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Resource for converting some gene formats

Discussion in 'Genetic Testing and SNPs' started by MeSci, Dec 29, 2013.

  1. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    I've been frustrated at having no idea what the 'rs' notation relates to with regard to my own results (from Scion/Cellf), and not being able to use links I have found here, so I just did some internet searching.

    If you can bring yourselves to use a CDC site :D you may find this page and pages linked from it useful - I have! :)
    Ninjas likes this.
  2. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    Still frustrated - they don't have all the pertinent genes or variations listed. I have some of the rs numbers now but not all. There are lots of links to promising-looking sites/databases from that one, but some are too large for this modest PC to cope with and others have so much info it's hard to locate what I need.
  3. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    Just done some more searching. This page looks more useful. So do the other SNPedia pages.
  4. Sea

    Sea Senior Member

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    What format are your results in MeSci? If you google a result in your format along with "snp" or "snpedia" or "dbsnp" you can often find a connection
  5. Hip

    Hip Senior Member

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    snpedia.com is a good database that many people use. Just type in the rs number into the search box.
    MeSci likes this.
  6. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    That's the one I'm using now (see above). What I need is to convert my results, which I have listed here, into rs format so that I can compare my results with other people's and read what they say about the alleles I have.

    @Sea - I find it much too time-consuming to use a search engine for each gene, and I don't use Google except as a last resort due to their tax avoidance in the UK. Tax avoidance means less money to spend on health, welfare, social services and many other things we depend on. I use the charity search engine EveryClick (see my signature).
  7. Hip

    Hip Senior Member

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    The easiest way to find the rsID is just to look at the GeneticGenie tables that people have posted on this forum. Mine are here, for example. This gives you the translation you are looking for.



    For better or for worse, it is very common for multinational corporations to avoid paying tax; it is not just Google that does it.

    But to say that it is wrong for multinationals to do this, you would have to demonstrate that paying less tax actually results in lower tax revenues received by the government. Lower tax may not necessarily reduce tax revenue: quite often, by lowering taxes, the government actually receives more tax revenue, paradoxical as that may sound. This is because lower taxes can spur more economic activity and economic fervor, like blowing oxygen over a smoldering fire, and then because of this increased economic activity, the government actually receives more tax.

    To be honest, I don't know the full ins and outs of the mathematics, but I do know it is not a straightforward picture.

    What I don't understand is why governments moan and moan about multinationals not paying enough tax. Governments are not here to moan. If they think that the multinationals not paying enough tax, then these governments should change the tax laws in order to levy more tax. That's what governments are here for: to pass the right laws that society needs. In other words, governments should not just sit there and moan; it makes them look impotent: if they have a problem, they should do something.
  8. Sea

    Sea Senior Member

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    @MeSci

    By "google" I just mean search by whatever search engine you use.

    For example by "googling" this from your list - APOC3 c3175g

    the following is one of the alternatives displayed and the rs number is easily found:

    http://alfred.med.yale.edu/alfred/recordinfo.asp?condition=sites.site_uid='SI001130F

    = rs5128

    or this one when searching IL6 g(-174)c

    http://snpedia.com/index.php/Rs1800795

    For those that don't display an rs number easily, there are other ways to find it using the position on the chromosome. Many studies don't include rs numbers but most will identify the position

    I can't see any way around finding them one by one.
  9. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    Thanks for the link to your results - that is very useful.

    It's not our government that is complaining about corporation tax avoidance (the corporations are registered in tax havens so really avoiding it). It's the public, and we are lobbying the governments to stop the avoidance by plugging loopholes.

    @Sea, thanks for your links.

    I understand that some (many) people use 'google' as a generic term for internet searches, but to me it is analogous to calling a health professional a 'Wessely' or a diagnosis a 'CDC', and it's effectively giving them free advertising.

    The search engine I use donates to a charity of your choice for every search you do and also has arrangements with numerous companies who donate percentages for everything you buy through them. The large lists of charities include ME ones.
  10. Hip

    Hip Senior Member

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    Well in all the news coverage I have seen about Google and other multinational's tax avoidance schemes, it has been government minsters bring up the subject, not the public. I have not seen any non-governmental groups or member sof this public mention this. So it seems to me as if the UK government initiated it.

    I bet the Irish government is not complaining though: they are receiving all the tax levied on all of Google's services sold in the UK.
  11. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    A quick search for 'google uk corporation tax' produces numerous hits on public anger over the avoidance by Google, Starbucks, Amazon etc., for example this one. I don't think it's generally government-led; there has been a lot of criticism of the government for over-taxing the poor (like many of us) and under-taxing the rich and powerful.

    I think the US and UK/European public opinions on tax are very different. Anyway, we are straying a bit - my fault perhaps - but I wanted to point out that there are alternatives to Google which can generate income for ME charities.

