Talk:Single-nucleotide polymorphism

message: I'm new, and before charging into anything, I'd like to understand better what is considered "fair use" in the Wiki world. To me, this article exceeds "fair use" guidelines, as the information is straight offf of this page:
  http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml
The source is not directly credited, with only an oblique attribution. Is this considered legit and consistent with Wiki guidelines?
Regards
--Daffyd 10:55, 27 October 2005 (UTC)
replies: text: "Fair use" usually refers to a specific legal definition within copyright law. The content in question is provided by the US Government and is not copyrighted at all, so legally there's nothing wrong with copying it verbatim. Not that it's polite. --Mike Lin 17:27, 27 October 2005 (UTC)
replies: text:  Thanks for the clarification, makes sense. --Daffyd 17:55, 27 October 2005 (UTC)
replies: text:  It is unethical to use the material without crediting the source.  If I had run across this in a student paper, the student would be charged with plagiarism.  What is even worse is that the definition is wrong and misleading.  The author(s) clearly don't know the meaning of polymorphism, and confuse cause and effect (e.g., "...a SNP might change the nucleotide sequence...." or "SNPs are generally considered to be a form of point mutation....").Ted 01:26, 20 January 2006 (UTC)
replies: text: The only problem there is that the author(s) get(s) SNP confused with what would be true of a UEP. Nagelfar 01:16, 14 March 2007 (UTC)
thread_title: "fair use"

message: Quoting from this article - "For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say that there are two alleles : C and T."
This definition of allele is incorrect.  C and T comprise a nucleotide pair.  DNA molecules are chains of nucleotide pairs.  Many nucleotide pairs are not located within a genetic locus.  Here is the definition of allele from the glossary section of the Human Genome Project Information website <http://public.ornl.gov/hgmis/external/search_term_action.cfm>
Allele: Alternative form of a genetic locus; a single allele for each locus is inherited from each parent (e.g., at a locus for eye color the allele might result in blue or brown eyes).
Lgfree 01:52, 17 June 2006 (UTC)
thread_title: Correction: allele

message: I'm not sure if this statement is correct:
Almost all common SNPs have only two alleles
My understanding is that there are only two possible options (alleles) at a single nucleotide locus. If I'm wrong, would it be useful to have an example of a SNP that has more than two alleles?
Buzwad 11:59, 22 March 2007 (UTC)
replies: text: They're quite difficult to find (mostly because most high-throughput genotyping assays don't work well with non-dimorphic SNPs), but they do exist. Here's a link to one that seems to have a fairly large amount of validation: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=1977161 gringer 01:17, 6 July 2007 (UTC)
replies: text:  Except I've just noticed that the reported frequencies do not include A/T, so it may not be a "real" SNP of this nature. Regardless, it indicates that people are allowing for the possibility of more than two alleles at a single nucleotide locus. gringer 01:23, 6 July 2007 (UTC)
replies: text:  rs332 is a tri allelic small indel, close enough to being a snp for the ncbi (dbsnp rs332). It is also the cause of 50% of Cystic Fibrosis cases . Cariaso 16:48, 19 August 2007 (UTC)

text:  rs3091244 is a legitimate triallelic snp ncbi rs3091244 Cariaso 16:09, 10 October 2007 (UTC)

text: This is contradictory:This is simply the lesser of the two allele frequencies for single-nucleotide polymorphisms.
'Almost all ... have only two' vs. 'the lesser of the two alleles for  single-nucleotide polymorphisms' seems to be contradictory.  —Preceding unsigned comment added by 98.207.80.224 (talk) 17:57, 17 February 2009 (UTC)
thread_title:  Definition query 

