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ME/CFS Genes Study by Dr. Nancy Klimas - Still Recruiting!

Discussion in 'Latest ME/CFS Research' started by Neunistiva, Dec 21, 2016.

  1. Neunistiva

    Neunistiva Senior Member

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    I first found out about Dr. Klimas' ME/CFS Genes Study during the IACFS/ME pre-conference. It seems it has been going on for several months already, but I've never heard of it before, so I thought I'd share it here in case anyone else missed it.

    I loved their idea, it's a great way for ME/CFS patients to help researchers with no budget to collect a lot of genetic data. The collected data will be shared with Dr. Davis (Do I remember this correctly @Ben Howell?)

    I participated as a ME/CFS patient and my parents as healthy controls so I thought we’d share our experiences.

    The whole study is done online and it’s possible to do every step without getting out of bed.

    You can start answering surveys before you even have your genetic data, and many patients already got tested for other reasons, but I waited to get everything I needed because I can’t keep several things in my head at once. I will write bullet points in the order I finished them.

    • Go to 23andme.com or dna.ancestry.com to order your kit and follow their instructions (we ordered our kits on 2nd of November, we mailed them together at the same time, and received our raw genetic data on different dates between 30th of November and 10th of December. Obviously all of this will vary depending on the time of the year, country you live in, type of shipping you choose etc.)

    • E-mail MECFSGenes@Nova.edu and state whether you have ME/CFS or you are a Healthy Control

    • They will send you a secure link in your e-mail inbox. You have several days to click it before it expires. Once you click it, you will be taken into an online NOVA mailbox. You will have one more e-mail there will clear instructions.

    • If you follow the instructions and click the next link you will be taken to a web form where you will fill out your real name, last name, choose a password and security question. (Write these down as you will probably not be able to fill out all the surveys at once and have to come back at a later time.)

    • Fill out a Pre-Screening Questionnaire consisting of 11 questions to see if you are eligible for the study (you may want to do this before ordering genetic test if this study is the only reason you want it)

    • Finally, fill out surveys and upload your raw genetic data. (You can take as much time as you need and even stop and come back whenever you want.)
    A few notes:

    I know this sounds like a lot to do and seems overwhelming, it did for me too, but I am severely ill and managed to do everything on my own, except read Informed Consent pdf file because that was several pages long. My mother read it for me and we were both satisfied that this was a professional and reliable research that will handle our genetic data carefully.

    Everything was pretty self-explanatory, but if you get confused there are simple instructions for everything with images for those who struggle reading text.

    I stretched out filling surveys over 3 days at a comfortable relaxed pace. Shortest survey had 1 question and longest one 162 (but that one didn’t take long to fill out either because it was actually 3 times less, 54 questions with additional symptom severity options). On the other hand, my parents who are healthy did it in about half an hour all in one day.

    I still had my mother monitor my answers because my brain does stupid mistakes all the time and I didn’t want to answer something wrong and influence the study.

    Those two private genetic companies, 23andMe and Ancestry offer several options when ordering your kit, but I e-mailed the researchers and they confirmed they only need raw genetic data so it doesn’t matter what you choose as long as you get raw genetic data.



    Relevant links:

    1. NOVA SOUTHEASTERN UNIVERSITY Institute for Neuro Immune Medicine ME/CFS Genes Study
    2. 23andMe
    3. Ancestry
     
    Last edited: Dec 22, 2016
  2. *GG*

    *GG* senior member

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    I hope to do something like this when my disability is approved, and finally have some income. Would like to get my parents data in their as well, they had good health most of their lives. Wonder why I didn't have as much success?

    GG

    PS You might want to break up the "bullet" section, to make it easier to read :)
     
    Last edited: Dec 21, 2016
    Comet likes this.
  3. Neunistiva

    Neunistiva Senior Member

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    Ah, SHIFT + ENTER is my friend :)
     
  4. Neunistiva

    Neunistiva Senior Member

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    Mel9, Invisible Woman, merylg and 2 others like this.
  5. btdt

    btdt Senior Member

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    Why a lull in research?
    I have my 23 and me data and uploaded it to a site called Genetic Genie to find out how to help with methylation .. I could never think well enough long enough to sort it. Genetic Genie was easy to use as it linked to 23 and me without help from me... does this research site do the same thing.

