A person’s genome (total DNA in a cell) is made up of a linear sequence of chemical units called nucleotides. There are four DNA nucleotides – adenine (a), thymine (t), guanine (g), and cytosine (c) – and their specific order in parts of the genome encodes important information that helps cells function. Most of any one person’s genome is identical in its sequence to another person’s. However, there are variations between genomes, and one class of variations is referred to as short tandem repeats (STRs). STRs are parts of the genome that feature consecutive repeats of a DNA sequence, often three to seven nucleotides in length. For example, gatagatagatagatagatagata features the four-nucleotide repeat gata. The STR variation between individuals is not found in the sequence of the repeat, but in how many times it is repeated. Some individuals might have the repeat 10 times, others 11, and still others 12. On top of that, every person has two versions (i.e., alleles) of each STR, one inherited from each parent. The number of repeats will either be the same for both alleles (e.g., 10,10 or 12,12) or different (e.g., 10,12). When multiple different STR regions (called “loci”) are simultaneously considered, differences between individuals emerge that can be used for DNA profiling. CODIS uses 20 different STR core loci to generate a DNA profile.
Analyzing a DNA sample for use in a US criminal investigation requires four steps:
- Extraction: DNA contained on swabs taken from a suspect or crime scene must be isolated to eliminate all other contaminating material (i.e. cotton, dust, etc.).
- Amplification: Short sequences of DNA from 20 different loci are amplified (i.e., copies are produced) using a technique called polymerase chain reaction (PCR). This amplification step allows for DNA analysis from a very small amount of starting DNA.
- Separation: Individuals contain different numbers of repeats within these STRs, which would be reflected in the size of the amplified DNA sequence. The amplified DNA can be separated by size using a technique called electrophoresis. There are two main types of electrophoresis, gel (traditional) and capillary (used in Rapid DNA).
- Detection: Each of the two STR alleles for each locus are compared to a control to determine its size (i.e., number of repeats). While each locus might have repeat sizes shared by 5-20% of the population, looking at the 20 different loci vastly decreases the odds of a duplicate profile within a population.
The FBI can use STR profiles to match DNA at crime scenes to STR profiles of individuals in their CODIS system. Rapid DNA instruments vastly speed up and simplify these four steps into a single process with minimal human interface.
Rapid DNA analysis provides several advantages over canonical DNA analysis. First, rapid DNA analysis eliminates the need for a DNA expert to handle a known sample. Little training is necessary to operate the machines, so the DNA analysis can be managed by an investigating police officer, booking agent, or other law enforcement personnel.
Second, any DNA picked up from gloves, countertops, door handles etc. during DNA analysis can serve as a contaminant, complicating the DNA profiling process and interfering with the accuracy of results. Rapid DNA analysis employs a hands-free method, effectively minimizing the chance of contamination.
Third, DNA analysis can be quite time consuming, taking a laboratory between 10 hours and several days to process a sample. Any backlog of samples will make this process even longer. Rapid DNA analysis can complete the process, “swab in” to “profile out” in about two hours, providing a high throughput system for DNA analysis.