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Mitochondrial disease confirmed!

Discussion in 'Genetic Testing and SNPs' started by pattismith, Feb 12, 2018.

  1. wigglethemouse

    wigglethemouse Senior Member

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    @pattismith
    @BeautifulDay

    Linda Avey's 23andMe data is posted her:
    https://www.snpedia.com/index.php/User:Lilly_Mendel

    And here is a direct link to her 23andMe v4 data as an example.
    https://s3.amazonaws.com/snpedia/User/Lilly_Mendel/genome_Lilly_Mendel_v4.txt.gz

    I believe here husbands file is also available somewhere.....

    I don't know how to decode the raw data file to see the 4 mutations of interest to get another data point without paying the $40 to Enlis. Maybe you are interested to take a look?

    As an aside - Linda was one of founders 23andMe and is now working on ME with precise.ly. One of her friends has ME. Precisely are part of one of the NIH centers working with Deva and Lucinda Bateman.

    In 1H2018 they will be updating their app to support HELIX genetic data specifically to look at ME aspects. Could be worth reaching out to her on things we'd like to see from the Precisely/Helix combination.
     
  2. pattismith

    pattismith Senior Member

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    @wigglethemouse

    if you just wish to control if you have the four false mutation in your MT DNA,
    you can go directly in your raw datas in the 23andme website.

    You write the name of the gene MT-ND1 in the window, and a list of snp will show up.

    You will check the position 3377, 3734, 3947 if you have the variant for it.

    Then you will ask for the other gene MT-CYB and you will check the pôsition 15198 to see if you got the variant
     
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  3. BeautifulDay

    BeautifulDay Senior Member

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    Thank you @wigglethemouse

    Linda Avey and her company's Precise.ly patient tracking platform that's being used in the ME/CFS Study is very interesting.
    http://www.prweb.com/releases/2017/10/prweb14763030.htm

    I had not realized Lily Mendel from 23andme was Linda Avey.
    https://www.snpedia.com/index.php/User:Lilly_Mendel

    As much as there are things that I'd like to see on such an app, there are also many pitfalls to such an app. For example, exercise must be dealt with appropriately. With exercise, it's not about pushing pushing pushing. With ME, it's all about listening to the body and pacing. Pushing too hard causes crashes and more damage. I'm one of those people that enjoys exercise when I feel well. I'll keep upping the exercise over the days and weeks slowly if I'm up to it. However, after decades, I also know too well that when the body says slow down the pace, do it in shorter increments, and take a day off - this is very important. Because ME patients can take nosedives in energy (for example from mid level energy to zero energy), having an app that realizes such changes and realigns goals accordingly (to where the person is currently at) without pushing is very important.

    Think about it in terms of a weight loss app. One day you weigh 150 pounds and are being applauded for the 20 pounds loss. Then you wake up the next day and weigh 170 pounds again. While this doesn't happen with weight, it does with regards to the ability to exercise for those with ME. Therefore, the app in no way can make one feel bad for opening the app (it can't be a downer) and make them feel bad about being back to square one on energy. For some ME patients, filling the dishwasher with dirty dishes brings them into anaerobic energy usage and the corresponding crash. I hope they have patient advocates on their team and not just researchers.
     
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  4. wigglethemouse

    wigglethemouse Senior Member

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    I checked the Lilly Mendel v4 file I linked to and these 4 positions are not listed. So it looks like these four positions were added in the v5 version of the chip.
     
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  5. pattismith

    pattismith Senior Member

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    yes this is what I thought :thumbsup:
     
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  6. wigglethemouse

    wigglethemouse Senior Member

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    @pattismith @BeautifulDay.

    I found the Personal Genome Project website that has v5 data files
    https://my.pgp-hms.org/public_genetic_data?data_type=23andMe

    I browsed the first 3 files and they are all the same as us
    MT-ND1 : 3,377 = G, 3,734 = G, 3,947 = G
    MT-CYB : 15,198 = T

    Sorry to disappoint but it looks like those locations are perfectly normal for v5 23andme data :(.

    Seems like the v5 chip appeared last summer.
     