    As an aside, the Danish come out consistently as one of the happiest nations, despite their cold dark winters. They have some of the most generous welfare payments and one of the fairest tax systems. I'm sure those are factors. Inequality is a major source of unhappiness.
  12. Hip

    Hip Senior Member

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    I have to admit that although when I was younger and healthy, I used to believe that the happiness of the people was one of the most important characteristics of a nation. But these days, especially given my experience of developing ME/CFS, I tend to think now that one of the most important characteristics of a nation is that it strives to tackle the nasty problems that humanity faces, such as chronic debilitating diseases like ME/CFS.

    Unfortunately, being hit will a nasty illness like ME/CFS seems to rob you of your "philosophical innocence" about the world; once you realize what degradations nature can throw at you, it changes your viewpoint on life.

    Capitalist nations may sometimes be a bit crueler to the populace than say more socialist nations like France, Spain and the Scandinavian countries, but capitalism appears to be more strident, in terms of moving forward scientifically, technologically and medically. I still have ample liberal/left leaning views, but I do recognize that nothing brings advancement like capitalism does. Of course, if we lived in a perfect world, were there was no disease, no crop failures, no natural disasters, etc, and thus no need to strive, then I'd be more socialist.
    Last edited: Dec 31, 2013
  13. S.A.

    S.A.

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    Have you looked into this one: www.nutrahackerblog.com. ? They have a service similar to mthfrsupport where you can run raw data to get a report but nutrahacker produces a report that gives you recommendations for diet and supplements. I can't recommend since I haven't actually tried it, but I've been concidering it. A friend is trying it and I'm waiting to see if she finds it useful.
  14. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    I can't find a page or section on the site where you can do that, but my brain is rather sluggish at the moment. Can anyone else point me to such a page?
  15. bel canto

    bel canto Senior Member

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  16. MeSci

    MeSci ME/CFS since 1995; activity level 6

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  17. Hip

    Hip Senior Member

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    @MeSci
    I take it that you got you genotype results from a company other than 23andme.com, and what you are trying to do is get the same Gene + Variation and rsID names as 23andme.com use to describe an SNP.

    The only other complexity is that when the alleles / mutations are given, there are unfortunately two different conventions used, and each organization and researcher may adopt either of these two conventions to give their results.

    The two conventions are: whether the mutations for an SNP are stated in terms of the negative DNA strand, or stated in terms of the positive DNA stand. Obviously DNA contains two strands in its double helix, and these two strands are mirror images of each other (mirror images in terms of the bases on these strands — the base A always mirrors T on the opposite strand, and the base C always mirrors G).

    23andme use the positive DNA strand for reporting all SNPs. You need to find out whether the company you got your gene results from report on the negative strand, or report on the positive strand.

    Once you know this, it is easy to convert: if your company also use the positive strand for reporting, no conversion is necessary. But if they use the negative strand, then you need to interchange the As with the Ts, and interchange the Cs with the Gs.

    If you read the comment by Sea in this post (and the posts that follow), it explains how this negative / positive strand business works.

    Best read when your brain fog is not too bad!
  18. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    Thanks. I have most of the RS numbers now and have just added them to my results thread here. I have also got info about the implications of the SNPs from the Nutrametrix document I posted a link to here.

    I have to get on with other stuff now and give my poor brain a rest but will try to come back to your message later.
  19. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    I thought I had come back to your message, @Hip, but my ME-brain has deceived me!

    As the company that did my test is defunct, I can't find out which strand they reported on, but I did find a patent application that says their probe may bind to either strand.

    So all I have is the name of the variation, e.g. CBS C699T, statements as to whether or not I have the variation, and my two letters, e.g. T,T. Does this tell me whether I am homozygous or heterozygous for the variation? As I understand from my rather distant science studies, C will always be opposite G on a chromosome, and A opposite T, so my two letters must presumably relate to the two chromosomes in a pair. In the example cited then, I guess that it means that I am homozygous for that variation - is this right? In the case of GSTP1 C341T (C,T), I guess that I must be heterozygous? Or am I hopelessly confused...? :confused:
  20. Hip

    Hip Senior Member

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    @MeSci
    Yes I think that is right: if you have the variation, and you have both letters the same, such as "TT", then this means that you are homozygous, but if you have the variation and you have different letters, such as "CT", then this means that you are heterozygous.

    I looked through my Genetic Genie results, and all the homozygous (shown in red) results have the two letters the same, and all the heterozygous (shown in yellow) results have the two letters different.


    You should also be able to work out which strand your company is reporting on by looking at my above Genetic Genie results, and then taking an SNP case where: both you have no variations at all, and my own results have no variations at all. Then if your two letters on this SNP example are the same as my two letters, it means your company is reporting on the positive strand, as used by 23andme. But if your letters in this SNP example are the complementary letters (A goes to T, and C goes to the G), then I guess it means your company reports on the negative strand.
    MeSci likes this.

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