Short tandem repeat
Encyclopedia
A short tandem repeat in DNA
occurs when a pattern of two or more nucleotide
s are repeated and the repeated sequences are directly adjacent to each other. The pattern can range in length from 2 to 5 base pair
s (bp) (for example (CATG)n in a genomic region
) and is typically in the non-coding intron
region. A short tandem repeat polymorphism (STRP) occurs when homologous STR loci differ in the number of repeats between individuals. By identifying repeats of a specific sequence at specific locations in the genome, it is possible to create a 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.
STR analysis is a relatively new technology in the field of forensics
, having come into popularity in the mid-to-late 1990s. It is used for the genetic fingerprinting
of individuals. The STRs in use today for forensic analysis are all tetra- or penta-nucleotide repeats (4 or 5 repeated nucleotides), 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 PCR 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 stain
ing (low sensitivity, 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. It is also used to follow up bone marrow transplant
patients.
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. The British
data base for STR loci identification is the UK National DNA Database
(NDNAD). The British system uses 10 loci, rather than the American 13 loci.
Y-STR
s (STRs on the Y chromosome
) are often used in genealogical DNA test
ing.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
occurs when a pattern of two or more nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s are repeated and the repeated sequences are directly adjacent to each other. The pattern can range in length from 2 to 5 base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
s (bp) (for example (CATG)n in a genomic region
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
) and is typically in the non-coding intron
Intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final...
region. A short tandem repeat polymorphism (STRP) occurs when homologous STR loci differ in the number of repeats between individuals. By identifying repeats of a specific sequence at specific locations in the genome, it is possible to create a genetic profile of an individual. There are currently over 10,000 published STR sequences in the human genome. STR analysis
STR analysis
Short tandem repeat analysis is a molecular biology method used to compare specific loci on DNA from two or more samples. A short tandem repeat is a microsatellite, consisting of a unit of two to thirteen nucleotides repeated hundreds of times in a row on the DNA strand. STR analysis measures...
has become the prevalent analysis method for determining genetic profiles
Genetic fingerprinting
DNA profiling is a technique employed by forensic scientists to assist in the identification of individuals by their respective DNA profiles. DNA profiles are encrypted sets of numbers that reflect a person's DNA makeup, which can also be used as the person's identifier...
in forensic cases.
Forensic analysis
Forensics
Forensic science is the application of a broad spectrum of sciences to answer questions of interest to a legal system. This may be in relation to a crime or a civil action...
, having come into popularity in the mid-to-late 1990s. It is used for the genetic fingerprinting
Genetic fingerprinting
DNA profiling is a technique employed by forensic scientists to assist in the identification of individuals by their respective DNA profiles. DNA profiles are encrypted sets of numbers that reflect a person's DNA makeup, which can also be used as the person's identifier...
of individuals. The STRs in use today for forensic analysis are all tetra- or penta-nucleotide repeats (4 or 5 repeated nucleotides), 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 PCR stutter and preferential amplification, as well as the fact that several genetic diseases are associated with tri-nucleotide repeats such as Huntington's disease
Huntington's disease
Huntington's disease, chorea, or disorder , is a neurodegenerative genetic disorder that affects muscle coordination and leads to cognitive decline and dementia. It typically becomes noticeable in middle age. HD is the most common genetic cause of abnormal involuntary writhing movements called chorea...
. Longer repeat sequences will suffer more highly from environmental degradation and do not amplify by PCR
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
as well as shorter sequences.
The analysis is performed by extracting nuclear DNA
Nuclear DNA
Nuclear DNA, nuclear deoxyribonucleic acid , is DNA contained within a nucleus of eukaryotic organisms. In mammals and vertebrates, nuclear DNA encodes more of the genome than the mitochondrial DNA and is composed of information inherited from two parents, one male, and one female, rather than...
from the cells of a forensic sample of interest, then amplifying specific polymorphic
Polymorphism (biology)
Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...
regions of the extracted DNA by means of the polymerase chain reaction
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
. Once these sequences have been amplified, they are resolved either through gel electrophoresis
Gel electrophoresis
Gel electrophoresis is a method used in clinical chemistry to separate proteins by charge and or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge...
or capillary electrophoresis
Capillary electrophoresis
Capillary electrophoresis , also known as capillary zone electrophoresis , can be used to separate ionic species by their charge and frictional forces and hydrodynamic radius. In traditional electrophoresis, electrically charged analytes move in a conductive liquid medium under the influence of an...
