View source for Biology:Variable number tandem repeat

A '''variable number tandem repeat''' (or '''VNTR''') is a location in a [[Biology:Genome|genome]] where a short nucleotide sequence is organized as a [[Biology:Tandem repeat|tandem repeat]].  These can be found on many [[Biology:Chromosome|chromosome]]s, and often show [[Biology:Polymorphism|variations]] in length (number of repeats) among individuals.  Each variant acts as an [[Biology:Heredity|inherited]] [[Biology:Allele|allele]], allowing them to be used for personal or parental identification.  Their analysis is useful in [[Biology:Genetics|genetics]] and [[Biology:Biology|biology]] research, forensics, and DNA fingerprinting.  
 
[[Image:VNTRDemo.gif|thumb|right|650px|{{center|Schematic of a Variable Number of Tandem Repeats in 4 alleles.}}]]
[[Image:D1S80Demo.png|thumb|right|350px|{{center|Variations of VNTR (D1S80) allele lengths in 6 individuals.}}]]

==Structure and allelic variation==

In the schematic above, the rectangular blocks represent each of the repeated DNA sequences at a particular VNTR location.  The repeats are in tandem – i.e. they are clustered together and oriented in the same direction. Individual repeats can be removed from (or added to) the VNTR via [[Biology:Genetic recombination|recombination]] or [[Biology:DNA replication|replication]] errors, leading to alleles with different numbers of repeats.  Flanking regions are segments of non-repetitive sequence (shown here as thin lines), allowing the VNTR blocks to be extracted with [[Biology:Restriction enzyme|restriction enzyme]]s and analyzed by [[Biology:Restriction fragment length polymorphism|RFLP]], or amplified by the [[Biology:Polymerase chain reaction|polymerase chain reaction]] (PCR) technique and their size determined by [[Biology:Gel electrophoresis|gel electrophoresis]].

==Use in genetic analysis==
VNTRs were an important source of RFLP [[Biology:Genetic marker|genetic marker]]s used in [[Biology:Genetic linkage|linkage analysis]] (mapping) of diploid genomes.  Now that many genomes have been [[Biology:Human Genome Project|sequenced]], VNTRs have become essential to forensic crime investigations, via DNA fingerprinting and the [[Biology:Combined DNA Index System|CODIS]] database.  When removed from surrounding DNA by the PCR or RFLP methods, and their size determined by gel electrophoresis or [[Biology:Southern blot|Southern blot]]ting, they produce a pattern of bands unique to each individual.  When tested with a group of independent VNTR markers, the likelihood of two unrelated individuals'<!--apostrophe here for the genitive case; that is, "the likelihood of THEIR having..." not "the likelihood of them having..."--> having the same allelic pattern is extremely low.  VNTR analysis is also being used to study [[Biology:Genetic diversity|genetic diversity]] and breeding patterns in [[Biology:Population genetics|populations]] of wild or domesticated animals. As such, VNTRs can be used to distinguish strains of bacterial pathogens. In this microbial forensics context, such assays are usually called Multiple Loci VNTR Analysis or MLVA.
[[Image:Codis_profile.jpg|thumb|right|350px|{{center|Chromosomal locations of the 13 VNTR loci in the CODIS panel.}}]]

==Inheritance==

In analyzing VNTR data, two basic genetic principles can be used:

* '''Identity Matching''' – both VNTR alleles from a specific location must match.  If two samples are from the same individual, they must show the same allele pattern.
* '''Inheritance Matching''' – the VNTR alleles must follow the rules of inheritance.  In matching an individual with his parents or children, a person must have an allele that matches one from each parent.  If the relationship is more distant, such as a grandparent or sibling, then matches must be consistent with the degree of relatedness.

==Relationship to other types of repetitive DNA==
 
[[Biology:Repeated sequence (DNA)|Repetitive DNA]], representing over 40% of the human genome, is arranged in a bewildering array of patterns.  Repeats were first identified by the extraction of [[Biology:Satellite DNA|Satellite DNA]], which does not reveal how they are organized.  The use of restriction enzymes showed that some repeat blocks were [[Biology:Interspersed repeat|interspersed]] throughout the genome.  [[Biology:DNA sequencing|DNA sequencing]] later showed that other repeats are clustered at specific locations, with [[Biology:Tandem repeat|tandem repeat]]s being more common than [[Biology:Inverted repeat|inverted repeat]]s (which may interfere with DNA replication).  VNTRs are the class of clustered tandem repeats that exhibit allelic variation in their lengths.

