Chapter 11 – DNA Analysis

Each individual has billions of cells that contain a nucleus. Within the nucleus is genetic material arranged in 23 pairs of chromosomes. These contain the polymeric molecule, DNA, that is responsible for genetic inheritance of all characteristics of the person. The DNA molecule is arranged in the form of a double helix containing base pairs linked to a chemical backbone. There are approximately 3 billion base pairs in the human genome and less than one percent differ from person to person. DNA typing methods utilize these differences in DNA to help identify people from biological evidence. The first method that was used commercially for DNA typing was restriction fragment length polymorphism (RFLP). This method isolates certain regions of DNA that are made up of core base pair sequences that are characterized by repeating a different number of times throughout the human population. The RFLP process isolates these sequences by the use of restriction enzymes and separates them by gel electrophoresis. They are visualized by radio-labeling or chemiluminescence. Modern methods of DNA typing rely on the polymerase chain reaction. Using enzymes, nucleotides, and DNA primers, sequences of DNA can be replicated automatically using a thermal cycler. The standard method for DNA analysis today exploits some of the thousands of short tandem repeats. These are 4 base pair polymorphic repeating sequences. The STRs are fluorescently labeled and separated by capillary electrophoresis. Currently, 15 loci are being typed for forensic purposes. Reliable population statistics have been developed for the various alleles of each of the 15 STRs. Since the DNA types at all 15 loci have been shown to be independent, the product rule can be used to calculate the probability of a chance occurrence of a given DNA profile within a chosen population. Each multilocus genotype derived from the 15 loci being used today is so rare that it is improbable that two people in the world would have the same exact type. This has resulted in forensic biology laboratories to conclude in STR cases, that a match of the DNA type of the evidence and the suspect (or other person of interest) is essentially an identification, except in the case of identical twins. Under the auspices of the FBI, a three-tiered (local, state, and national) Combined DNA Indexing System (CODIS) database has been created that contains nearly 10 million DNA profiles. Starting at the local LDIS database, any accredited forensic science laboratory can mount a CODIS search to see if a DNA sample recovered from a crime matches an entry in the database. This has resulted in hundreds of hits, some of which have come in cold cases that have been open for many years. The ability to test biologic evidence for DNA years after it was collected (as long as it has been properly preserved) has given rise to the Innocence Project that uses DNA typing to reexamine criminal convictions where the case was originally adjudicated without the benefit of DNA typing. In more than 300 instances, prisoners have been exonerated by postconviction DNA typing. mtDNA is present in all cells. There are two hypervariable regions in mtDNA. Unlike nuclear DNA which has only one copy per cell, there are hundreds of copies of mtDNA in each cell. All mtDNA comes from the mother and each person has the same DNA as his or her mother. mtDNA is useful for typing old, degraded samples and in cases where nuclear DNA may not be present such as in old bones, hairs with no root, teeth, etc.