, 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 stain
Silver stain
Silver staining is the use of silver to selectively alter the appearance of the target.-Use in medicine:It is used to stain histologic sections. This kind of staining is important especially to show proteins and DNA. It is used to show both substances inside and outside cells...
ing (low sensitivity, safe, inexpensive), or an intercalating dye such as ethidium bromide
Ethidium bromide
Ethidium bromide is an intercalating agent commonly used as a fluorescent tag in molecular biology laboratories for techniques such as agarose gel electrophoresis. It is commonly abbreviated as "EtBr", which is also an abbreviation for bromoethane...
(fairly sensitive, moderate health risks, inexpensive), or as most modern forensics labs use, fluorescent dyes
Fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation of a different wavelength. It is a form of luminescence. In most cases, emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation...
(highly sensitive, safe, expensive). Instruments built to resolve STR fragments by capillary electrophoresis also use fluorescent dyes to great effect. It is also used to follow up bone marrow transplant
Bone marrow transplant
Hematopoietic stem cell transplantation is the transplantation of multipotent hematopoietic stem cell or blood, usually derived from bone marrow, peripheral blood stem cells, or umbilical cord blood...
patients.
In the United States
United States
The United States of America is a federal constitutional republic comprising fifty states and a federal district...
, 13 core STR loci
Locus (genetics)
In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...
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. The British
United Kingdom
The United Kingdom of Great Britain and Northern IrelandIn the United Kingdom and Dependencies, other languages have been officially recognised as legitimate autochthonous languages under the European Charter for Regional or Minority Languages...
data base for STR loci identification is the UK National DNA Database
UK National DNA Database
The United Kingdom National DNA Database is a national DNA Database that was set up in 1995. As of the end of 2005, it carried the profiles of around 3.1 million people...
(NDNAD). The British system uses 10 loci, rather than the American 13 loci.
Y-STR
Y-STR
A Y-STR is a short tandem repeat on the Y-chromosome. Y-STRs are often used in forensics, paternity, and genealogical DNA testing.-Nomenclature:Y-STRs are assigned names by the HUGO gene nomenclature committee....
s (STRs on the Y chromosome
Y chromosome
The Y chromosome is one of the two sex-determining chromosomes in most mammals, including humans. In mammals, it contains the gene SRY, which triggers testis development if present. The human Y chromosome is composed of about 60 million base pairs...
) are often used in genealogical DNA test
Genealogical DNA test
A genealogical DNA test examines the nucleotides at specific locations on a person's DNA for genetic genealogy purposes. The test results are not meant to have any informative medical value and do not determine specific genetic diseases or disorders ; they are intended only to give genealogical...
ing.
See also
- tandem repeatTandem repeatTandem repeats occur in DNA when a pattern of two or more nucleotides is repeated and the repetitions are directly adjacent to each other. -Example:An example would be:in which the sequence A-T-T-C-G is repeated three times.-Terminology:...
- variable number tandem repeatVariable number tandem repeatA Variable Number Tandem Repeat is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length between individuals. Each variant acts as an inherited allele, allowing them to be used for...
- nucleotide sequences
- Microsatellite
- MinisatelliteMinisatelliteA minisatellite is a section of DNA that consists of a short series of bases 10-60 bp. These occur at more than 1,000 locations in the human genome...
- Y-STRY-STRA Y-STR is a short tandem repeat on the Y-chromosome. Y-STRs are often used in forensics, paternity, and genealogical DNA testing.-Nomenclature:Y-STRs are assigned names by the HUGO gene nomenclature committee....
- List of X-STR markers
- List of Y-STR markers
- Genetic fingerprintingGenetic fingerprintingDNA profiling is a technique employed by forensic scientists to assist in the identification of individuals by their respective DNA profiles. DNA profiles are encrypted sets of numbers that reflect a person's DNA makeup, which can also be used as the person's identifier...
- Single-nucleotide polymorphism (SNP)
- SnpstrSnpstrA SNPSTR is a compound genetic marker composed of one or more SNPs and one microsatellite . SNPSTRs were first described by MOUNTAIN et al. who developed experimental protocols for autosomal SNPSTRs which contain a SNP and a microsatellite within 500 base pairs of one another...
- StrbaseStrbaseSTRBase is a database of Short Tandem Repeats...