    I attempted to download my raw data once and could not do it... not so sure my computer connections are secure either.. it is a shared internet access the virus program says it is not secure but the owner of the connection does not want to fix it as he does not believe it.

    Testing so far as been no use to me as I can't think well enough long enough to make use of it.

    I could use some help but not sure there is any fixing things on my end... so maybe nothing can be done.
    Still putting this out ...
    I certainly would join the project at least add my dna data if they can do the easy connection that genetic genie uses.
     
  6. Dakota15

    Dakota15 Senior Member

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    Hey PR, Happy Friday and cheers. Hope everyone is hanging in there.

    Not sure if this was already posted, but Dr. Nancy Klimas and Nova Southeastern University are currently recruiting for a ME/CFS Genes Study.

    In Dr. Klimas's own words (in the quick video in the link below), "The idea is to better understand which gene mutations put patients at a better shot or a worse shot at a particular kind of therapy or treatment". She's hopeful of at the minimum of receiving 1,000 samples of genetic data and compared this study to what helped move Diabetes forward to better understand.

    http://www.nova.edu/nim/research/mecfs-genes.html

    A couple quick points:

    - Will I have to come to your clinic or see your provider?

    No. Participating in this study is purely web based, meaning communication will be completed via email. Completing the surveys and uploading your genetic data will also be completed at your leisure using RedCap, a secure web based platform.

    - I completed my genetic testing from a website. Which companies do you accept?

    At this time, we are only accepting raw genetic data from 23andme.com and dna.ancestry.com

    They are currently recruiting for ME/CFS patients AND Healthy Controls

    I know many on PR have leveraged 23andme or DNA.Ancestry - would be great if we could give Dr. Klimas as much information as we have out there to help!

    Dr. Klimas asks at the end of her video for our help with anything we can do to help this go viral and pass this on
     
    Last edited: May 18, 2018
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  7. Neunistiva

    Neunistiva Senior Member

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    I posted this before, but it's good you posted it again. It's kind of disappointing to see that this has been going on for years and still 1000 people haven't been reached. Especially because so many of us had genetic tests done.

    It's really easy to do and I've written step-by-step guide for the brain-fogged.

    Also, a reminer that Robert Phair also needs our genetic data for research on metabolic trap: WES (whole exome sequencing) or WGS (whole genome sequencing), but not 23andme anymore. Apparently, WES is cheaper than WGS.
     
    Last edited: May 18, 2018
    Mary and Dakota15 like this.
  8. Dakota15

    Dakota15 Senior Member

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    @Neunistiva When I tried to click on the link within the article to send to Robert Phair, it redirected me it seems....did you send to Robert Phair by chance or have any idea how to navigate it?
     
  9. bertiedog

    bertiedog Senior Member

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    I believe that Robert Phair has said he now has sufficient data and didn''t need anymore at this stage.

    Pam
     
  10. John Mac

    John Mac Senior Member

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    @Neunistiva Do you know if this is limited to people in the US or can anyone upload their DNA results?
     
    Last edited: May 18, 2018
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  11. J.G

    J.G

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    Thank you for posting this here, @Dakota15. I've contacted them for participation.
     
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  12. Neunistiva

    Neunistiva Senior Member

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    I'm not sure which link you were clicking, but it's just an e-mail address where you're supposed to send it to.

    "You can reach me at rphair@integrativebioinformatics.com"

    Maybe an e-mail client was attempting to start up? Let me know if I misunderstood.

    Could you please try and remember where you heard this? It would be a pity to discourage people from sending more if he needs it. Especially because the issue with link was that it's not a link but an e-mail address.

    I also can't find anything about not needing any more data on his project page. The request is still there.

    Anyone. It's open internationally. I am Croatian.
     
    John Mac likes this.
  13. bertiedog

    bertiedog Senior Member

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    My guess would be either here on PR or alternatively it would have been Healthrising. I took an active interest in this because I did send my data to him but I am 99% sure that he said he had sufficient data of people who had 23andme results but he was still wanting to receive a specific type of genetic testing which I gather not many of us would have undertaken because it was very expensive.

    Pam
     
  14. bertiedog

    bertiedog Senior Member

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    Just checked and it was on Healthrising The type of testing Dr Phair wanted was called WGS testing. There were 150 comments that followed Cort's blog including some from Dr Phair himself.


