Invest in ME Conference 12: First Class in Every Way
OverTheHills wraps up our series of articles on this year's 12th Invest in ME International Conference (IIMEC12) in London with some reflections on her experience as a patient attending the conference for the first time.
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Download for Rare SNP Analysis

Discussion in 'Genetic Testing and SNPs' started by Valentijn, Aug 29, 2013.

  1. Jenny TipsforME

    Jenny TipsforME Senior Member

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    @Valentijn Coursera is great I'm doing a personalised medicine /genetics course ignoring coursework. I'm also doing Graphic Design keeping to deadlines.
     
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  2. Paralee

    Paralee Senior Member

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    Hummm......I'm hetero on those three.
     
  3. Paralee

    Paralee Senior Member

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    @Valentijn , is that wonderful program of yours still usable? Also, I have windows 10 and haven't learned it well yet. Thank you.
     
  4. Valentijn

    Valentijn Senior Member

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    Yes, it's still usable. Windows 10 shouldn't be too different. The main thing is to download the program (and extra files, if desired), and unzip all of them into the same directory.
     
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  5. Paralee

    Paralee Senior Member

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    @Valentijn , thank you so much. I'll ask someone what that means.
     
  6. Loachi

    Loachi

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    Thumbs up @Valentijn , I am a step further in my investigations.
    On my old XP , I had following happening :
    - Before downloading the comment file, the safe as PDF gave an completely empty file.
    - But the text file was OK
    - After adding the comments file the save as PDF suddenly worked.
    - The sorting by first collumn works on the PDF file , but not on the TXT file.
    And now ? Learn how to lookup .... and not panic when I find a scary one :)
    From
    i3000469 2 T 0.060 CT Mutation T105I (-1) Clinsig is other Genes HNMT Renamed rs11558538
    i3003198 15 T 0.010 CT Genes LIPC Renamed rs35511894
    i5008401 1 A 0.001 AG Mutation P20L (-3) Clinsig is Patho Genes NPHS2 Renamed rs74315344
    i5900152 5 C 0.050 CT Genes PDE6A Renamed rs112771183
    I find only info about 74315344
     
  7. Valentijn

    Valentijn Senior Member

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    Ah, that makes sense. We only added the pdf file option recently I think, at the same time the "remarks" database was added. We still need to repackage the latest versions of the files so everything that goes together gets downloaded together :p

    With the text file, the best approach is to open it from Excel. Then each field will be in a sortable column.

    You can look them up by rsID (rs11558538, etc) at www.ncbi.nlm.nih.gov/projects/SNP/ . That will often link to any pathogenic info, or you can directly look up a gene at OMIM.org.

    There are usually multiple different positions given for missense mutations, as more info about the protein created is uncovered, so positions given in the report can be wrong. But the amino acid abbreviations are always the same. So the report might say the mutation is "T105I" but it's reported elsewhere as "T71I". So on OMIM and similar, it can be important to look for nearby numbers with the same amino acids.

    So for HNMT T105I, there's no link to pathogenic info about it, though you can see links to all the research if you hover over the cyan box in the map view. But at OMIM that SNP is listed at http://omim.org/entry/605238#0001 and the research is summarized. Some says its a risk factor for asthma, some says it isn't. So it's not pathogenic, and might or might not mean asthma is more likely.

    Your NPHS2 mutation is more interesting. http://www.omim.org/entry/604766#0006 shows that it's pathogenic when autosomal recessive (homozygous or compound heterozygous) but also indicates that people heterozygous for this mutation can have a milder form of Nephrotic Syndrome which is sometimes responsive to steroids. Though as it says in the summary on OMIM, it can't be ruled out that there's another heterozygous mutation on the same gene which causes them to be compound heterozygous. 0.4% of the general population is heterozygous for that mutation, so it's quite rare.
     
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  8. Waverunner

    Waverunner Senior Member

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  9. Moof

    Moof

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    Somewhat behind the curve, as usual, I've just gone through this fascinating thread this evening. @Valentijn, are you still collecting 23andMe data from confirmed M.E. patients? Happy to send mine if you are...been ill with it for more than 40 years, so will contribute to any project that may yield interesting results! (No worries if you've long since left it behind.) And happy new year, all!
     

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