Sequence-tagged site

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Simple sequence length polymorphism

A sequence-tagged site (or STS) is a short (200 to 500 base pair) DNA sequence that has a single occurrence in the genome and whose location and base sequence are known.

STSs can be easily detected by the polymerase chain reaction (PCR) using specific primers. For this reason they are useful for constructing genetic and physical maps from sequence data reported from many different laboratories. They serve as landmarks on the developing physical map of a genome.

When STS loci contain genetic polymorphisms (e.g. simple sequence length polymorphisms, SSLPs, single nucleotide polymorphisms), they become valuable genetic markers, i.e. loci which can be used to distinguish individuals.

They are used in shotgun sequencing, specifically to aid sequence assembly.

STSs are very helpful for detecting microdeletions in some genes. For example, some STSs can be used in screening by PCR to detect microdeletions in Azoospermia (AZF) genes in infertile men.

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The Sequence-Tagged Site (STS) is a relatively short, easily PCR-amplified sequence (200 to 500 bp) which can be specifically amplified by PCR and detected in the presence of all other genomic sequences and whose location in the genome is mapped.

The STS concept was introduced by Olson et al. (1989). In assessing the likely impact of the Polymerase Chain Reaction (PCR) on human genome research, they recognized that single-copy DNA sequences of known map location could serve as markers for genetic and physical mapping of genes along the chromosome. The advantage of STSs over other mapping landmarks is that the means of testing for the presence of a particular STS can be completely described as information in a database: anyone who wishes to make copies of the marker would simply look up the STS in the database, synthesize the specified primers, and run the PCR under specified conditions to amplify the STS from genomic DNA.

STS-based PCR produces a simple and reproducible pattern on agarose or polyacrylamide gel. In most cases STS markers are co-dominant, i. e., allow hetorozygotes to be distinguished from the two homozygotes.

The DNA sequence of an STS may contain repetitive elements, sequences that appear elsewhere in the genome, but as long as the sequences at both ends of the site are unique and conserved, researches can uniquely identify this portion of genome using tools usually present in any laboratory.

Thus, in broad sense STS include such markers as microsatellites (SSRs, STMS or SSRPs), SCARs, CAPs, and ISSRs.