping
Other EVCs as FDP targets
DNA methylation and age prediction
The VISAGE initiative and the future of FDP
FDP for forensic anthropology purposes
Final remarks
References
17 - Forensic applications of epigenetic (DNA methylation) markers through NGS
Introduction
Emerging MPS methods for forensics
Illumina NovaSeq
Illumina's MiSeq FGx sequencing system
Oxford Nanopore Technologies MinION device
Ion Torrent PGM and Ion S5
Body fluid identification by MPS
Age estimation by MPS
Improvements in the application of epigenetic markers via MPS
Future considerations
References
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
Acknowledgments
References
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
References
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
MiniSTRs
Mitochondrial DNA typing
Single nucleotide polymorphism typing
Application of NGS in challenging DNA evidence
Degraded samples and low-template DNA evidence.
DNA mixture profile
Conclusion: The main challenges of NGS in forensic applications
References
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
References
22 - NGS-based detection and differentiation of forensically relevant body fluids using conventional, molecular, an ...
Background
Existing technologies for human body fluid detection
Conventional techniques
Semen
Blood
Vaginal fluid
Saliva
Urine
Sweat
Molecular techniques
Semen
Blood
Vaginal fluid
Saliva
Urine
Sweat
Rapid techniques
Microbial-based body fluid detection
Technological advancements in microbial forensics
Conclusions
List of abbreviations
References
23 - Application of next-generation sequencing technology and investigative genetic genealogy to solving cold cases
Introduction
Methods
Results
Discussion and conclusion
References
Case Reports
3 - Challenges in implementing NGS in forensic laboratories
24 - Troubleshooting and challenges of Next-generation sequencing technology in forensic use
Forensic genetics: timeline of technology evolution
First generation sequencing
Second generation sequencing
Third generation sequencing
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
References
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
National DNA Index System
FBI's quality assurance standards
SWGDAM validation guidelines for DNA analysis methods
Developmental validation process
Developmental validation process—subsection 3.10
Internal validation process
Addendum to “SWGDAM interpretation guidelines for autosomal STR typing by forensic DNA testing laboratories” to address nex ...
SWGDAM interpretation guidelines for mitochondrial DNA analysis by forensic DNA testing laboratories
Peer-reviewed publications on validation studies of NGS systems
Funding for forensic laboratories to adopt and validate NGS technology
References
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
Errors
DNA mixtures
Degraded or low-quality forensic samples
Need for standards
Direct-to-customer genomic services
False identification
Use of unproven or invalid testing methods
Biospecimen and hacking threats
Intrusion to privacy
Genomic privacy
Bypassing codes of informed consent
Genetic surveillance
Via genealogical databases
Ethical issues
Forced collection of DNA samples from arrested individuals
Lack of a law protecting privacy
Case studies
Phoenix canal killings
Golden State serial killer or case of Joseph DeAngelo
Way forward
Conclusions
References
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
References
Further reading
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
References
29 - Ethical, legal, and social challenges of next-generation sequencing technologies (NGS) in forensic criminal id ...
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
Acknowledgment
References
Index
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