message: In most academic publications, abbreviations are acceptable in the text as long as they have been defined previously. Given the short form (SNP, pronounced "snip") is significantly quicker to say than the expanded form (Single nucleotide polymorphism), and the abbreviation has been stated in the first sentence, wouldn't it be reasonable to use SNP for subsequent uses in this article? I notice that there have been two instances in the revision history where there has been a change from the abbreviated form to the expanded form (or vice versa). I'm mostly mentioning this because 65.40.126.255 has changed the text back to the expanded form without noticing the previous history comment by 82.139.86.128 on 17 April. 
gringer 01:56, 12 July 2007 (UTC)
replies: text: I would say it is ok to use "SNP" once the abbreviation has been stated in the first sentence. — fnielsen (talk) 08:24, 4 September 2008 (UTC)
thread_title:  SNP vs Single Nucleotide Polymorphism 

message: I just reverted this because it was an anonymous IP's only, unexplained edit which changed a word to its opposite. Could someone make sure it was vandalism? 128.240.229.65 (talk) 15:50, 10 January 2008 (UTC)
thread_title:  Possible vandalism? 

message: How does this relate to the "missense mutation" article. This layman needs clarification.  —Preceding unsigned comment added by 212.24.80.93 (talk) 12:32, 11 August 2008 (UTC)
replies: text: This concept was not explained and should be: A missense mutation is a nonsynonymous mutation. I have now made a section title "Types of SNPs" and expanded it with a infobox. There is room for improvements. — fnielsen (talk) 08:28, 4 September 2008 (UTC)
thread_title:  Missense mutation 

message: I see that there is nothing said about how many SNPs have currently been mapped in humans. I would like to see a short table of species and how many SNPs are currently known in each... (This would need to be date stamped though.) See: 
dbSNP summary 
--Jahibadkaret (talk) 16:22, 3 September 2008 (UTC)
thread_title:  More Info 

message: This article mentions a SNP called 4Qk10 that should be common in Ashkenazi Jews and rare in Cubans. I can't find any references to back this up - neither dbSNP nor Google can clarify this. Does anyone have a reference for this?
Stinusl (talk) 12:05, 25 November 2008 (UTC)
replies: text: Agreed. That name does not follow common patterns for naming snps. Furthermore while Ashkenazi populations are well researched, this is far less common for Cubans. The statement was added by an IP with no previous history of edits. I encourage the next interested party to remove the text. Cariaso (talk) 07:50, 26 November 2008 (UTC)

text: done. Cariaso (talk) 20:46, 28 November 2008 (UTC)
thread_title:  Reference for 4Qk10 SNP? 

message: I believe in the more traditional way of using hyphens.  They got lax about teaching it so long ago that even most professors no longer use it habitually, but magazines and newspapers do, so everybody still understands it, and that makes it possible to save it, and its worth saving for reasons noted below.
: 
In some cases it disambiguates and adherence to a single style is preferable.  One may, for example, omit a question mark at the end of many questions and still expect the reader to recognize them as questions, but in some cases the question mark conveys substantial information, and adhering to a single style—that of always including it—is therefore better than adhering to a style that always excludes it.
: 
This is about polymorphisms involving a single nucleotide, NOT about "nucleotide polymorphisms" that are single.  In this case, such a disambiguation may be like adding a question mark to a sentence that people would already have recognized as a question, but adhering to the style helps maintain the habit so that it's there for cases where it helps more than that.
: 
See also hyphen for more on this.
: 
That is why I changed the article's title, adding the hyphen. Michael Hardy (talk) 19:38, 28 December 2008 (UTC)
thread_title:  hyphen 

message: grammar is not my forte but I feel this change is not correct. When I read the text out loud I hear "a snip" not "an S-N-P". Cariaso (talk) 15:53, 22 April 2009 (UTC)
thread_title:  a SNP / an SNP 

message: Firstly, the Example section needs work. Secondly, what do we consider a "valid example" of a SNP? Annotated SNPs? Notable SNPs?.. Geno-Supremo (talk) 16:17, 21 May 2009 (UTC)
thread_title:  Example Section 

