Variable number tandem repeat

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Schematic of a Variable Number of Tandem Repeats in 4 alleles. VNTRDemo.gif
Schematic of a Variable Number of Tandem Repeats in 4 alleles.

A variable number tandem repeat (or VNTR) 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 (number of repeats) among individuals. Each variant acts as an inherited allele, allowing them to be used for personal or parental identification. Their analysis is useful in genetics and biology research, forensics, and DNA fingerprinting.

Contents

Structure and allelic variation

Variations of VNTR (D1S80) allele lengths in 6 individuals. D1S80Demo.png
Variations of VNTR (D1S80) allele lengths in 6 individuals.

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 recombination or replication errors, leading to alleles with different numbers of repeats. Flanking regions are segments of repetitive sequence (shown here as thin lines), allowing the VNTR blocks to be extracted with restriction enzymes and analyzed by RFLP, or amplified by the polymerase chain reaction (PCR) technique and their size determined by gel electrophoresis.

Use in genetic analysis

VNTRs were an important source of RFLP genetic markers used in linkage analysis (mapping) of diploid genomes. Now that many genomes have been sequenced, VNTRs have become essential to forensic crime investigations, via DNA fingerprinting and the CODIS database. When removed from surrounding DNA by the PCR or RFLP methods, and their size determined by gel electrophoresis or Southern blotting, 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' having the same allelic pattern is extremely low. VNTR analysis is also being used to study genetic diversity and breeding patterns in 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.

Chromosomal locations of the 13 VNTR loci in the CODIS panel. Codis profile.jpg
Chromosomal locations of the 13 VNTR loci in the CODIS panel.

Inheritance

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

Relationship to other types of repetitive 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 Satellite DNA, which does not reveal how they are organized. The use of restriction enzymes showed that some repeat blocks were interspersed throughout the genome. DNA sequencing later showed that other repeats are clustered at specific locations, with tandem repeats being more common than inverted repeats (which may interfere with DNA replication). VNTRs are the class of clustered tandem repeats that exhibit allelic variation in their lengths.

Classes

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. VNTRexample.png
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 minisatellite in which the size of the repeat sequence is generally ten to one hundred base pairs. Minisatellites are a type of DNA 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 microsatellites, 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. [1] [2]

See also

Related Research Articles

In molecular biology, restriction fragment length polymorphism (RFLP) is a technique that exploits variations in homologous DNA sequences, known as polymorphisms, populations, or species or to pinpoint the locations of genes within a sequence. The term may refer to a polymorphism itself, as detected through the differing locations of restriction enzyme sites, or to a related laboratory technique by which such differences can be illustrated. In RFLP analysis, a DNA sample is digested into fragments by one or more restriction enzymes, and the resulting restriction fragments are then separated by gel electrophoresis according to their size.

A microsatellite is a tract of repetitive DNA in which certain DNA motifs are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. They have a higher mutation rate than other areas of DNA leading to high genetic diversity. Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as simple sequence repeats (SSRs) by plant geneticists.

<span class="mw-page-title-main">DNA profiling</span> Technique used to identify individuals via DNA characteristics

DNA profiling is the process of determining an individual's deoxyribonucleic acid (DNA) characteristics. DNA analysis intended to identify a species, rather than an individual, is called DNA barcoding.

In genetics, tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other, e.g. ATTCG ATTCG ATTCG, in which the sequence ATTCG is repeated three times.

In genetics, a minisatellite is a tract of repetitive DNA in which certain DNA motifs are typically repeated two to several hundred times. Minisatellites occur at more than 1,000 locations in the human genome and they are notable for their high mutation rate and high diversity in the population. Minisatellites are prominent in the centromeres and telomeres of chromosomes, the latter protecting the chromosomes from damage. The name "satellite" refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA. Minisatellites are small sequences of DNA that do not encode proteins but appear throughout the genome hundreds of times, with many repeated copies lying next to each other.

Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA. Satellite DNA is the main component of functional centromeres, and form the main structural constituent of heterochromatin.

<span class="mw-page-title-main">Haplotype</span> Group of genes from one parent

A haplotype is a group of alleles in an organism that are inherited together from a single parent.

Variable number of tandem repeat locus is any DNA sequence that exist in multiple copies strung together in a variety of tandem lengths. The number of repeat copies present at a locus can be visualized by means of a Multi-locus or Multiple Loci VNTR Analysis (MLVA). In short, oligonucleotide primers are developed for each specific tandem repeat locus, followed by PCR and agarose gel electrophoresis. When the length of the repeat and the size of the flanking regions is known, the number of repeats can be calculated. Analysis of multiple loci will result in a genotype.

A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change, or a long one, like minisatellites.

<span class="mw-page-title-main">Random amplification of polymorphic DNA</span>

Random amplified polymorphic DNA (RAPD), pronounced "rapid", is a type of polymerase chain reaction (PCR), but the segments of DNA that are amplified are random. The scientist performing RAPD creates several arbitrary, short primers, then proceeds with the PCR using a large template of genomic DNA, hoping that fragments will amplify. By resolving the resulting patterns, a semi-unique profile can be gleaned from an RAPD reaction.

