mathematics

Variable number tandem repeat

Variable number tandem repeat is a mathematics topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Variable number tandem repeat rather than just read about it. In short: 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.

Key takeaways

Variable number tandem repeat belongs to mathematics; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Variable number tandem repeat to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Variable number tandem repeat from memory before moving on to harder problems.

Reference excerpt

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.

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 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.

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 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

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.

See also AFLP MLVA Short tandem repeat Tandem repeat BioNumerics

References

External links Examples : VNTRs Archived 2020-11-09 at the Wayback Machine – info and animated example Databases : The Microorganisms Tandem Repeats Database Archived 2019-01-04 at the Wayback Machine The MLVAbank Archived 2007-11-28 at the Wayback Machine Short Tandem Repeats Database Tandem Repeats Database (TRDB) Search tools : TAPO: A combined method for the identification of tandem repeats in protein structures Tandem Repeats Finder Mreps Archived 2011-09-29 at the Wayback Machine STAR TRED TandemSWAN Microsatellite repeats finder JSTRING – Java Search for Tandem Repeats in genomes Phobos – a tandem repeat search tool for perfect and imperfect repeats – the maximum pattern size depends only on computational power Variable+Number+of+Tandem+Repeats at the U.S. National Library of Medicine Medical Subject Headings (MeSH)

Illustrations

Variable number tandem repeat: Variations of VNTR (D1S80) allele lengths in six individuals. — Variations of VNTR (D1S80) allele lengths in six individuals.

Variable number tandem repeat: Chromosomal locations of the 13 VNTR loci in the CODIS panel. — Chromosomal locations of the 13 VNTR loci in the CODIS panel.

Worked examples

Example 1 — a first encounter with Variable number tandem repeat

Start with the simplest possible case. Write down what Variable number tandem repeat claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In mathematics, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Variable number tandem repeat before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Variable number tandem repeat ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Variable number tandem repeat

In research: Variable number tandem repeat appears in mathematics research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Variable number tandem repeat in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Variable number tandem repeat is common in secondary-school and first-year university syllabi. It links to neighbouring topics Repetitive DNA sequences, so understanding it makes those chapters shorter.
In everyday life: Look for Variable number tandem repeat outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

Ask Teacher Smith questions about this articleOpens your AI tutor with a question about “Variable number tandem repeat” →

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study Variable number tandem repeat in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Variable number tandem repeat means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Variable number tandem repeat out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Variable number tandem repeat in simple terms?

Why does Variable number tandem repeat matter?

Because it connects several mathematics ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Variable number tandem repeat?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Variable number tandem repeat.