Untitled Notes

1. Lesson Objectives

By the end of this lesson, you should be able to:

Provide comprehensive definitions for all key terms.
Explain the technology of polymerase chain reaction (PCR) and how it applies to forensic DNA typing.
Explain the latest DNA typing technique, short tandem repeat (STR) analysis.
Be familiar with the 13 CODIS STRs and their chromosomal locations.
Calculate the frequency of occurrence of a DNA profile.
Explain the difference between traditional STR analysis and Y-chromosome STR determination.
Explain the difference between nuclear DNA and mitochondrial DNA.
Discuss the application of a computerized DNA database to criminal investigation.
List the necessary procedures for the proper preservation of bloodstained evidence for laboratory DNA analysis.
Determine familial relationships based on DNA evidence.
Calculate the probability of occurrence of a DNA profile using demographic data.

2. Relevance Connection – DNA Case Study

Solving Cold Cases with DNA: The Boston Strangler Case

By Philip Bulman
NIJ funding helped the Boston Police Department solve a rape and murder case almost 50 years after the crime.

Mary Sullivan, a 19-year-old woman, was found dead in January 1964 shortly after moving to Boston. She had been raped and strangled, and her body was one of many associated with the infamous Boston Strangler.
Albert DeSalvo confessed to the murders but later recanted, leading many to believe the actual assailant was still at large. He was sentenced to life imprisonment on unrelated charges and was murdered in prison in 1973.
In July 2013, DNA evidence finally connected DeSalvo to Sullivan's murder, establishing a critical link to historical unsolved cases.

NIJ’s Program on Cold Cases

The NIJ program provides funding to help police departments investigate and analyze cold cases that could be solved through DNA analysis, often applicable when DNA testing was not available at the time of the crime.

Y-Chromosome Research

Y-chromosome DNA testing focuses on the male-specific DNA in cases where male DNA is present among female DNA, particularly relevant in sexual assault cases.
NIJ has funded various Y-chromosome research projects, including:
- Validation of Y-STR multiplex kits
- Development of DNA typing systems targeting the male-specific portion of the genome
- Creation and maintenance of the U.S. Y-STR Database
- Evaluation of new strategies to enhance male DNA detection.

3. DNA Evidence Collection

Sources of DNA

Multiple different sources of DNA exist; however, not all are suitable for extraction. In cases where no optimal source exists, alternative sources may be utilized.

DNA Collection Guidelines

Evidence should be photographed and sketched before collection.
Use gloves frequently to prevent contamination, utilizing disposable tools whenever possible.
To avoid personal DNA contamination, do not touch surfaces unnecessarily.
Air-dry damp samples before packaging; avoid airtight containers to prevent moisture-related degradation.
Package samples separately in well-ventilated paper bags or boxes.
All biological evidence must be stored in cool conditions until delivered to the laboratory.
Collect standard/reference DNA specimens, such as blood or buccal swabs (swabbing the mouth and cheek).

4. DNA Analysis

DNA analysis can be categorized based on the analysis's ultimate purpose:

DNA Barcoding: Used for species differentiation, often requiring STR analysis.
DNA Profiling/Fingerprinting: Aims to compare evidence with reference samples, identify familial relationships, or exonerate suspects through nuclear, STR, RFLP, or mtDNA techniques.
DNA Phenotyping: Helps identify physical attributes without reference samples, utilizing SNPs, STRs, and mtDNA.

4.1. Polymerase Chain Reaction (PCR)

PCR is a laboratory procedure that generates multiple copies of specific DNA segments, making it critical for forensic DNA typing.
Two primers bind to the target DNA sequence, and a PCR machine cycles through temperature variations to denature the DNA, anneal primers, and synthesize new DNA strands, resulting in exponential amplification of the target.
PCR's accurate amplification makes it usable on small or partially degraded samples, crucial for forensic applications.

4.2. Restriction Fragment Length Polymorphisms (RFLPs)

RFLP is early DNA typing that uses restriction endonucleases to cut DNA into fragments at specific nucleotide spots (A, T, C, G).
DNA samples undergo gel electrophoresis, separating fragments by size. Bands are visualized using Southern blotting with radioactive probes and then detected on X-ray film.
RFLP is slow (taking weeks to months for results) and requires large sample sizes, often not suitable for small or degraded samples.

4.3. Short Tandem Repeats (STRs)

STR analysis is a modern and effective profiling technique focusing on short repeating sequences in DNA.
It is characterized by short sequences (3-7 bases) and smaller fragment lengths, enabling PCR amplification, suitable for degraded samples, and ideal for multiplexing.
The FBI has established 13 STRs for CODIS, yielding an exceedingly low probability of coincidental matches in unrelated individuals (~1 in 575 trillion).
As little as 125 picograms of DNA is sufficient for STR analysis, making it advantageous over RFLP methods.

4.4. Y-STR

Y-STR analysis specifically targets male Y chromosomes and is useful in cases involving multiple males or cell admixture.
It produces single-band patterns due to its haploid nature and can trace male lineage over generations.

4.5. Short Nucleotide Polymorphisms (SNPs)

SNPs represent alterations at single nucleotide sites and can aid in predicting complex phenotypic traits.
They allow analysis of traits such as facial features using statistical correlations across multiple loci.

4.6. Mitochondrial DNA (mtDNA)

mtDNA is maternally inherited and found in mitochondria outside the nucleus, less discriminative than nuclear DNA.
It is more time-consuming and costly to analyze, often used when nuclear DNA is not available.
The sequencing of specific highly variable mtDNA regions is employed for forensic characterization.

4.7. Novel Techniques

Touch DNA: Refers to DNA left on surfaces from skin cells when objects are touched.
M-Vac: A non-destructive surface sampling device that recovers DNA efficiently by applying a DNA-free buffer and simultaneously vacuuming suspended particles.
Rapid DNA: Automation advances allow DNA profiling within hours, contrasting with the longer timelines of traditional techniques.

4.8. Activity

1. What is polymerase chain reaction (PCR) and how is it useful to forensic scientists?
2. What are tandem repeats and how are they useful to forensic scientists?
3. What are short tandem repeats (STRs) and what is their significance to DNA typing?
4. List two advantages STRs have over restriction fragment length polymorphisms (RFLP).
5. What are the three main differences between nuclear DNA and mitochondrial DNA?
6. Name two advantages and two disadvantages of mitochondrial DNA analysis compared to nuclear DNA analysis.