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  7. pattismith

    pattismith Senior Member

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  8. wastwater

    wastwater Senior Member

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    I was just looking at LHON genetic mitochondria desease as it often has MS or cfs like features
    I’m getting a full genome scan and wonder will it rule in or out mitochondrial desease

    Some more rare ones mentioned in this paper
    Monogenic diseases masquerading as MS
     
    Last edited: Feb 27, 2018
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  9. wigglethemouse

    wigglethemouse Senior Member

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    @BeautifulDay I contacted Linda Avey and she said that they are currently building up their ME network in preparation for their Pecisely Helix app launch and would love suggestions for a patient advocacy group to provide feedback.

    I'm new to PR, and don't really have the energy to pursue this right now. Do you think this topic might interest others here - perhaps you might be interested to explore further as you have a pretty good knowledge of genetics & ME (in my eyes anyway) - or you might know someone who would?

    @Sushi - I've no idea if this sort of thing is allowed for a commercial product here on PR. Can you advise?
     
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  10. aquariusgirl

    aquariusgirl Senior Member

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    @wastwater who are you going with for the full genome? how much is it? thanks
     
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  11. wastwater

    wastwater Senior Member

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    It’s the uk 100,000 genomes project
    It’s free because I have a rare genetic condition
    Sorry I know that probably doesn’t help you but as a whole I know the price of a genome scan is coming down
     
    Last edited: Feb 28, 2018
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  12. Learner1

    Learner1 Forum Support Assistant

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    I'm interested in knowing if I have any of the SNPs Neil McGregor or any of the other researchers have found to be associated with ME/CFS, and what pathways to relate to.

    Seems like it would be useful for so many of us. :hug::hug::hug::hug::hug:


    On another note, this popped up on my Google feed today. Wonder if she can help...

    https://directorsblog.nih.gov/2018/03/01/creative-minds-looking-for-common-threads-in-rare-diseases/
     
  13. wigglethemouse

    wigglethemouse Senior Member

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    @Learner1 I did ask if there would be a Precisely tie in with data such as that presented by Neil McGregor at the OMF symposium last August - such as the significance of G-Protein Receptor mutations to sensory issues, and some feedback on MTHFR mutations, and she responded that this was "right in line with what we’re developing" with the Helix tie-in.

    Precisely had also said they were hoping to release the app in 1H2018, hopefully this Spring. That's all I know.

    My 23andme data was recent and came from the v5 chip. There was insufficient SNP data to tie into either the Melbourne Bioanalytics gene data or the Gold Coast gene data when I tried to see what I could learn. Here's hoping Helix will cover those SNP's.
     
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  14. Learner1

    Learner1 Forum Support Assistant

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    Do you happen to know if v2, 3, or 4 will work?
     
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  15. wigglethemouse

    wigglethemouse Senior Member

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    I'm afraid I don't know. I suspect v4 is no good for Melbourne Bioanalytics gene analysis as I seem to remember Neil McGregor saying that they could no longer get the data they needed to continue the analysis (OMF August presentation?).

    FYI - Livewello has a template for "Genes Associated With Chronic Fatigue Syndrome (CFS) OR ME (Myalgic Encephalopathy) Griffiths University Study TRPA1 TRPC4 TRPM3" - I only had data for three items, all mutated. Would have liked to see more.
     
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  16. pattismith

    pattismith Senior Member

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    Would you share your mutations on these genes?
     
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  17. wigglethemouse

    wigglethemouse Senior Member

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    Here are my mutations according to the "Griffiths" template on Livewello
    Griffiths.PNG
     
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  18. pattismith

    pattismith Senior Member

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  19. wigglethemouse

    wigglethemouse Senior Member

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    @pattismith

    Here is line 1824 in my raw text file. Maybe you can look at this location or search the other number.
    rs1504401 9 73916953 CT

    Here is the full list that I checked from the Livewello Griffiths template
    Griffiths_Full_list.PNG

    I only had data for 3 of them.
     
  20. pattismith

    pattismith Senior Member

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    Strangely my raw datas stop after genomic position "73736167", so I had to look into Enlis and found I am homozygous mutated for that one, which is not surprising as it a a very frequent mutation (80%)

    rs11142508 has a mutation frequency of 44%
    rs7865858 has a frequency of 61%

    So given the high frequency of these mutations, what we should look for is higher numbers of homozygous in CFS/ME for these snp, and maybe some interesting haplotypes (associations between some of these snp that could be more frequent in CFS/ME)
     
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