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Doing a Whole Genome Sequencing (WGS)

Discussion in 'Genetic Testing and SNPs' started by jamienoble, Nov 12, 2015.

  1. Valentijn

    Valentijn Senior Member

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    I'm not sure what you're asking. Genetic mutations are a possible cause of disease, but so are many other things. Nothing can be assumed.
     
  2. shoponl

    shoponl

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    It sounds really great!

    I had a notice today that the new version is available on SourceForge. I am a little spooked by downloading a zip file from SourceForge, though, because of their bad press regarding adware and malware since 2013. i.e. http://www.howtogeek.com/218764/warning-don’t-download-software-from-sourceforge-if-you-can-help-it/ , http://www.information-age.com/indu...google-discovers-588-pages-malicious-software

    Is the program available on another site?
     
  3. Valentijn

    Valentijn Senior Member

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    Nope. And it sounds like the SourceForge problem went away shortly after that article was published, based on the update at the bottom.

    The extra data file is downloaded separately, to keep the basic program bundle nice and small for people with downloading or other limits. It's the "remarks.zip" file at https://sourceforge.net/projects/analyzemygenes/files/Databases/ and just needs to go into the same folder with the other files from the program.
     
    shoponl likes this.
  4. shoponl

    shoponl

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    You mean the update on the bottom of the SourceForge landing page? Yes, I see that they've changed management in Jan 2016... https://sourceforge.net/blog/sourceforge-acquisition-and-future-plans/ So presumably downloads are clean again, since they've been bitten once.

    I took a quick look at the java and I can see someone spent a lot of time on this! It's great you created this resource and offer it free to the world. Many thanks to you and Jan.
     
  5. Valentijn

    Valentijn Senior Member

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    No, on the bottom of the article you cited above.
     
  6. jamienoble

    jamienoble

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    My results will be ready in around 2 months from Gene by gene.
    Correct me if im wrong, finding information related to my disease is like finding a needle in haystack pretty much?
    And if my symptoms are from an infection or something i wasn't born with, this information wont be in the data at all?

    When the data is ready, could you teach me what i can do myself to find anything useful from this?
     
  7. Valentijn

    Valentijn Senior Member

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    Yes ... but there are ways to search through the haystacks more efficiently. Mythbusters had a fun episode on that :D
    Even if it's not a strictly genetic disease, there could still be a genetic susceptibility. For example, there are missense mutations in the genes involved in innate immunity which can result in reacting poorly to a few specific infections. But unless/until someone with one of those mutations runs into one of those infections, everything is going to be pretty normal.
    Yes. Currently I'm working on getting the 23andMe files for Analyze My Genes to include more of the rare SNPs (some were omitted from earlier versions due to being difficult), but after that my next project is to attempt something similar for at least the exome, maybe the genome depending on how huge the data files get.

    But even without that sort of program you can probably still manually focus on the genes which are most likely to contribute to your disease/symptoms.
     
  8. jamienoble

    jamienoble

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    Hello again,

    My results are now ready, not sure which one of these i should upload for you tho?

    https://www.dropbox.com/s/uhbnait3ythnhz1/Namnlös.png?dl=0

    Very much looking forward to begin searching for any clues in this data. I know its just a small chance that we find anything related to my symptoms but im willing to spend time each day looking as long as you teach me how and what im suppose to look for. :)
     
  9. Valentijn

    Valentijn Senior Member

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    The files are zipped, so I can't tell what the file extensions are :p The interesting ones should be in .vcf format, but the visible exome.vcf file is too small to contain much data.

    Based on the naming, the "post" files probably all go with the "post.bam" file. .bam is basically the raw string of alleles.

    So the more useful ones are probably "exome.vcf" and the files after it are probably .vcf files too, but broken into smaller parts so the files aren't too large to be copied or downloaded. So I'd like to see the "exome.vcf" file and at least the first two following it, so we can get a version of the Analyze My Genes program working with the specific formatting and multiple files.

    I'll send you a PM (conversation) with my contact info.
     
    Helen, jamienoble, Sea and 1 other person like this.
  10. jamienoble

    jamienoble

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    Just sent you the links to exome.vcf and all the files beneath it. Just tell if you want the first 5 files in the list as well.
    Hope it works well! ;)
     
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  11. merylg

    merylg Senior Member

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    Valentijn and Sea like this.
  12. OkRadLakPok

    OkRadLakPok Senior Member

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    I did what is almost that at a University. I do have a large duplication over 8 genes, one of which is PACSIN1. They say it is clinically sig in terms of my hyper sensitivity. It makes me happy to have that dx after YEARS of hell, telling me I a crazy.

    Now when I go to Dr and tell them, and tell them it is NOT 23 and Me which they laugh at ( I do NOT know why because 23 and me showed my some stuff!!) then they perk up and stop making me feel like crap

    Yes, I will do WGS soon. It is worth every thousand I will spend . It may show nothing more, but if you are dumped in that psych boat, you will n otice how differently they treat you when you really do have a genetic issue.
     
    SickOfSickness and merylg like this.
  13. jamienoble

    jamienoble

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    Please update how it goes, who will go through your WGS data?
     
  14. merylg

    merylg Senior Member

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  15. merylg

    merylg Senior Member

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    Sydney, NSW, Australia
  16. wastwater

    wastwater Senior Member

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    Just marking this as a point of interest
     
  17. parpar

    parpar

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    what do you mean when you used accutane you are cured , i took it and i got CFS in the 3rd month
     
    pattismith likes this.
  18. parpar

    parpar

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    you seem knowledgeable in the field of genetic analyzing , i would ask you if you have done any genetic testing WGS or WES ?
     
    merylg likes this.
  19. wastwater

    wastwater Senior Member

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    Arnt people with me/cfs going in for these genome projects and making data public to see what can be learnt from this if anything
    They are studying rare diseases and cancer I think so it might not be easy to get in
     
    Last edited: Nov 11, 2017

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