A Y-STR is a short tandem repeat (STR) on the Y-chromosome. Y-STRs are often used in forensics, paternity, and genealogical DNA testing. Y-STRs are taken specifically from the male Y chromosome. These Y-STRs provide a weaker analysis than autosomal STRs because the Y chromosome is only found in males, which are only passed down by the father, making the Y chromosome in any paternal line practically identical. This causes a significantly smaller amount of distinction between Y-STR samples. Autosomal STRs provide a much stronger analytical power because of the random matching that occurs between pairs of chromosomes during the zygote-making process.

<span class="mw-page-title-main">STR analysis</span> Biological DNA analysis for allele repeats

Shorttandemrepeat (STR) analysis is a common molecular biology method used to compare allele repeats at specific loci in DNA between two or more samples. A short tandem repeat is a microsatellite with repeat units that are 2 to 7 base pairs in length, with the number of repeats varying among individuals, making STRs effective for human identification purposes. This method differs from restriction fragment length polymorphism analysis (RFLP) since STR analysis does not cut the DNA with restriction enzymes. Instead, polymerase chain reaction (PCR) is employed to discover the lengths of the short tandem repeats based on the length of the PCR product.

<span class="mw-page-title-main">Molecular-weight size marker</span> Set of standards

A molecular-weight size marker, also referred to as a protein ladder, DNA ladder, or RNA ladder, is a set of standards that are used to identify the approximate size of a molecule run on a gel during electrophoresis, using the principle that molecular weight is inversely proportional to migration rate through a gel matrix. Therefore, when used in gel electrophoresis, markers effectively provide a logarithmic scale by which to estimate the size of the other fragments.

SNP genotyping is the measurement of genetic variations of single nucleotide polymorphisms (SNPs) between members of a species. It is a form of genotyping, which is the measurement of more general genetic variation. SNPs are one of the most common types of genetic variation. An SNP is a single base pair mutation at a specific locus, usually consisting of two alleles. SNPs are found to be involved in the etiology of many human diseases and are becoming of particular interest in pharmacogenetics. Because SNPs are conserved during evolution, they have been proposed as markers for use in quantitative trait loci (QTL) analysis and in association studies in place of microsatellites. The use of SNPs is being extended in the HapMap project, which aims to provide the minimal set of SNPs needed to genotype the human genome. SNPs can also provide a genetic fingerprint for use in identity testing. The increase of interest in SNPs has been reflected by the furious development of a diverse range of SNP genotyping methods.

<span class="mw-page-title-main">DNAPrint Genomics</span>

DNAPrint Genomics was a genetics company with a wide range of products related to genetic profiling. They were the first company to introduce forensic and consumer genomics products, which were developed immediately upon the publication of the first complete draft of the human genome in the early 2000s. They researched, developed, and marketed the first ever consumer genomics product, based on "Ancestry Informative Markers" which they used to correctly identify the BioGeographical Ancestry (BGA) of a human based on a sample of their DNA. They also researched, developed and marketed the first ever forensic genomics product - DNAWITNESS - which was used to create a physical profile of donors of crime scene DNA. The company reached a peak of roughly $3M/year revenues but ceased operations in February 2009.

The cleaved amplified polymorphic sequence (CAPS) method is a technique in molecular biology for the analysis of genetic markers. It is an extension to the restriction fragment length polymorphism (RFLP) method, using polymerase chain reaction (PCR) to more quickly analyse the results.

<span class="mw-page-title-main">Gene polymorphism</span> Occurrence in an interbreeding population of two or more discontinuous genotypes

A gene is said to be polymorphic if more than one allele occupies that gene's locus within a population. In addition to having more than one allele at a specific locus, each allele must also occur in the population at a rate of at least 1% to generally be considered polymorphic.

<span class="mw-page-title-main">Multiple loci VNTR analysis</span>

Multiple loci VNTR analysis (MLVA) is a method employed for the genetic analysis of particular microorganisms, such as pathogenic bacteria, that takes advantage of the polymorphism of tandemly repeated DNA sequences. A "VNTR" is a "variable-number tandem repeat". This method is well known in forensic science since it is the basis of DNA fingerprinting in humans. When applied to bacteria, it contributes to forensic microbiology through which the source of a particular strain might eventually be traced back, making it a useful technique for outbreak surveillance.

Multiple Annealing and Looping Based Amplification Cycles (MALBAC) is a quasilinear whole genome amplification method. Unlike conventional DNA amplification methods that are non-linear or exponential, MALBAC utilizes special primers that allow amplicons to have complementary ends and therefore to loop, preventing DNA from being copied exponentially. This results in amplification of only the original genomic DNA and therefore reduces amplification bias. MALBAC is “used to create overlapped shotgun amplicons covering most of the genome”. For next generation sequencing, MALBAC is followed by regular PCR which is used to further amplify amplicons.

<span class="mw-page-title-main">Forensic DNA analysis</span> Genetic analyses in crime analysis

DNA profiling is the determination of a DNA profile for legal and investigative purposes. DNA analysis methods have changed countless times over the years as technology changes and allows for more information to be determined with less starting material. Modern DNA analysis is based on the statistical calculation of the rarity of the produced profile within a population.

References

  1. "VNTR" (PDF). Archived (PDF) from the original on 2017-05-01. Retrieved 2024-01-13.
  2. Dubrova, Yuri E. "Minisatellites and microsatellites – similar names but different biology" (PDF). Archived from the original (PDF) on 2017-12-15.