SNP Analysis
Page 1: Introduction
Focus on emerging forensic DNA technologies.
Course: SNP FRSC 370 Fall 2024.
Page 2: Understanding SNPs
Definition
SNP (Single Nucleotide Polymorphism): type of polymorphism.
STR (Short Tandem Repeat): refers to length polymorphism.
Characteristics
Typically bi-allelic: occurring in two forms.
Extremely abundant within the genome:
Lower mutation rate than STRs.
May or may not indicate phenotypic advantages.
Different analytical approach is necessary for casework.
Page 3: Forensic Applications of SNPs
Key Applications
SNP-STR analysis as a crucial method.
Identity informative SNPs:
Serve as alternatives to STRs.
Small size allows them to perform well in degraded samples.
Applications include Forensic (Investigative) Genetic Genealogy (FIGG/FGG) and Forensic DNA Phenotyping (FDP).
Page 4: Old vs. New SNP Analysis
Old Methods
Sanger sequencing:
Conducts sequencing one fragment at a time.
Produces small fragments with multiple reads for base “calls.”
Lengthy and slower process.
New Methods
Massively Parallel Sequencing (MPS) / Next Generation Sequencing:
Analyzes many small fragments concurrently.
Increased coverage deemed important for accuracy.
Page 5: Sanger Sequencing Overview
Developed by Frederick Sanger in 1975.
Received Nobel Prize in Chemistry in 1980.
Major Applications
Human Genome Project completion in 2003.
Used for predictive genomic testing such as BRCA1 variants for breast cancer.
Page 6: Mechanics of Sanger Sequencing
Components
Discussion of DNA forms:
DNA: deoxyribonucleic acid (lacking -OH on 2'C).
ddDNA: didoxyribonucleic acid (lacking -OH on 2'OH or 3'C).
Issues with the incorporation in PCR reactions involving both dNTPs and ddNTPs, leading to distinct color coding.
Page 7: Sanger Sequencing Process
Process Description
Given DNA template strand undergoes primer annealing.
Extension produces ddNTP terminated products, varying in length, each tagged by different color fluorescent dye.
Data Interpretation
Peaks noticed in an electropherogram aid in determining sequence.
Page 8: Introduction to MPS
Overview with a focus on Next Generation Sequencing techniques.
Page 9: Basics of MPS Preparation (Part 1)
Process Steps
DNA cutting into fragments enzymatically.
Addition of “linkers” using ligases, which are complementary to immobilized oligos on sequencing tools.
Page 10: Basics of MPS Preparation (Part 2)
Process Continuation
Initial library exposed to chip.
Linkers hybridize with oligos for PCR extension, serving as templates during sequencing.
Page 11: Sequencing Methods
Detection Methods in PCR
All PCR methods require a mechanism to track nucleotide incorporation.
Common techniques:
Fluorescent dye labeling (Illumina).
pH detection (Ion Torrent).
Page 12: Ion Torrent System
Reference to the video about the Ion Torrent sequencing technology.
Page 13: Miseq by Illumina
Highlighting the significance of the Illumina sequencing technology.
Page 14: Evaluating Identity
Comparison Techniques
STR-SNP Analysis:
Evaluates variations within STRs.
Identity SNPs:
Follows similar principles to STRs but is less functional.
Requires more SNPs to match STR power of discrimination.
Page 15: Filtering SNPs for Analysis
Techniques
Guidelines for SNP filtering:
Identify SNPs with high heterozygosity and low F-statistics.
Focus on SNPs with known functional capabilities, quality sequences, and conserved flanking regions.
Page 16: Insights from Research
Key Takeaways
Proposal of 70-plex SNP panel for close relative differentiation.
Higher resistance to DNA degradation due to smaller amplicon sizes.
Page 17: Identity SNPs in Challenging Samples
Overview of funding evaluation for SNP genotyping for skeletal remains.
Page 18: Forensic DNA Phenotyping
Comprehensive Analysis
Analysis of SNP data for phenotypic traits (e.g., hair/eye color).
Kits available for phenotyping.
Page 19: Biogeographic Ancestry (BGA)
Population Analysis
Studying SNP similarities within geographic populations.
Importance of considering overrepresentation within genetic databases for European descent.
Page 20: Research Reference
Citation on SNP variation in ethnic groups for forensic intelligence.
Page 21: Relationships in FIGG
Techniques Utilized
Comparing SNP profiles in databases from evidence to individuals.
Concerns about privacy and data usage in direct-to-consumer kits (Ancestry, 23 & Me).
Page 22: Shared DNA
Measurement and Implications
Focus on shared genetic fragments to understand relationships.
Measurement in centimorgans (cM) evaluates relatedness across chromosomes.
Page 23: Emerging Technology Issues
Concerns Raised
Bias in identity.
Privacy issues.
Admissibility and informed consent challenges.
Page 24: Genetic Racial Essentialism
Research Article Reference
Exploration of the implications of biogeographic ancestry on race-based judgments.
Page 25: Race vs. Genetic Ancestry
Key Issues
Challenge in connecting genetic ancestry with the socially constructed race concept.
Race as a social and political construct rather than a biological marker.
Page 26: Unethical Studies
Discussion
Overview of unethical biometric research studies involving ethnic minorities in China and associated controversies.
Page 27: Privacy Implications
Statistics and References
Significant percentage of European descent individuals at risk of identification through familial searches.
Page 28: Ethical Considerations
Informed Consent
Importance of ethical clarity in research participation.
Highlight of historical case (HeLa cells) illustrating the need for consent.
Page 29: Timeline Overview of Events
Uyghur Minority Surveillance
Timeline regarding DNA collection initiatives in Xinjiang by Chinese authorities.
Page 30: Backlash Overview
Responses
Timeline of events relating to allegations of ethical misconduct in genetic research
Page 31: Continued Frustration
Slow Progress on Ethical Concerns
Discussion on activists' concerns over the retraction of unethical studies on minority groups.
Page 32: Final Thoughts on SNPs in Forensics
Evolution of Science
Advantages of SNP analysis over traditional methods.
Need for checks and balances in ethics and admissibility.
Page 33: SNP Resources
References for Further Study
STRbase, SWGDAM guidelines, ISFG information, VISAGE consortium resources.