SNPedia:FAQ

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[edit] General

[edit] How many SNPs are in SNPedia?

There are 12914 snps in SNPedia.


  • 4989 are tested by 23andMe and deCODEme
  • 1977 are tested by 23andMe and Navigenics
  • 1957 are tested by deCODEme and Navigenics
  • 1576 are on all 3 platforms above
  • 1343 are tested by 23andMe and FamilyTreeDNA


There are also

[edit] How can I get tested to determine which SNPs I carry?

See the testing page.


[edit] Can you refer me to a physician or genetic counselor to discuss my SNP testing results or Promethease report?

Not yet. If you are a qualified physician or genetic counselor interested in helping individuals interpret their genomic test results, please email us at info@snpedia.com.


[edit] What are the basics of using or editing SNPedia?

See our Wiki Basics page.


[edit] Legal / Licensing

The content in SNPedia is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License. The Terms of Use of SNPedia and related software such as Promethease are also posted.

[edit] What is SNPedia?

See the articles at About SNPedia


[edit] Do you have a logo available?

http://www.snpedia.com/skins/common/images/SNPedia_logo_155x46_transColor.png

[edit] Which SNPs are selected to go into the Wiki? And where are they selected from?

Anything for which we can find something worthy of recording. Recent candidates can be found here. The definition of 'worthy' is very subjective, but the gold standard is a link to published, peer-reviewed paper showing some sort of significance. SNPs mentioned in OMIM have been added in the past, and recently 40 more were added simply on the basis of being very close to known microRNAs.

It would be possible to load all ~10M SNPs from dbSNP, but then the only thing we could say about 99.99% of them would be 'this is a SNP' and perhaps which microarrays it occurs on. Few people would care.

If you know of a SNP you think should be added, and you're willing to put it in (citing a published reference for your information), it probably qualifies, so please do enter it. If you're not familiar with entering information in a Wiki, pretty much everything that applies to Wikipedia applies to SNPedia, so you can go to the How To Edit page at Wikipedia for plenty of information. If you're confused or lazy you can send an email info@snpedia.com telling us about the SNPs you'd like to see added.

[edit] SNPs only? what about CNVs, indels, inversions, epigenetics ... ?

dbSNP already assigns rs#s to small indels. A notable example is rs332. This is not a true single nucleotide polymorphism. Instead it is a deletion of three nucleotides with 2 different insertion texts. dbSNP handles it fine, and so does SNPedia. We also handle

As naming standards emerge for other types of variations SNPedia will be able to handle them too.

[edit] Bulk Info

http://kokki.uku.fi/bioinformatics/varietas/ provides a web interface which includes SNPedia content

[edit] Where can I get a list of all the snps in SNPedia?

The file at http://www.snpedia.com/files/gbrowse/snpedia is updated semi-regularly and can be parsed to provide a reasonable list. You can also consider using MediaWiki-Bot or pywikipedia to get current information on demand with a script such as 

use MediaWiki::Bot;
my $bot = MediaWiki::Bot->new();
$bot->set_wiki('www.snpedia.com','/');
my @rsnums = $bot->get_pages_in_category('Category:Is_a_snp');
print "@rsnums";


[edit] How can I grab the text from pages?

#!/usr/bin/env perl
use MediaWiki::Bot;
my $bot = MediaWiki::Bot->new();
$bot->set_wiki('www.snpedia.com','/');

foreach my $rs ('rs1815739',
                'rs4420638',
                'rs6152') {
   my $text = $bot->get_text($rs);
   print '=' x 20,"$rs\n";
   print $text;
}


I need genotypes and their magnitude 

#!/usr/bin/env perl;
use strict;
use warnings;
use MediaWiki::Bot;

my $bot = MediaWiki::Bot->new();
$bot->set_wiki('www.snpedia.com','/');
my $text = $bot->get_text('rs1234');
print '=' x 20,"$text\n";
print "\n\nThe above text should prove that we can read from SNPedia\n";
print "Getting some more info from SNPedia\n";

my @genotype = $bot->get_pages_in_category('Category:Is a genotype') ;

foreach my $geno (@genotype) {
   my $genotext       = $bot->get_text($geno);
   my ($magnitude)    = $genotext =~ m/magnitude\s*=\s*([+-\.\d]+)/;
   my ($beginingtext) = $genotext =~ m/\}\}(.{3,30})/s;
   $beginingtext = $genotext unless $beginingtext;
   $beginingtext =~ tr/\n/ /;
   $magnitude = '' unless defined $magnitude;
   print "Magnitude\t${magnitude}\tfor\t${geno}\t${beginingtext}\n";
}

[edit] Cite

[edit] Can it be used for peer reviewed publications?

These researchers at the CDC seem to think so. If you choose to do so, you may wish to link to versioned 'Permanent link' found in the lower right corner of every SNPedia wiki page. This wikipedia article should further inform your consideration.

