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I am booked in to see Prof. de Meirleir in January

Discussion in 'ME/CFS Doctors' started by snowathlete, Nov 27, 2012.

  1. maryb

    maryb iherb code TAK122

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    Can someone explain what haplotypes are please?
     
  2. Sushi

    Sushi Moderator and Senior Member Albuquerque

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    He didn't comment to me, but he is in touch with Shoemaker, so he has probably tracked this. Sorry, I just don't know.

    Sushi
     
  3. Sushi

    Sushi Moderator and Senior Member Albuquerque

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    It is confusing as it is in Dutch! Looks like he tested HLA-Dr at UZ Brussel.

    Best,
    Sushi
     
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  4. Thomas

    Thomas

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    @maryb its a genetic test that shows susceptibility to certain things but for us its important as it relates to mold, lyme and other biotoxin illnesses and our response to antibiotics and abilities to detoxify neurotoxins. Look at survivingmold.com and the work of Ritchie Shoemaker for more info.
     
  5. maryb

    maryb iherb code TAK122

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    Will it be on my 23 and me test?
     
  6. cigana

    cigana Senior Member

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    There was some discussion on another thread about whether or not it could be worked out from 23andme results and I think the answer was no.
     
  7. maryb

    maryb iherb code TAK122

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    okay thanks, have a massive problem with mould just wondering if I should get it done? but where?
     
  8. cigana

    cigana Senior Member

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  9. maryb

    maryb iherb code TAK122

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    @Thomas
    thanks for the link - I'm not up to reading a lot but am familiar with a lot of Shoemaker's views. So are you saying this gene is important as it affects how we respond to antibiotics?
     
  10. Thomas

    Thomas

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    @maryb yes, essentially. In so much that antibiotics alone won't resolve the problem. As for how to get around that, that's another huge animal altogether.
     
  11. maryb

    maryb iherb code TAK122

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    @Thomas
    so Shoemaker doesn't have the answer?
     
  12. Thomas

    Thomas

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    Maybe for some people sure, who knows. He claims to have helped people. I don't think anyone has "the answer" yet. Trial and error until we/they figure more things out.
     
  13. Valentijn

    Valentijn Activity Level: 3

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    HLA-DR haplotypes are determined based on up to 5 genes. They aren't really tested well enough by 23andMe to determine genotypes with certainty.

    For HLA-DRA you have DRA*010101 and DRA*010203. But for myself and a couple other patients, it can only be narrowed down to three possibilities, of which we have any two.

    23andMe only tests in one relevant location on HLA-DRB1, and they're looking at insertion/deletion instead of allele, which is not helpful for HLA purposes. They don't test HLA-DRB3 or HLA-DRB4 at all, and just one SNP on HLA-DRB5.

    So a LOT more data is needed to figure out HLA-DR haplotypes. Many mainstream testing services probably do it, as that sort of testing is necessary for organ transplants.
     
  14. cigana

    cigana Senior Member

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    Which lab did you use?
     
  15. Valentijn

    Valentijn Activity Level: 3

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    I haven't used any labs - basically I don't know any of my HLA types.
     
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  16. maryb

    maryb iherb code TAK122

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    @Valentijn

    "HLA-DR haplotypes are determined based on up to 5 genes. They aren't really tested well enough by 23andMe to determine genotypes with certainty.
    For HLA-DRA you have DRA*010101 and DRA*010203. But for myself and a couple other patients, it can only be narrowed down to three possibilities, of which we have any two.
    23andMe only tests in one relevant location on HLA-DRB1, and they're looking at insertion/deletion instead of allele, which is not helpful for HLA purposes. They don't test HLA-DRB3 or HLA-DRB4 at all, and just one SNP on HLA-DRB5.
    So a LOT more data is needed to figure out HLA-DR haplotypes. Many mainstream testing services probably do it, as that sort of testing is necessary for organ transplants"

    Can you explain that to me again - I can't understand it, having a bad fog day.....
     
  17. Valentijn

    Valentijn Activity Level: 3

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    HLA phenotypes can be determined based on the HLA genes. An HLA gene might have 1000 or so alleles, and due to pretty extensive documenting of it, we know that certain alleles in certain places result in the different pre-defined and categorized phenotypes.

    The easiest and most certain way to figure out the phenotype is to look at the entirety of the relevant HLA gene, and see which version it matches up with, since there can be dozens of SNPs to look at to determine which phenotype someone has. So instead of looking at a single letter (SNP) to determine risk or other characteristics, you're looking at an entire sentence of consecutive alleles, where all the possible variations of that sentence are already known.

    As an example, the possible "sentences" might be:
    A) There is a dog on the roof.
    B) There is a cat on the roof.
    C) There is a dog in the roof.
    D) There is a dog in the room.
    E) There is a dog on the roof and it smells funny.


    These different versions of the gene will basically line up like the sentences above. Some might be a bit longer or shorter, but most will have tiny variations resulting in the different phenotypes. If you can see the full sentence with complete sequencing of the gene, then it's simple to see what version you have - it's spelled out!

    But if you just test a few SNPs, it can get more complicated. Testing focused on HLA could get away with incomplete testing of the gene, because it's known where the important variations are. Thus we might figure out the sentence by testing in certain positions (numbered) while ignoring the unimportant ones:
    There is a 1 2n the roo34
    So to figure out the haplotype from the above options, we can just look at 1 for "dog" or "cat", 2 for "i(n)" or "o(n)", 3 for "(roo)f" or "(roo)m", and 4 tells us if the sentence stops or continues.

    But 23andMe isn't really testing the places that make a difference - they're mostly just telling you that "T???? ?s a ??? o? ??? ????." So entirely the wrong data we need to determine HLA phenotypes, though little bits and pieces can give clues. For HLA-DRA we get enough clues from 23andMe to figure out some patients phenotypes but not others. For the other HLA genes, there doesn't seem to be any useful clues from 23andMe.

    The biggest issue is that 23andMe is very binary. If it's not A, it's G. If it's not I, it's D. For the vast majority of the SNPs that isn't a problem, but HLA SNPs are extremely whacky. Most will have 3 or 4 possible alleles instead of 2, and I don't think 23andMe can handle that at all. Hence they're not capable of testing for HLA phenotypes with the technology they use, and just avoid testing the useful HLA SNPs to keep things simple for them.
     
    Last edited: May 12, 2014
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  18. maryb

    maryb iherb code TAK122

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    @Valentijn
    thanks for taking the time to explain that - I'll keep looking at it until it sinks in:)
     
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  19. Jenny

    Jenny Senior Member

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    Yes, I was diagnosed with Lyme and other infections at the Breakspear. But I have very little confidence in their testing. And they weren't able to give me any sensible interpretations of my test results. I had long courses of about 6 different abx.

    Gave up with them and with abx years ago.
     
  20. maryb

    maryb iherb code TAK122

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    @Jenny
    thanks - I think the testing may have improved since?? But not good you didn't see any improvement, so many report this, and then others recover....
    Hope you've found something to help you improve.
     

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