Have questions? Visit https://www.reddit.com/r/SNPedia

SNPedia:FAQ

From SNPedia

General[edit]

How many SNPs are in SNPedia?[edit]

There are currently 111702 SNPs in SNPedia.


There are also

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

See the testing page.

How can I improve SNPedia?[edit]

See the new editors or the wiki Basics pages.

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

We can refer you to a genetic counselor; see our Find a genetic counselor page for more information.

Legal / Licensing[edit]

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.

What is SNPedia?[edit]

See the articles at About SNPedia or the wikipedia article

Do you have a logo available?[edit]

https://files.snpedia.com/data/SNPedia_logo_155x46_transColor.png in SVG or on a messenger bag

Bulk Info[edit]

If you need a lot of SNPedia at one time, see Bulk


Science[edit]

What are some good sources for learning the basics about DNA and genetics?[edit]

We recommend these sites:

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

Anything for which we can find something worthy of recording. Our emphasis is on SNPs and mutations that have significant medical or genealogical consequences and are reproducible (for example, the reported consequence has been independently replicated by at least one group besides the first group reporting the finding). These are typically found in meta-analyses, studies of at least 500 patients, replication studies including those looking at other populations, genome-wide significance thresholds of under 5 x 10e-8 [PMID 25666886] for GWAS findings, and/or mutations with historic or proven medical significance. GWAS findings with odds ratios anywhere near 1.0 are in general not particularly interesting. The definition of 'worthy' is very subjective, but the gold standard is a link to published, peer-reviewed paper with credible statistics. And if they are not already in SNPedia, SNPs cited as significant in other credible sources such as OMIM, ClinVar, Coriell, or by the ACMG are certainly worthy of consideration.

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. Some information for newbies is here. 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 unsure or confused by any of this, you can send an email info@snpedia.com telling us about the SNPs you'd like to recommend be added.

Whether captured as genosets or in some other form, polygenic risk scores (PRS) are likely to be added to SNPedia in the future. The criteria for deciding which genetic risk scores is evolving, but for the moment, important ones are (1) AUC >0.75, and preferably >0.85, (2) at least two independent concordant GRS scores per condition, (3) internal and external validation, (4) clear statements as to the ethnicities studied, (5) at least 20 patients cases per parameter in study to reduce chances of overfitting, (6) preferably, the inclusion of high penetrance mutations in addition to lower penetrance risk factors, and (7) clinical applicability on the personal rather than population level. If you have feedback about these criteria, we encourage you to contact us. A straightforward discussion about current PRSs and their questionable clinical utility is available here.

For every complex problem, there is an answer that is clear, simple, and wrong. - H.L. Mencken

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

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

dbVar now assigns names to CNVs, however we've not yet found any notable literature which uses these identifiers. As naming standards emerge for other types of variations SNPedia expects be able to handle them too

Cite[edit]

How do I cite SNPedia?[edit]

SNPedia: a wiki supporting personal genome annotation, interpretation and analysis 
Michael Cariaso; Greg Lennon
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr798

[PMID 22140107] Read the Abstract or Full Text

The paper above should be cited when discussing SNPedia generally. To cite specific content in SNPedia you may wish to link to versioned 'Permanent link' found in the lower left corner of every SNPedia wiki page. This wikipedia article should further inform your consideration.

SNPedia Citings[edit]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245045/citedby/ shows the citations of the SNPedia paper.

Here are some publications which cited SNPedia before the paper was published:

  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
  3. [PMID 20164091] Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.
  4. PMC2847765 Genetic Risk for Recurrent Urinary Tract Infections in Humans: A Systematic Review
  5. PMC2997604 Varietas: a functional variation database portal
  6. PMC2901858 Personal Genomics and the Future of American Medicine
  7. PMC3013672 Ensembl 2011
  8. ERIC TOPOL, M.D. comments
  9. cdc workshop
  10. fda workshop 2009
  11. A highly annotated whole-genome sequence of a Korean individual Nature 460, 1011-1015 20 (August 2009) 10.1038/nature08211
  12. Linking genes to diseases with a SNPedia-Gene Wiki mashup The Journal of Biomedical Semantics (April 2012) news August 05, 2011 By Uduak Grace Thomas genomeweb Aug 2011. accessible cache
  13. Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries
  14. ENSEMBL 2011

Newer

  1. [PMID 24136352] CAN I ACCESS MY PERSONAL GENOME? THE CURRENT LEGAL POSITION IN THE UK.

Nomenclature[edit]

Many additional terms are defined on the Glossary page.

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

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

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. This is because SNPedia wants to maintain backwards compatibility with its earliest versions which required uppercasing the first letter. Now existing software expects the capital letter. Enabling this feature would cause Rs1234 and rs1234 to be 2 different pages, causing information about a given snp to be scattered in 2 locations. In time I hope to have SNPedia supporting both styles smoothly.

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

The explanation from 23andMe is a good resource.

Most snps in SNPedia have their Orientation set to either plus or minus. If it says minus you will sometimes find other sources (such as 23andMe) have the flipped form 

A -> T
T -> A
C -> G
G -> C

If the snp is A/T or C/G, we call the homozygous genotypes ambiguous flips because interpreting the literature is prone to confusion.

What do all of these names mean?[edit]

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.

Addendum from Ann Turner: the question came from someone who has 1438G in his complete mitochondrial DNA sequence (called FGS by FTDNA). It is practically universal, since the Cambridge Reference Sequence has the rare allele there. The number 1438 in the mtDNA molecule is unrelated to the site of the mutation in HTR2A.

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

There appear to be discrepancies between my 23andme data and my Promethease report. For example, for 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 numbers, 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 your report because Promethease was able to handle this.

Indel notation[edit]

See also Talk:Rs5030655


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

Retrieved from "https://www.SNPedia.com/index.php?title=SNPedia:FAQ&oldid=1612078"
Powered by MediaWiki
Powered by Semantic MediaWiki
Powered by the NCBI