==Classes==
[[File:VNTRexample.png|thumb|500x500px|This shows a theoretical example of a VNTR in two different individuals. A single strand of DNA from each individual is displayed in which there is tandem repeat sequence that the individuals share. The sequence presence is a VNTR because one individual has five repeats, while the other has seven repeats (number of repeats varies in different individuals). Each repeat is ten nucleotides, making it a minisatellite, rather than a microsatellite in which each repeat is 1-6 nucleotides.]]
VNTRs are a type of [[Biology:Minisatellite|minisatellite]] in which the size of the repeat sequence is generally ten to one hundred base pairs. Minisatellites are a type of DNA [[Biology:Tandem repeat|tandem repeat sequence]], meaning that the sequences repeat one after another without other sequences or nucleotides in between them. Minisatellites are characterized by a repeat sequence of about ten to one hundred nucleotides, and the number of times the sequence repeats varies from about five to fifty times. The sequences of minisatellites are larger than those of [[Biology:Microsatellite|microsatellite]]s, in which the repeat sequence is generally 1 to 6 nucleotides. The two types of repeat sequences are both tandem but are specified by the length of the repeat sequence. VNTRs, therefore, because they have repeat sequences of ten to one hundred nucleotides in which every repeat is exactly the same, are considered minisatellites. However, while all VNTRs are minisatellites, not all minisatellites are VNTRs. VNTRs can vary in number of repeats from individual to individual, as where some non-VNTR minisatellites have repeat sequences that repeat the same number of times in all individuals containing the tandem repeats in their genomes.<ref>{{cite web| url=https://www.nlm.nih.gov/visibleproofs/education/dna/vntr.pdf | title=VNTR | access-date=2024-01-13}}</ref><ref>{{cite web| url=https://www2.le.ac.uk/departments/mathematics/redundant-content/event-microsites/bio/Dubrova.pdf | title=Minisatellites and microsatellites – similar names but different biology | first=Yuri E. | last=Dubrova| archive-url=https://web.archive.org/web/20171215111344/https://www2.le.ac.uk/departments/mathematics/redundant-content/event-microsites/bio/Dubrova.pdf | archive-date=2017-12-15}}</ref>

==See also==

* [[Biology:Amplified fragment length polymorphism|AFLP]]
* MLVA
* Short tandem repeat
* [[Biology:Tandem repeat|Tandem repeat]]

=== Software for MLVA typing ===

* [[Software:BioNumerics|BioNumerics]] (using the [http://www.applied-maths.com/bionumerics/plugins/miru.htm BioNumerics MIRU-VNTR plugin] specifically developed for running a popular MLVA assay genotyping ''[[Biology:Mycobacterium tuberculosis|Mycobacterium tuberculosis]]'' strains)

==References==
{{Reflist}}

== External links ==
*Examples : 
** [http://www.rvc.ac.uk/review/DNA_1/4_VNTRs.cfm VNTRs] – info and animated example
*Databases :
** [http://minisatellites.u-psud.fr/   The Microorganisms Tandem Repeats Database]
** [http://mlva.u-psud.fr/ The MLVAbank]
** [http://www.cstl.nist.gov/div831/strbase/ Short Tandem Repeats Database]
** [http://tandem.bu.edu/ Tandem Repeats Database (TRDB)]
*Search tools :
**[https://dali.crbm.cnrs.fr/index.php?route=tools&tool=2 TAPO: A combined method for the identification of tandem repeats in protein structures]
** [http://tandem.bu.edu/trf/trf.html Tandem Repeats Finder] 
** [http://bioinfo.lifl.fr/mreps Mreps]
** [http://atgc.lirmm.fr/star STAR]
** [http://www.sci.brooklyn.cuny.edu/~sokol/tandem TRED]
** [https://web.archive.org/web/20060712070732/http://strand.imb.ac.ru/swan/index.html TandemSWAN] 
** [https://web.archive.org/web/20060709203109/http://www.biophp.org/minitools/microsatellite_repeats_finder/demo.php   Microsatellite repeats finder]
** [https://web.archive.org/web/20060404015058/http://bioinf.dms.med.uniroma1.it/JSTRING/ JSTRING – Java Search for Tandem Repeats in genomes]
** [http://www.rub.de/spezzoo/cm/cm_phobos.htm Phobos – a tandem repeat search tool for perfect and imperfect repeats – the maximum pattern size depends only on computational power]
* {{MeshName|Variable+Number+of+Tandem+Repeats}}


[[Category:Repetitive DNA sequences]]

{{Sourceattribution|Variable number tandem repeat}}