Chapter 10 Notes

CHAPTER 10 – DNA Polymorphisms & Human Identification (MASTER SHEET)

1. DNA Polymorphisms: Core Concepts

  • Polymorphism = genetic variation present in ≥1% of population.

  • Applications: forensics, paternity testing, ancestry, population genetics, disease association.

  • Basis of individualization.

2. Major Types of Polymorphisms

A. SNPs

  • Single base changes.

  • Biallelic → lower discrimination.

  • Used for ancestry, degraded samples, pharmacogenomics.

B. RFLPs

  • Variation in restriction enzyme cut sites.

  • Requires large, intact DNA.

  • Largely obsolete in modern forensics.

C. VNTRs (Minisatellites)

  • 10–100 bp repeats.

  • Highly variable.

  • Used in early DNA fingerprinting.

D. STRs (Microsatellites)

  • 2–7 bp repeats.

  • Highly polymorphic.

  • PCR‑based; works with small or degraded samples.

  • Current forensic gold standard.

  • Used in CODIS.

3. STR Analysis Workflow

  1. DNA extraction

  2. Multiplex PCR amplification

  3. Capillary electrophoresis

  4. Allele calling

  5. Profile comparison and statistics

Key Terms

  • Allelic ladder = reference for allele sizing.

  • Stutter peaks = PCR slippage artifact.

  • Dropout = allele fails to amplify.

  • Drop‑in = spurious allele appears.

  • Mixture = multiple contributors.

4. Special Marker Systems

A. Y‑STRs

  • Paternal lineage.

  • Useful in male‑female mixtures.

  • Lower discrimination due to shared haplotypes.

B. mtDNA

  • Maternal inheritance.

  • High copy number → useful for degraded samples.

  • Lower discrimination.

  • Sequencing of HV1 and HV2 regions.

C. Amelogenin

  • Sex determination marker.

  • X and Y alleles differ in size.

  • Rare Y‑deletions can cause false female result.

5. Human Identification Applications

A. Forensics

  • STR profiling.

  • Mixture interpretation.

  • Degraded samples → mtDNA or miniSTRs.

B. Paternity/Relationship Testing

  • Mendelian inheritance.

  • CPI (Combined Paternity Index).

  • Probability of paternity.

C. Disaster Victim Identification

  • STRs, mtDNA, SNPs for severely degraded remains.

6. Bone Marrow Engraftment (Chimerism Analysis)

Purpose

  • Monitors donor vs recipient cell populations after hematopoietic stem cell transplantation (HSCT).

  • Detects engraftment success, relapse, or graft failure.

Chimerism Types

  • Complete donor chimerism: 100% donor cells.

  • Mixed chimerism: donor + recipient cells present.

  • Graft failure: increasing recipient cells.

Method (Gold Standard: STR Analysis)

  • Uses autosomal STR loci to distinguish donor vs recipient genotypes.

  • Requires pre‑transplant reference samples from both individuals.

  • Post‑transplant samples analyzed by multiplex PCR + capillary electrophoresis.

Informative Loci

  • STR loci where donor and recipient differ.

  • Only these loci are used for quantification.

Percent Engraftment Calculation

  • Based on peak area ratios of informative alleles.

  • General formula:
    % Donor = (Donor allele peak area) / (Donor + Recipient peak areas) × 100

Clinical Interpretation

  • Increasing donor % → successful engraftment.

  • Stable mixed chimerism → monitor closely.

  • Increasing recipient % → relapse or graft rejection.

  • Sudden drop in donor % → urgent concern.

Special Cases

  • Sex‑mismatched transplants may also use amelogenin or X/Y FISH.

  • STR‑based methods remain most sensitive and quantitative.

7. Statistics & Population Genetics

  • Hardy–Weinberg equilibrium.

  • Random Match Probability (RMP).

  • Likelihood ratios.

  • Combined Paternity Index (CPI).

  • RMP uses product rule across independent loci.

8. Quality Assurance

  • Chain of custody.

  • Contamination control.

  • Positive and negative controls.

  • Proficiency testing.

  • Validation of new STR kits.

9. Legal & Ethical Points

  • CODIS core loci.

  • Privacy considerations.

  • Admissibility standards (Daubert/Frye).

High‑Yield Facts to Memorize

  • STRs = primary forensic marker.

  • Y‑STRs = paternal lineage, male‑specific.

  • mtDNA = maternal lineage, degraded samples.

  • Stutter = PCR artifact.

  • Allelic ladder = sizing reference.

  • RMP uses product rule.

  • CODIS = standardized STR loci set.

  • Engraftment uses STR peak area ratios to quantify donor vs recipient.

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