Week 9.1 Forensic Identity Testing and DNA Fingerprinting Lecture Notes

Overview of Diagnostics and the Role of the UCLA Laboratory

• Dr. Wayne Brody and the UCLA Laboratory: Dr. Brody is the founding director of the Diagnostic Molecular Pathology Laboratory at UCLA. This facility was one of the first in the United States to offer DNA-based testing for a wide variety of diseases and conditions.

• Diverse Applications of Molecular Testing: The laboratory and its affiliates at UCLA engage in several specialized areas of testing:

  • Neoplastic/Cancer Genetics: Testing tumor DNA to diagnose or characterize cancers.

  • Genetic Disease Testing: Diagnosing inherited conditions, which is a core focus of the medical genetics curriculum.

  • Identity Testing: Using DNA to identify individuals or determine familial relationships.

  • HLA Typing (Immuno-genetics/Histocompatibility): Used for bone marrow and solid organ transplants. UCLA’s immuno-genetics lab is considered a world leader, housing the International Bone Marrow Registry.

  • Molecular Microbiology: Testing for infectious diseases, typically performed in the clinical microbiology lab.

  • Pharmacogenetics: Evaluating how genetic variation affects drug response, particularly for biologic drugs in cancer treatment. Dr. Brody expressed skepticism regarding the current "hype" versus substance in this field.

• The Power of PCR in Forensics: The Polymerase Chain Reaction (PCR) has revolutionized forensics because it allow researchers to start with very tiny amounts of target DNA and exponentially amplify it for analysis. Unlike clinical biopsies or blood draws which provide fresh, high-quality samples, crime scenes often yield:

  • Tiny, dried blood spots.

  • Skin cells trapped under a victim’s fingernails from a struggle.

  • Trace amounts of saliva on stamps or envelopes (though self-adhesive materials in the US have limited this specific source recently).

The Evolution of DNA Testing Methodologies

• Restriction Fragment Length Polymorphisms (RFLP): Used in the early days involving southern blots. This process was laborious, taking $3$ to $4$ weeks and requiring dangerous radioactive tracers.

• Variable Number of Tandem Repeats (VNTR): These involve large regions in the genome repeated many times (kilobases or megabases long) and still required southern blotting.

• Short Tandem Repeats (STR): The current standard facilitated by PCR. These are polymorphic repeats in non-coding regions that vary in length between individuals. They can be mono-, di-, tri-, or tetra-nucleotide repeats.

• Single Nucleotide Polymorphisms (SNP): Base changes in the genome (especially non-coding regions). While historically expensive, Next Generation Sequencing (NGS) is beginning to make SNP analysis more viable for forensic labs.

• Target Selection Criteria: For a marker to be useful, it must have many different alleles (e.g., $14$, $16$, or $18$ repeats) and no single allele should be predominantly common in a population. Ideally, markers should have alleles occurring at low frequencies (e.g., $2\%$) to increase the power of exclusion.

Historical Milestones in DNA Fingerprinting

• Alec Jeffries: Often called the father of DNA identity testing, Jeffries (University of Edinburgh) discovered that non-coding regions of DNA are highly distinct between individuals. He coined the term "DNA fingerprinting" based on the complex patterns produced by multi-locus DNA probes on southern blots.

• The Blooding (Leicestershire, England): The first case solved by DNA fingerprinting. In $1983$ and $1986$, two $15$-year-old girls were raped and strangled. Despite a mass DNA screening of $5,000$ men, the killer, Colin Pitchfork, was only caught after he was overheard in a pub admitting he had a friend impersonate him for the blood draw. He was sentenced to life in $1988$.

• Tommy Lee Andrews ($1987$): The first individual convicted in the United States using DNA evidence for a rape and burglary case in Orlando, Florida.

• The Innocence Project: While DNA identifies the guilty, its primary use is often exoneration. Roy Crider was released in Texas after serving $10$ years of a sentence for a murder he did not commit, following DNA testing of a cigarette butt and vaginal swab that did not match him.

The O.J. Simpson Trial and Its Impact on Forensic Science

• The Case: O.J. Simpson was accused of the double murder of Nicole Brown Simpson and Ron Goldman in the mid-$1990$s.

• The Evidence:

  • Side Walk/Bundy Drive: A pool of blood matched Nicole Brown.

