Forensic Biology (POL5009) - Lesson 2: DNA Interpretation

Lesson 2 continues the investigation into DNA, its applications, and limitations.
Review of DNA electropherograms and interpretation, random match probability (RMP), and current issues with DNA profiling.
Key text: Understanding Forensic DNA (Bell & Butler, 2022).
Live session for reviewing content and questions.

1. Understand and explore the use of DNA, analysis, and application in forensic investigations.
2. Identify and analyze epithelial and body fluids and their contributions to forensic investigations.
3. Explore and interpret bloodstain patterns in relation to the theoretical components of blood dynamics.
4. Analyze botany and animal genetics' roles in forensic investigation.
5. Gain knowledge of forensic biology's role in investigations.

Short Tandem Repeats (STRs) are sequences in DNA where certain patterns of two or more nucleotides are repeated.
Each STR loci has multiple alleles, depending on the number of times the repeat occurs.
An allelic ladder is run alongside the sample during capillary electrophoresis to provide a baseline comparison for peak heights.

DNA size is plotted on the x-axis (time taken to migrate), and fluorescence intensity (DNA amount) is plotted on the y-axis.
Example electropherograms demonstrate:
- Clear peaks indicating homozygous or heterozygous genotypes.
- Mixture profiles where peaks from different individuals may overlap, thus complicating interpretation.
- LCN (Low Copy Number): Describes samples undergoing extensive PCR cycles, producing complex patterns that complicate interpretation.

Full profile: Includes all STR markers from a single individual.
Partial profile: Only some STR alleles are obtained.
Mixed profile: More than one individual's DNA is present in the profile.
Major profile: Exhibits higher peaks for one or two contributors, making it easier to identify them.
Low-level DNA samples: Often difficult to interpret due to multiple contributors.
- Suitable for comparison: Discernible peaks at some loci.
- Not suitable for comparison: No identifiable peaks present.

PCR inhibitors can interact with DNA or DNA polymerases, complicating the amplification.
Common inhibitors: soil, mold, plant material, feces, and hemoglobin.
Importance of limiting sample size to reduce the effect of inhibitors when swabbing.

Allelic drop out: Occurs with low DNA quantity; may result in missing peaks.
Silent or Null Alleles: Mutations affecting primer binding can result in peaks appearing homozygous when one allele is not represented.
Non-allelic peaks: Peaks that do not represent true STR alleles caused by various effects, including:
- Stutter Peaks: Minor peaks before a true peak caused by DNA polymerase slippage.
- Pull-up Peaks: Result from fluorescence bleed-through between alleles in multiple channels.
- Drop-ins: Contaminants that lead to the presence of external DNA fragments.

To match profiles, analysts will determine if peaks in a known reference sample match those in an unknown sample.

The model predicts genotype frequencies in an ideal population (large, randomly mating, unaffected by migrations, selections, or mutations).
For alleles p and q in heterozygous scenarios:
- The probabilities for genotypes are calculated as:
- Equation: p^2 + 2pq + q^2.
- Example Punnett Square calculation for alleles where p = 0.7 and q = 0.3 to determine genotype probabilities.

Calculated as the ratio of specific allele occurrences versus total alleles sampled.
The example: 32 million brown-haired individuals among a population of 67 million yields an allele frequency of approximately 0.48.

RMP calculated using the combined probabilities of all analyzed loci.
The methodology involves multiplying the probabilities of each locus together and then determining the inverse for the final RMP figure.
RMP reported in court represents the chance of randomly matching profiles.

The Forensic Science Regulator advises reporting a 1 in 1 billion match probability as a maximum figure.
If RMP is lower, include this in reports as it affects interpretation weight.

Prosecutor's Fallacy: Misinterprets RMP as the probability of innocence rather than probability of matching if innocent.
- Illustrated mathematically: P(E|I) for evidence given innocence versus P(I|E) (wrong transposition).
- Example: Assessing the probability of a characteristic being true given an animal is a monkey does not apply valid probabilistic reasoning.
Defence Fallacy: Assumes all individuals equally likely to match DNA regardless of extra implicating evidence.
- Focus on context: suspect's prior knowledge or presence.

Covered DNA electropherogram interpretation, challenges in analyzing results, statistical analysis for RMP, legal presentations of DNA evidence, and highlighted critical fallacies in interpreting DNA evidence.
The next lesson will focus on different methodologies for obtaining genetic information.

Bell, S. & Butler, J.M. (2022). Understanding Forensic DNA. Cambridge: Cambridge University Press.
Gunn, A. (2019). Essential Forensic Biology. Wiley.
Klug, W.S. et al. (2021). Essentials of Genetics. Pearson.
ALamoudi, E. et al. (2018). DNA Profiling Methods and Tools: A Review.
Forensic Science Regulator (2020). The Interpretation of DNA Evidence.
Puch-Solis, R. et al. (2012). Assessing the probative value of DNA evidence.

Various articles and materials referenced to deepen understanding of DNA evidence, profiling, and implications in a forensic context.