[edit] How do I cite SNPedia and/or Promethease?

Cariaso, Michael and Lennon, Greg. SNPedia. Available at: http://www.SNPedia.com/. Accessed [date of access].

Cariaso, Michael and Lennon, Greg. Promethease. Available at: http://www.promethease.com/. Accessed [date of access].

[edit] SNPedia Citings

  1. The need for genetic variant naming standards in published abstracts of human genetic association studies Wei Yu,corresponding author1 Renée Ned, Anja Wulf, Tiebin Liu, Muin J Khoury, and Marta Gwinn1
  2. Tests for candidate-gene interaction for longitudinal quantitative traits measured in a large cohort Dörthe Malzahn, Yesilda Balavarca, Jingky P Lozano and Heike Bickeböller

[edit] Nomenclature

Many additional terms are defined on the Glossary page.

The various non-standardized snp names can be translated with the Variant Name Mapper.

[edit] Why do I sometimes see lowercase rs1234 and other times Rs1234

Mediawiki (the software which runs this website) prefers all wiki pages to begin with a uppercase letter, but the NCBI prefers to use the lowercase when referring to a snp. SNPedia prefers the lowercase, but sometimes the uppercase is visible. There is the ability to allow lowercase but so far SNPedia has not adopted this.

[edit] Why does dbSNP list rs737865 as a C/T variant whereas other sources list it as an A/G variant?

A C/T variant on one strand of the DNA, is equivalent to an A/G on the opposite strand. This same sort of logic usually works, except in cases we call ambiguous flips.

In this particular case, the switch first becomes visble at the dbSNP submission section. Here you will see that 4 different groups (CSHL, EGP_SNPS, ABI, and Illumina) have all submitted this snp. CSHL and Illumina both submitted a fwd/B (forward bottom strand) oriented read, while the other two submitted a rev/T (reverse top strand) read.


[edit] What do all of these names mean?

I tested my FGS with familytreeDNA. I had heard that the results contain health related information,
and curious, I came to SNPedia to try and see what info I could learn about my FGS mutations. 
Unfortunately I cannot make heads or tails of what my search yielded. For example, one of my 
mutations is 1438G, so I searched that got rs6311. This is where I begin feel like I am trying to 
read Klingon... " rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A)". To me, that says rs6311 
times (negative1438A is greater than A minus 1438G OR negative 1438G is greater than A divided by G
minus 1438A). I know that cannot be right. I get further confused the more I read. I just wanted to
know what 1438G meant health-wise, as well as my other mutations.

SNPedia didn't make up all of these names and we frequently experience the same pain. In fact, this is the specific reason why we prefer rs#s. rs# names are meaningful names across the entire genome. Names such as the ones above are ambiguous unless there is other information such a gene or chromosome name is involved. For your specific cases, the gene of interest is HTR2A. The 1438 indicates that the SNP is 1438 bases/nucleotides/letters away from the start of that gene. The minus sign indicates that the SNP is upstream of the start site. A>G means that the reference genome has a A, but that a G was instead observed.

It gets worse. DNA is made of 2 complementary strands, SNPedia uses the same strand as dbSNP, but many sources, including 23andMe, will sometimes use the other strand. When this happens all nucleotides need to be switched to the form which is found on the other strand. So an A becomes a T, and a T becomes an A. C becomes a G, and G becomes a C. For reasons I can't explain the source you've chosen is referring to As and Gs, which is the opposite strand from dbSNP. In this case its unambiguous, but there are some nastier cases called ambiguous flips.

As a specific answer to your questions. You have a G at rs6311. Its not clear from your wording, if you have one or two copies of the SNP, so you are either rs6311(C;C) or rs6311(C;T). At present the SNPedia page shows several papers about this snp, but a clear consensus on the consequences is not yet known. It seems as though you should expect a lower risk of anorexia, bulimia, and tardive dyskinesia but may experience more anger- and aggression-related behavior.


[edit] Why don't some genotype names match between SNPedia and 23andMe

There appear to be discrepancies between my 23andme data and my Promethease report. For example rs1051730

  • My genotype according to 23andme is AA.
  • Yet the SNPedia literature says that the genotypes are (C;C), (C;T), and (T;T).

Both 23andMe and SNPedia are using RS#s so they should be the same SNP?!


your rs1051730(A;A) is also known as rs1051730(T;T). These are two different, but equally valid names for exactly the same thing.

SNPedia has chosen to call it (T;T) because this is consistent with what we consider to be the highest authority -- a database called dbSNP run by NIH.gov . You can see a specific example of that here

23andMe has in this case chosen to instead call it (A;A) for an entirely reasonable reason (this snp is on the minus strand). It doesn't matter, it is still the same thing. And you're seeing it in you report because Promethease was able to handle this.


If you have a general question not answered by this FAQ, add the question to this page, or email info@snpedia.com.

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