A short tandem repeat (STR) in DNA is a class of polymorphisms that occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. The pattern can range in length from 2 to 10 base pairs (bp) (for example (CATG)n in a genomic region) and is typically in the non-coding intron region, making it junk DNA. By examining several STR loci and counting how many repeats of a specific STR sequence there are at a given locus, it is possible to create a unique genetic profile of an individual. There are currently over 10,000 published STR sequences in the human genome. STR analysis has become the prevalent analysis method for determining genetic profiles in forensic cases.
Forensic STR Analysis
STR analysis is a relatively new technology in the field of forensics, having come into popularity in the mid-to-late 1990's. The STRs in use today for forensic analysis are all tetra- or penta-nucleotide repeats (4 or 5 repeat units), as these give a high degree of error-free data while being robust enough to survive degradation in non-ideal conditions. Shorter repeat sequences tend to suffer from artifacts such as stutter and preferential amplification, as well as the fact that several genetic diseases are associated with tri-nucleotide repeats such as Huntington's disease. Longer repeat sequences will suffer more highly from environmental degradation and do not amplify by PCR as well as shorter sequences.
The analysis is performed by extracting nuclear DNA from the cells of a forensic sample of interest, then amplifying specific polymorphic regions of the extracted DNA by means of the polymerase chain reaction. Once these sequences have been amplified, they are resolved either through gel electrophoresis or capillary electrophoresis, which will allow the analyst to determine how many repeats of the STR sequence in question there are. If the DNA was resolved by gel electrophoresis, the DNA can be visualized either by silver staining (not very high resolution, safe, inexpensive), or an intercalating dye such as ethidium bromide (fairly sensitive, moderate health risks, inexpensive), or as most modern forensics labs use, fluorescent dyes (highly sensitive, safe, expensive). Instruments built to resolve STR fragments by capillary electrophoresis also use fluorescent dyes to great effect.
In the United States, 13 core STR loci have been decided upon to be the basis by which an individual genetic profile can be generated. These profiles are stored on a local, state and national level in DNA databanks such as CODIS.
Y-STRs (STRs on the Y chromosome) are often used in genealogical DNA testing.