message: The reference I snarfed from the TASR2R38 article for the PTC tasting and number of SNPs only mentions 3 SNPs, not 6, but it could be that it's only talking about SNPs that affect PTC tasting, not all the SNPs in that gene. (Assuming there's a difference.) Being mostly clueless, I won't touch that bit. The Crab Who Played With The Sea (talk) 03:56, 24 March 2010 (UTC)
thread_title:  Number of SNPs in TAS2R38 (Examples section) 

message: http://en.wikipedia.org/w/index.php?title=Single-nucleotide_polymorphism&diff=prev&oldid=358109401 . This unsourced statement makes the first sentence even harder to read. Proposed for rapid removal. Cariaso (talk) 00:57, 5 May 2010 (UTC)
replies: text: Google suggests the name should be Stephen B. Liggett (we appear to have no article). I agree that it is just noise in the lead, and since the lead is supposed to be a summary of the article (which has no mention of the name), I support removal. An edit summary might be "unsourced, see talk". Johnuniq (talk) 01:58, 5 May 2010 (UTC)
thread_title:  Dr. Steve Ligget 

message: I would consider changing the colours of the picture. I don't like the two strands having tgnbvhjgvbhe same colour as adenine and thymine nucleotides.
212.126.224.100 (talk) 10:24, 27 August 2010 (UTC)
thread_title:  The picture 

message: For someone who is trying to figure out SNP genotyping, the picture caused me a lot of confusion. It shows a C/A polymorphism; however, C/A is rare because the usual pairs are C/T and G/A. The picture also does not match up with the example in the first paragraph (a CT SNP). I think that it would be better to us the picture found on this page:
http://www.isogg.org/wiki/Single-nucleotide_polymorphism
71.93.120.216 (talk) 01:26, 10 April 2015 (UTC)
replies: text: So sorry about that. The article has several issues and needs a rewrite. I'll set aside some time this weekend to sort it. SW3 5DL (talk) 03:34, 8 May 2015 (UTC)

text: I've now updated the image to G/A. gringer (talk) 13:28, 8 May 2021 (UTC)
thread_title:  Picture should be changed 

message: Quite a few papers and books define common SNP to be what this article (and Nature) define as just SNP. So I'm guessing they use a wider definition of SNP. 86.127.104.145 (talk) 05:27, 14 October 2017 (UTC)
thread_title:  Common SNP 

message: The information regarding use of SNPs vs STR fingerprinting for forensic use in identifying criminal suspects and crime victims is significantly out of date; see https://en.wikipedia.org/wiki/Genetic_genealogy#Law_enforcement and https://en.wikipedia.org/wiki/Forensic_genealogy Pseudonymous Cognomen (talk) 04:11, 4 August 2019 (UTC)
thread_title:  Forensics 

message: I think this part of the article should be punctually revised:
 "LD is affected by two parameters: 1) The distance between the SNPs [the larger the distance, the lower the LD]. 2) Recombination rate [the lower the recombination rate, the higher the LD].[7]".
Instead, it should read:
LD is affected by two parameters: the distance between the SNPs (the larger the distance, the lower the LD) and the recombination rate (the lower the recombination rate, the higher the LD).[7]
In addition, I think it's worth noting that even though this statement is accurate to a degree, there are several other factors that also affect linkage disequilibrium that are worth noting. Some of those factors include gene flow, mutations, natural selection, and genetic drift within the population. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124487/>. This source I provided to support my suggested edit is also a more recently written article (2008) versus the 2001 article cited as source [7]. Grahamla44 (talk) 00:52, 7 February 2020 (UTC)
thread_title:  Linkage disequilibrium 

message: — Assignment last updated by JustinxLane (talk) 19:04, 2 June 2023 (UTC)
thread_title: Wiki Education assignment: PHMD 2040 Service - Learning Spring 2023

message: Citation added regarding the redundancy of the genetic code and citation added supporting the difference between types of SNPs mutations. Statistic updated about SNPs within the population accompanied by appropriate reference and citation --Monoclonalantibodies (talk) 03:15, 22 March 2023 (UTC)
thread_title:  Citation Added