DNA profiling Study Guide

📖 Core Concepts DNA profiling – Identifying an individual (or species) by analysing characteristic DNA regions. STR (Short Tandem Repeat) analysis – PCR‑amplified repeat loci; the most common modern forensic method. RFLP (Restriction Fragment Length Polymorphism) – Early technique that cuts DNA with restriction enzymes and separates fragments by size; requires high‑molecular‑weight DNA. PCR (Polymerase Chain Reaction) – Enzyme‑based method that copies a specific DNA segment through denaturation, annealing, and extension cycles. Match probability – The chance that a random, unrelated person would share the same DNA profile; calculated with the product rule across independent loci. Cold hit – A crime‑scene profile that matches a profile already stored in a DNA database. Partial match (CODIS) – A profile that shares at least one allele at every locus with the query, but does not meet the full‑match criteria. Familial DNA searching – Database query that looks for close relatives of an unknown contributor, not exact matches. Surreptitious DNA collection – Obtaining DNA from discarded items without the person’s knowledge (e.g., coffee cups). --- 📌 Must Remember STR loci used: CODIS 20‑core loci (US), DNA‑17 (UK), 18 core markers (Australia). Match‑probability magnitude: As low as \(1 \times 10^{-18}\) (one in a quintillion) for full STR profiles. DNA quantity needs: RFLP ≥ 100 ng (high‑MW DNA). Multiplex PCR can work with \< 1 ng, even on degraded samples. Degraded vs. low‑template DNA: Degraded → fragmented, unsuitable for RFLP; Mini‑STRs improve success. Low‑template → stochastic effects (allelic dropout, drop‑in). Mixture complexity limit: > 3 contributors become unreliable; 4+ generally too complex. Key legal thresholds: US: DNA can be collected on arrest for serious crimes (Maryland v. King, 2013). UK: Human Tissue Act 2004 restricts private covert collection; law‑enforcement allowed. Jury instruction (UK): Match probability ≠ guilt probability (R v. Doheny, 1996). Partial profiles admissibility: Permitted if limitations are clearly explained (R v. Bates). --- 🔄 Key Processes STR PCR Workflow Extract DNA → Quantify → Multiplex PCR with primers flanking repeat region → Capillary electrophoresis → Generate allele calls. Mini‑STR for Degraded Samples Design primers that bind close to repeat → Produce ≤ 100 bp amplicons → Amplify low‑quality DNA. Probabilistic Genotyping (Mixture Interpretation) Input raw electropherogram → Algorithm computes likelihoods for each possible genotype combination → Generates statistical weights for contributors. Familial Searching Procedure Run standard CODIS search → If no direct hit, run “close‑relatives” algorithm → Rank candidates by kinship index → Follow up with Y‑STR or mtDNA as needed. Surreptitious Collection (Police) Retrieve discarded item → Extract DNA → Process with standard STR PCR → Compare to database or suspect profile. --- 🔍 Key Comparisons RFLP vs. STR PCR RFLP: needs ≥ 100 ng high‑MW DNA, long processing, low sensitivity → unsuitable for degraded samples. STR PCR: works with \< 1 ng, tolerates degradation, faster, standard today. Full match vs. Partial match Full match: All loci identical; extremely low random match probability. Partial match: At least one allele shared at every locus; higher random match risk; often used for familial leads. Y‑STR vs. mtDNA analysis Y‑STR: Paternal lineage, male‑specific, useful for distinguishing male contributors in mixtures. mtDNA: Maternal lineage, abundant in hair/old bone, lower discrimination power. Cold hit vs. Direct suspect match Cold hit: Database‑generated lead; evidentiary weight lower because the match is indirect. Direct match: Sample taken from suspect; stronger probative value. --- ⚠️ Common Misunderstandings “A DNA match proves guilt.” – Match probability only tells how rare a profile is; it does not establish the individual’s presence at the crime scene. “Identical twins have different DNA profiles.” – Twins share virtually identical nuclear DNA; profiling cannot differentiate them. “Partial matches are as reliable as full matches.” – Partial matches lack the statistical power of full profiles and can miss sibling relationships without Y‑STR analysis. “All DNA databases work the same way.” – CODIS (US) and NDNAD (UK) differ in loci, retention policies, and whether arrest‑based or conviction‑based samples are collected. --- 🧠 Mental Models / Intuition Product rule analogy: Treat each STR locus as an independent coin flip; the chance of matching all flips equals the product of individual odds → explains why adding more loci drives the overall probability down dramatically. Mixture “puzzle” picture: Imagine overlapping transparent sheets, each representing a contributor’s alleles; the more sheets, the harder to see any single pattern. Cold hit as “tip‑off”: Think of a cold hit like a detective’s anonymous tip – useful, but you still need corroborating evidence. --- 🚩 Exceptions & Edge Cases Monozygotic twins: Same nuclear DNA; profiling cannot separate them (≈ 0.2 % of population). Highly degraded DNA: Even Mini‑STRs may fail if fragments < 50 bp; alternative mtDNA may be the only viable source. Low‑template stochasticity: Allelic dropout can mimic a homozygous genotype; labs must set stochastic thresholds. Legal jurisdiction differences: Some US states collect DNA at arrest, others only after conviction; retention periods vary. --- 📍 When to Use Which Degraded sample → Mini‑STR or mtDNA analysis. Small DNA quantity (< 1 ng) → Multiplex PCR (STR) rather than RFLP. Mixture with ≤ 3 contributors → Standard STR interpretation; consider probabilistic genotyping for higher confidence. Need for male‑specific info → Y‑STR analysis (e.g., sexual assault cases). Investigative lead for unknown perpetrator → Familial searching (if database permits). Court presentation in UK → Emphasize match probability separate from guilt probability; avoid Bayes’ theorem (R v. Doheny precedent). --- 👀 Patterns to Recognize “Allelic dropout + low template” → Expect missing alleles, especially at larger loci. “Extra allele (drop‑in) in a single‑source profile” → May indicate contamination or mixture. “Consistent partial match across many loci but not full” → Possible close relative; trigger familial search. “High match probability but no corroborating evidence” → Red flag for potential lab error or contamination. --- 🗂️ Exam Traps Choosing RFLP for degraded DNA – Wrong; RFLP needs high‑MW DNA. Equating a cold hit with a direct match – Mistake; cold hits have less evidential weight. Assuming a full STR match guarantees the suspect’s guilt – Incorrect; must consider other evidence and the possibility of lab error. Ignoring stochastic effects in low‑template DNA – Leads to false conclusions about homozygosity. Over‑relying on partial matches without explaining limitations – May be penalized in UK exam questions referencing R v. Bates. ---