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Investigating SNP Polymorphisms for Functional Understanding

Discussion in 'Genetic Testing and SNPs' started by Journeyman, Sep 29, 2016.

  1. Journeyman

    Journeyman Senior Member

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    Hi Folks,

    After experiencing some benefits and costs with implementing dietary/supplement changes from my 23&Me results (V3) since mid 2013 I'm now looking to really understand the various SNP's and get past the roadblocks and perhaps have some chance at self actualisation?

    I've found some invaluable posts from Valentijn who has both generously given useful analysis and directed me to useful resources, however I need to improve my understanding and abiliity to use those resources. For example I redownloaded my 23&me raw data and started looking at RS numbers of interest.

    This then led me to using Valentijn's great '1%' programme which I'm particularly a big fan of since it allows you to get the info you need without putting what might become your most precious personal info out on the interwebs, and at no cost! So I've got some results and I've copied and pasted the RSID's into DbSNPedia but for all of them I get virtually nothing other than one instance which interestingly just said "This is frequently misinterpreted by 23&Me as being GG when its actually AA" - rs8176928

    So where to from here? Promethease seems to offer the next best thing after the obligatory (and great) genetic genie but is there anything else.

    I was able to use google scholar (great for bringing up peer reviewed journal articles on SNP's of interest) and found one RS which came up as 'homozygous only' in the 1% programme... rs8176928 which relates to SLE (lupus) and then led me to this article - http://online.liebertpub.com/doi/abs/10.1089/dna.2014.2368
    Now this seems genuinely useful. I've got a 0.37% SNP polymorphism that is associated with SLE (not sure of the strength of the relationship but it seems apparent)

    Is anyone else familiar with this SNP and its implications (Is it strongly linked with SLE?) and if you were in my situation where should I go to understand the interplay of all my SNP's better - a NUTREVAL test seems like the next step... ?

    Regards

    Journeyman
     
  2. Valentijn

    Valentijn WE ARE KINA

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    @Journeyman - There's been some updates to the program, though we still need to repackage the basic download to be more user-friendly.

    The latest version of the program is 0.6, so if you have something older (0.5 or lower) you can get the newer version at https://sourceforge.net/projects/analyzemygenes/files/Analyze My Genes 0.6/

    The 1% database doesn't generate a lot of results. The 10% generates a huge amount of results, and can be downloaded at https://sourceforge.net/projects/analyzemygenes/files/Databases/ as the ten_percent.zip file. The remarks.zip file can also be downloaded there, and this one is hugely helpful, since it automatically labels missense/nonsense mutations, pathogenic status (when known), gene names, etc. So that takes most of the work out of looking up your rare results.

    The 10% file is also useful for seeing potential compound heterozygous pathogenic mutations. Basically the csv or text file can be opened in Excel, then re-arranged by mutation, gene name, etc.
     
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  3. JamBob

    JamBob Senior Member

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    Hi @Valentijn - I'm interested in trying this - do you just download from source forge and then run the program? Does it work on macs?
     
  4. Valentijn

    Valentijn WE ARE KINA

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    Yup, just download all the files and unzip them into the same directory.

    It should work on Macs, unless yours is set to reject unverified programs (might be a default setting). It costs around $100 for developers to get programs registered as verified, and it isn't sensible to spend that on a free program :p
     
  5. JamBob

    JamBob Senior Member

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    @Valentijn - thanks for the info - I'm going to try and see!
     
  6. Journeyman

    Journeyman Senior Member

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    I'm able to get the 1% report working on my Mac but not the 10% (and yes fully aware of the default setting that prevents non verified programs etc.). I had some difficulty even getting it to show the 10% button in the main menu (can't replicate it now) but did at one point back on 30/9, however when I generate the PDF it appears per the attached (nothing sensible) Any ideas how to get it working and can you remind me how to get the main menu to actually show the 10% options tab (I tried putting the genes.jar in the same DIR as the ten_percent.hb.db and with my 23& me file but still no joy)
     

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  7. Valentijn

    Valentijn WE ARE KINA

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    @Journeyman - Is everything unzipped? And the downloaded files all is the same directory with each other? 23andMe results can be in a different directory, but should also be unzipped.
     

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