    Pam
     
  15. Neunistiva

    Neunistiva Senior Member

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    Ok, I went through the effort and searched for it and this is what I found in the comments on Healthrising

    Many of you have sent me 23andMe data, which I really appreciate. Recently, I received my first version 5 (v5) 23andMe data set from a CFS patient and to my surprise, 23andMe v5 appears to be no longer measuring ANY of the 5 single nucleotide variants (SNVs) (aka SNPs) that are important to the metabolic trap hypothesis.

    I did a brief search and found this post on Reddit

    https://www.reddit.com/r/23andme/comments/3dd3lp/snp_coverage_analysiscomparisons_23andme_v3v4/

    that compares 23andMe v3 and v4. This analysis asserts that each version both adds and subtracts SNVs. If someone reading this has the programming skills to verify this analysis and extend it to v5, that would be awesome.

    So at least for my metabolic trap project, please don’t spend your money on 23andMe v5. It won’t help.

    From what I can tell, he's not saying not to send 23andme any more, just not to send the newest version. People who tested it before and have v3 and v4 can still send it. Am I right?


    No, this is what Dr Phair said

    Also, if you’re thinking paying for sequencing data, I’d recommend whole exome sequencing, not the more expensive whole genome sequencing (WGS). Just sayin’.

    This thread is becoming a mess...
     
  16. bertiedog

    bertiedog Senior Member

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    We are seeking CFS/ME patients who have had their genomes sequenced and who would be willing to share their data for research purposes.* Your data would help us test theories about gene variants that may have predisposed you to developing CFS/ME when you encountered the infection or other stress that was the cause of your case of CFS/ME. We cannot provide feedback or use the data in studies. Nevertheless, confirmation or refutation of what we find in professionally acquired and processed WGS or exome sequencing data could help us a lot in our search for something that helps every ME/CFS patient.

    The above is a copy taken from Cort's original blog before all the comments.

    Pam
     
  17. Silencio

    Silencio Senior Member

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  18. bertiedog

    bertiedog Senior Member

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    Actually I read it here in this post on The Metabolic Trap thread -

    [Moderator note: according to this post, Dr. Phair now now has enough 23andMe data but could still use whole exome or whole genome data.]

    Help Dr. Phair with his research and send in your genome!

    rphair@integrativebioinformatics.com


    Your data would be most comprehensive and powerful in the form of .VCF (Variant Call Format) file but we will work to find a way to analyze your data in any format you are able to provide.

    Please also tell us your age and gender and write a paragraph or a page with a description of how you came down with ME/CFS. A list of current symptoms is optional, but desirable.

    E-mail from Dr. Phair regarding 23andme data:

    Yes, the .txt format will work. 23andMe only covers three of the five genetic variants that are important for the metabolic trap theory, but I can say that even this limited information is useful.

    The 23and Me file that I need has a filename like this: genome_firstName_lastName_Full_date_time_in_digits.txt
    so if it was mine it would be something like
    genome_Robert_Phair_Full_20180315085441.txt
    .zip instead of .txt is also fine
    If you can open the file in a text editor it should begin with a header that looks like this:
    # This data file generated by 23andMe at: Wed Jun 14 12:04:30 2017
    #
    # This file contains raw genotype data, including data that is not used in 23andMe reports.
    Regards,

    Robert D Phair PhD | Chief Science Officer | Integrative Bioinformatics Inc
    Mountain View, CA
    www.integrativebioinformatics.com



    Edit: Dr. Phair now now has enough 23andMe data but could still use whole exome or whole genome data

    Pam
     
  19. Silencio

    Silencio Senior Member

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    @bertiedog You still have left a post above which is quite misleading stating that he “doesn’t need any data”. This is not accurate, and probably should be deleted.
     
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  20. Wishful

    Wishful Senior Member

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    If this is just blood testing, it might be missing the critical part: cerebral mtDNA. Cerebral mtDNA is supposedly slightly different from the mtDNA elsewhere in the body (I can't find the paper claiming that, but it seemed plausible). Also, the mtDNA mutates in the cells, and keeps copying the errors, so potentially our ME could be from cerebral mtDNA errors which might not show up in blood samples.

    I'd hate for the research to show 'no DNA mutations linked to ME/CFS' which would close down further research into that possibility. Hopefully they'll compare some cerebral mtDNA (from autopsies?) with the blood mtDNA to see if there are differences.
     

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