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Download for Rare SNP Analysis

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

  1. Valentijn

    Valentijn Activity Level: 3

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    "I" is an insertion and "D" is a deletion.
     
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  2. Valentijn

    Valentijn Activity Level: 3

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    The location data (chromosome # and position on that chromosome) can be used to look up the rs number, but the rare allele program also includes the rs number "translation" when 23andMe uses an i number.
     
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  3. Valentijn

    Valentijn Activity Level: 3

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    Yeah, it's something I've been thinking about. But it would mean another database which needs to be downloaded and added complexity to the program. I'll talk to the programmer about it :p
     
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  4. snowathlete

    snowathlete

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    So the double II means both base pairs got inserted?
     
  5. Valentijn

    Valentijn Activity Level: 3

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    Yup. It's pretty common to have insertions and deletions, and it's usually not indicating anything interesting.
     
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  6. snowathlete

    snowathlete

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    @Valentijn - does your program have a report for those mutations that are greater than the 10% rarity? I'm thinking specifically of those which are labeled with an "i" code by 23andme. I'm thinking these might also be interesting to identify?
     
  7. Valentijn

    Valentijn Activity Level: 3

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    Well, it will pick up heterozygous mutations where the minor allele is at 10% prevalence. That means that the heterozygous genotypes would be reported going up to a (calculated) 18% prevalence rate for that genotype.

    It's also then easy to sort out the "i" numbers, if you save the results as a .txt file and open it in excel. Then you can sort based on the RSID (starts with "i" instead of "rs") or ETC columns (has an rs number instead of being empty). You could also do this with your full 23andMe file.
     
  8. snowathlete

    snowathlete

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    So I got round to seeing my GP today. I had to wait several weeks to get an appointment with her anyway. I explained about my 23andme results, which was hard work because she didnt know what 23andme was - so I had to explain that. She didn't seem to understand the difference between a predisposition and a mutation that definately results in a condition. I found that quite a surprise but anyway, she's referring me to a neurologist who should be more familiar with this stuff.
     
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  9. Waverunner

    Waverunner Senior Member

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    Genome analysis is fun. I have three homozygous SNPs (no clinical data available). All three are located in intron regions of my genome. Can we therefore conclude, that their importance is probably minor? I'd love to have my whole genome sequenced and run through this analysis tool.
     
  10. Valentijn

    Valentijn Activity Level: 3

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    Yeah, those are probably not important. Similarly, known missense mutations are a lot more interesting as well.
     
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  11. bel canto

    bel canto Senior Member

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    Val - Is there a database somewhere accessible that lists known missense mutations?
     
  12. Valentijn

    Valentijn Activity Level: 3

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    Probably, but I've never looked for it. I'd start with dbSNP, 1000 genome project, and/or OMIM.
     
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  13. kyzcreig

    kyzcreig

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    this is neat, i analyzed my genome - now what? is there an easy way to interpret the SNPs? should we use SNPedia?
     
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  14. Valentijn

    Valentijn Activity Level: 3

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    SNPedia is a good start. I prefer dbSNP, where I can easily see missense mutations and such, plus links to more of the research. Basically SNPedia is more user friendly, but contains less data and fewer SNPs.
     
  15. Jackie M

    Jackie M

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    This is such a great program. Thank you for creating it @Valentijn and for all you do to help others learn how to navigate their 23andMe data. Are you still collecting people's data and compiling it?
     
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  16. Valentijn

    Valentijn Activity Level: 3

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    I am, but only for patients who have CCC/ICC-defined ME with post-exertional malaise if they exceed their limitations.
     
  17. Jackie M

    Jackie M

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    Looking at the criteria in an ICC primer I found on here, I do meet the ICC standards and I definitely have PEM. I have had a lot of the testing mentioned done, but have not been formally diagnosed so I will leave it up to you if you want to add it or not.

    I remember how when CFS used to be on my charts, I'd be treated differently. They removed it when they found POTS, but little did I know, POTS seems to be more of a symptom than a cause of my problems in and of itself. For that reason, I am not quite ready to allow ME to be put on my charts since is lumped in with CFS and I am able to get treatment for symptoms/abnormalities without the label. I know this is not a new thought in this community, but I hold out hope that a reason for my symptoms will be found and worry a commonly misunderstood label will cause some doctors to not do testing they would otherwise do.
     

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