  • Blood Drops: DNA from both victims and O.J. Simpson were found at the scene.

  • Ford Bronco: Blood smears inside the vehicle matched O.J. Simpson and Nicole Brown.

  • The Bloody Glove: Found at Simpson's Rockingham estate, it contained a mixture of DNA from O.J., Nicole, and Ron Goldman.

• The Verdict and Repercussions: Despite overwhelming genetic evidence, the defense successfully created "reasonable doubt" by attacking the reliability of PCR and highlighting "Chain of Custody" failures (e.g., a detective carrying a blood sample in his pocket overnight).

• Public Perception: The acquittal led to a temporary belief that DNA testing was unreliable, affecting clinical practice where patients with suspected genetic diseases (like Cystic Fibrosis) expressed skepticism toward genetic tests.

Statistics, CODIS, and State Databases

• Statistical Power (The Product Rule): The FBI mandates the use of at least $13$ (now potentially more) STR markers on different chromosomes. If survival of one allele is seen in $12\%$ of the population and another in $7\%$, the chance of a random match for both is the product ($0.12 \times 0.07$). By the time $13$ markers are used, the probability of a coincidental match is often less than $1$ in many billions.

• CODIS (Combined DNA Index System): Established by Congress in $1994$, it digitizes STR patterns to allow cross-state matching. This is essential for "Cold Cases" where there is no witness or suspect.

• State Legislative Variation: Laws regarding who is entered into DNA databases vary. All $50$ states include sex offenders. Two-thirds include burglars. Some states are "arresting states," taking DNA samples upon arrest regardless of conviction.

• Expungement: The process of removing one's DNA from a database if released or exonerated also varies significantly by state; some require a formal request while others have no set policy.

Ethical Concerns and Familial Searching

• Guilt by Association: Familial searching involves looking for partial matches in CODIS. While CODIS is designed for exact matches, lowering the stringency can identify relatives of a perpetrator.

• The Grim Sleeper (Lonnie David Franklin Jr.): Responsible for at least $10$ murders in LA between $1984$ and $2007$. The case was solved through a partial match to his son, who was in CODIS for a weapons charge. Detectives then obtained the father's DNA from a pizza crust.

• The Golden State Killer (Joseph James DeAngelo): A former police officer responsible for $13$ murders and over $50$ rapes. He was identified using the public genealogy database Ancestry.com to track family members. This "genetic genealogy" method raises privacy concerns as users may not realize their data could be used in police investigations.

• Racial Bias: Dr. Brody noted that CODIS has a racial bias, containing a disproportionate number of African American genotypes due to systemic issues in the justice system.

Specialized Applications of Identity Testing

• Military Personnel: All members of the armed services must provide blood spots and fingerprints. This ensures that no soldier remains "unknown," even if only fragments are found after an explosion. Refusal can lead to a dishonorable discharge because genetic privacy is not protected within the military.

• Ancient DNA and Historical Mysteries: Mitochondrial DNA (maternally inherited) was used to identify the remains of Tsar Nicholas II and the Romanov family. Prince Philip (Queen Elizabeth's husband) provided DNA for comparison as a maternal descendant.

• Disaster Victim Identification (DVI): Used in plane crashes and mass tragedies like the World Trade Center attacks on $9/11$. Lab workers have matched over $1,000,000$ pulverized tissue fragments back to victims.

• Humanitarian Efforts: In Argentina, DNA was used to reunite children stolen by the fascist dictatorship with their biological grandparents (the Plaza de Abuelas).

• Clinical Specimen Identification: Dealing with mislabeled biopsies. If two breast biopsies are swapped, DNA extracted from the paraffin wax block can be compared to the patients’ blood to prevent erroneous surgeries.

Paternity Testing

• The Biological Rule: Every DNA fragment in a child must be present in either the biological mother or the biological father. If a child possesses an allele not found in either parent, the alleged father is excluded.

• Economic Implications: Often revolves around child support ("heartstrings and pursestrings").

• Anomalies: Occasionally, a paternity test reveals that the "mother" does not match the child's DNA. This often indicates a specimen mix-up or undisclosed family dynamics (e.g., surrogacy or abduction) that the parties choose not to clarify.

• Market Competition: Paternity tests are now highly commercialized, with costs often around $\$450$, even for high-profile cases involving significant wealth.