Talk:Short tandem repeat

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A redirection should be added from STR to this entry. I'm not sure how to do that. Arnon. 212.235.121.129 21:11, 13 Dec 2004 (UTC)

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[edit] Make a seperate entry for STR analysis?

I felt I could write a lot more about STR analysis, but it seems like that might warrant its own article rather than muddying up this article with tangential information. Is that typically done, or would it just be asking for a merge in the future? Sekiyu 10:31, 5 March 2006 (UTC)

[edit] Difference between Microsatellite and short tandem repeat?

I can't see the difference between "microsatellite" and "short tandem repeat". I would appreciate if anybody wrote it. A good way would include adding "short tandem repeat" somewhere in the neat assortment on Repeated sequence (DNA). Thank you. Mortsggah 16:36, 6 April 2007 (UTC)

[edit] There is no difference

Microsatellite and short tandem repeat describe the same thing similar to simple sequence repeat, they should be merged. sdobrin 21:49, 7 July 2007 (UTC)

[edit] STR and microsatellites are not the same...

I'd like to point out that merging STR and microsatellite entries will cause problems. Microsatellites are defined as 1-4 bp repeats on their wiki page whereas STRs are defined as 1-10 bp repeats. So they overlap but are not the same. I am also concerned that the boundaries are arbitrary. Note that 'minisatellites' are defined as 10-100bp repeats. Note also there is an entry for 'Y-STRs', which are probably actually microsatellites but the Y-STR terminology is widely used and accepted. To my mind, STRs cover both mini- and micro-satellites and the short 'gap' in between the two definitions. I happen to work on repeats that are most commonly between 7 and 12bp in unit length. In part because the definitions of mini/micro- satellites are not clear I have chosen to call them STRs. At the moment I am tussling with a journal referee who wants me to call them all mini/micro- satellites but I feel that STR is more appropriate in this case. I vote for keeping STR as an entry with links to both mini- and micro-satellite entries. Entamoeba 12:26, 24 September 2007 (UTC)

[edit] Literatures on categorizing tandem repeats

  • Minisatellite is initially termed by Jeffreys et al. [1] for repetitive region having 10-15 bp core unit.
  • Microsatellite is coined for 2 bp repeat by Litt & Luty [2].
  • Short tandem repeat seems a rather descriptive phrase; however, to my knowledge, Ali & Wallace [3] are the first authors using it in abbreviated form (STR), and they recognized Jeffreys' minisatellites as examples of STR.
  • Some authors (for example, Li [4]) recognize microsatellite of 1-2 bp unit, STR of 3-5 bp, minisatellite of 9 bp or longer; however, microsatellite and STR are often synonymized (with 1-5 bp in each unit) while minisatellite is discriminated (with 9-100 bp units). Tautz [5] discussed on this nomenclature, but it is unfortunately unavailable for me.
  • In human genomics, tandem repeats with a unit size of 6 bp or longer are usually recognized as minisatellites (Näslund et al. [6], for example). I guess the reason is that people recognize telomere-associated minisatellites and human telomere has 6 bp unit length.
  1. ^ Jeffreys AJ, Wilson V, Thein SL (1985). "Hypervariable 'minisatellite' regions in human DNA.". Nature 314 (6006): 67-73. PMID 3856104. 
  2. ^ Litt M, Luty JA (1989). "A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene.". Am J Hum Genet 44 (3): 397-401. PMID 2563634. 
  3. ^ Ali S, Wallace RB (1988). "Intrinsic polymorphism of variable number tandem repeat loci in the human genome.". Nucleic Acids Res 16 (17): 8487-8496. PMID 2901724. 
  4. ^ Li W (1997). Molecular Evolution. Sunderland, MA: Sinauer. ISBN 0878934634. 
  5. ^ Tautz D (1993). "Notes on the definition and nomenclature of tandemly repetitive DNA sequences", in Pena SDJ, Chakraborty R, Epplen JT, Jeffreys AJ (eds.): DNA fingerprinting: state of science.. Basel: Birkhäuser Verlag, pp. 21-28. ISBN 3764329068. 
  6. ^ Näslund K, Saetre P, von Salomé J, Bergström TF, Jareborg N, Jazin E (2005). "Genome-wide prediction of human VNTRs". Genomics 85 (1): 24-35. doi:10.1016/j.ygeno.2004.10.009. 

My opinion is that Microsatellite, Short tandem repeat, and Simple sequence repeat should be merged, because they are generally regarded as synonyms regardless of size definition. Just FYI, NLM defines a MeSH term "Microsatellite Repeats" including STRs.--Mzaki 14:20, 11 October 2007 (UTC)

[edit] Merge but as what?

Mzaki illustrates one of my points very well - there is clearly no universally accepted definition for these three terms. I have no objection to the entries being merged, but under what name? Short Tandem Repeat may be 'rather descriptive' but to me that's a good thing! Entamoeba 22:20, 11 October 2007 (UTC)

[edit] Microsatellite/STR differentiation issues

(NOTE: This is my first post to a talk page, so forgive me if the rules aren't followed. I skimmed them first, and I'll try my best...) While the two terms are utilized in all genetic sciences and may be used interchangably by some individuals, I can speak from a Forensic Science standpoint (I'm a FS Masters student). I still have to look into it and I can add more later under this post, but as far as I know, terms like "minisatellite" and "microsatellite" are considered generic and encompassing of several different types of tandem repeats (VNTRs, AmpFLPs, etc.). An "STR", however, is a specific term for just one variant and has its own internal categories (YSTRs, miniSTRs, autosomal STRs, mtDNA STRs). I'd vote to keep the STR page separate from "microsatellite", but not create a new page for the specifc STR variants until they are relevant enough in their own right. Autosomal STRs (and that is the term forensic scientists/criminalists use) have been used for several years now in allele typing for criminals (especially the 13 loci used for the CODIS database), and their specific relevance to the scientific community gives them the importance to have their own page apart from "microsatellite". YSTRs and miniSTRs are just now coming into vogue, and I'd say they are still in developmental stages, so I'd add them to this page for the time being, and then break them out if they ever become significant in their own right. PatrickTaormina (talk) 15:40, 11 March 2008 (UTC)

I agree, microatellite & STR pages should remain separate. Nagelfar (talk) 10:28, 10 May 2008 (UTC)