DNA fingerprinting as evidence

Definition: Laboratory procedure for analyzing patterns of sequence variation in DNA samples for the purpose of identifying evidence in forensic investigations.

Significance: The development of DNA fingerprinting represents one of the major breakthroughs in forensic science. Using techniques from molecular biology and increasingly detailed databases, investigators are able to examine the DNA contained within biological evidence obtained from crime scenes and compare their findings with known samples, resulting in a high degree of probability that particular pieces of evidence can be associated with individual suspects or victims.

In 1985, the English geneticist Alec Jeffreys proposed that newly discovered repetitive sequences in DNA (deoxyribonucleic acid) could be used as a form of genetic fingerprint to identify individuals. DNA fingerprinting represents a combination of both molecular biology and population genetics in that in this process, pieces of DNA are examined for the presence of specific markers and the findings are compared against known samples in a database to establish the prevalence of those markers in the general population.

Types of Genetic Markers

The human genome comprises more than 3.2 billion nucleotides, the letters that are responsible for coding for the proteins that make up and carry out bodily functions. The sequences of the human genome that code for these proteins are called genes. Humans are believed to have approximately twenty-five thousand genes. Between these genes are vast stretches of DNA that do not code for proteins. Within these areas are repetitive sequences called variable number of tandem repeats, or VNTRs. One class of VNTRs is made up of the minisatellites, sequences of up to one hundred nucleotides that may be repeated in tandem up to one thousand times. In addition to the minisatellites, microsatellites have been identified. These are also known as short tandem repeats (STRs) or simple sequence repeats (SSRs). Microsatellites are sequences of two to seven nucleotides that may be repeated hundreds of times. An example is the CA repeat (CACACACA) that occurs on average every thirty-thousand base pairs in the human genome.

Every human being has two copies of genetic information in each cell. This represents the genetic information contributed by each of the individual’s parents. Each STR thus exists in two copies. Often, the number of repeats within a specific STR differs in the parents. These differences are called alleles. In a population, a given STR may be polymorphic, meaning that many different forms (or alleles) of the STR exist in the population. For each allele used in forensic analysis, population geneticists have determined the percentage of the population at large that contains that given allele. This information forms the basis of DNA fingerprinting.

Analysis of DNA Fingerprints

When DNA fingerprinting was initially developed, analysts examined DNA patterns using a procedure called the Southern blot. In a Southern blot, DNA is extracted from cells and then cut with a special enzyme called a restriction endonuclease. Restriction endonucleases recognize specific sequences of nucleotides in the DNA. When the sequence has been identified, the enzyme makes a cut in the DNA, generating short fragments that may be separated by size through gel electrophoresis. A radioactive probe is then used to identify specific fragments that contain sequences of nucleotides of interest. Initially, analysts accomplished this task by using minisatellites and restriction fragment length polymorphisms (RFLPs). When exposed to photographic film, the radioactive probes revealed patterns in the DNA that could be used to identify evidence.

Soon after DNA fingerprinting began, the entire process was greatly simplified by the invention of the polymerase chain reaction (PCR). Instead of cutting the DNA with restriction enzymes, the analyst copies specific sections of the genome, in this case the area containing the microsatellite repeats, millions of times. The amplified sections are then separated by gel electrophoresis, stained, and photographed. Because the fragments are much smaller than those generated during a Southern blot, the results may be ready in just a few hours of time. As with a Southern blot, the length of the fragment is determined by the number of repeats. The larger the number of repeats in the amplified section of DNA, the slower its movement during gel electrophoresis. This allows the analyst to discriminate among STRs that differ in the numbers of repeats within the amplified sequence.

In the United States, thirteen STRs have been identified for use during forensic and criminal investigations. Most investigative laboratories also include an additional test for amelogenin, a gene associated with dental pulp, which allows an investigator to determine whether a sample comes from a male or a female subject. For each of the STRs, researchers have determined the prevalence of that allele in the general population. Although the allele for one STR may be shared by a large percentage of the population, the power of discrimination becomes much greater as the number of STRs being analyzed is increased. For example, when three STRs (A, B, and C) are used, the probability of a certain combination (A¹, B³, C²) is equal to the product of the frequency of that allele in the population (A B C). As the number of STRs increases, the chances that two individuals will share the same identical pattern decrease.

When coupled with additional evidence found at a crime scene, DNA fingerprinting can be a powerful tool for proving the guilt or innocence of a suspect. DNA fingerprinting is also used to identify human remains that have degraded over time or that have been badly damaged by exposure to chemicals or fire.

Bibliography

Butler, John M. Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers. 2d ed. Burlington, Mass.: Elsevier Academic Press, 2005. Provides a detailed examination of DNA fingerprinting analysis using STR markers. Intended for readers with background in the sciences.

Jeffreys, A. J., V. Wilson, and S. L. Thein. “Individual-Specific ’Fingerprints’ of Human DNA.” Nature 316 (1985): 76-79. Landmark paper that introduced the concept of DNA fingerprinting as a method of identification.

Kobilinsky, Lawrence F., Louis Levine, and Henrietta Margolis-Nunno. Forensic DNA Analysis. New York: Chelsea House, 2007. Presents a comprehensive introduction to the use of STRs in DNA fingerprinting. Includes discussion of future directions, including mitochondrial and Y chromosome analyses.

Rudin, Norah, and Keith Inman. An Introduction to Forensic DNA Analysis. 2d ed. Boca Raton, Fla.: CRC Press, 2002. Provides a good introduction to the use of biological evidence in forensics as well as the history and application of DNA fingerprinting in forensic investigations.