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GAP6

Sequence Tagged Sites (STS) mapping is a powerful technique for generating detailed physical maps of large genomes using short DNA sequences that are unique to specific locations. The mapping process involves collecting overlapping DNA fragments and determining which contain the STSs, typically using PCR for efficiency. STS mapping has applications in criminal identification, paternity testing, and disease diagnosis.

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11 views10 pages

GAP6

Sequence Tagged Sites (STS) mapping is a powerful technique for generating detailed physical maps of large genomes using short DNA sequences that are unique to specific locations. The mapping process involves collecting overlapping DNA fragments and determining which contain the STSs, typically using PCR for efficiency. STS mapping has applications in criminal identification, paternity testing, and disease diagnosis.

Uploaded by

azhagar_ss
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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STS Mapping

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Sequence tagged sites (STS)
• To generate a detailed physical map of a large genome we need, ideally, a
high-resolution mapping procedure.

• This should be rapid and not technically demanding.

• Restriction mapping is rapid, easy, and provides detailed information, but


it cannot be applied to large genomes.

• FISH can be applied to large genomes, and modified versions such as


fiber-FISH can give high-resolution data, but FISH is difficult to carry out and
data accumulation is slow.

• Map positions for no more than three or four markers being obtained in a
single experiment.

• For detailed physical maps we need a more powerful technique.

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STS Mapping
• One of the most powerful physical mapping techniques.

Responsible for generation of the most detailed maps of large genomes.

A sequence tagged site or STS is simply a short DNA sequence.

It is generally between 100 and 500bp in length.

It is easily recognizable and occurs only once in the chromosome or genome


that is being studied.

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How does one map STS?
• To map a set of STSs, a collection of overlapping DNA fragments from a
single chromosome or from the entire genome is needed.

• Each point along the chromosome represented on average five times in the
collection.

• The data from which the map will be derived are obtained by determining
which fragments contain which STSs.

• This can be done by hybridization analysis but PCR is generally used.

• It is quicker and has proven to be more amenable to automation.

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Fragments used for STS Mapping
• The fragments span the entire length of a chromosome, with each point on the
chromosome present in an average of five fragments. The two blue markers are close
together on the chromosome map and there is a high probability that they will be found
on the same fragment. The two green markers are more distant from one another and so
are less likely to be found on the same fragment.
•

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• The chances of two STSs being present on the same fragment will, depend on
how close together they are in the genome.

• If they are very close then there is a good chance that they will always be on
the same fragment.

• If they are further apart then sometimes they will be on the same fragment and
sometimes they will not.

• The data can therefore be used to calculate the distance between two markers,
in a manner analogous to the way in which map distances are determined by
linkage analysis.

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• In linkage analysis a map, distance is calculated from the frequency at which
crossovers occur between two markers.

• STS mapping is essentially the same, except that each map distance is based
on the frequency at which it breaks.

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How would a sequence qualify as an STS?
• To qualify as an STS, a DNA sequence must satisfy two criteria.

• 1) Its sequence must be known, so that a PCR assay can be set up to test for
the presence or absence of the STS on different DNA fragments.

• 2) The second requirement is that the STS must have a unique location in the
chromosome being studied, or in the genome as a whole if the DNA fragment
set covers the entire genome.

• If the STS sequence occurs at more than one position then the mapping data
will be ambiguous.

• Care must therefore be taken to ensure that STSs do not include sequences
found in repetitive DNA

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DNA Fingerprinting
• An individual's unique sequence of DNA base pairs.

• This is determined by exposing a sample of the person's DNA to molecular


probes.

• DNA fingerprints are often used as evidence in criminal law cases. Also called
genetic fingerprint.

• Different methods used in fingerprinting:


• 1) Restriction fragment length polymorphism
• 2) PCR
• 3) Amp FLP: Amplified fragment length polymorphism
• 4) Short tandem repeats (STR)

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Applications
• Identification of criminal suspects.

• Paternity issues

• Identification of the diseased.

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