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ENLIS decoding mitochondria related genes...lost!

Discussion in 'General ME/CFS Discussion' started by pattismith, Sep 6, 2017.

  1. pattismith

    pattismith Senior Member

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    I try to explore my 23andme genome via Enlis, but I'm lost....:D

    In the mitochondrial part for example, here what I can see...Any significance?

    (I have a rare mutation of unknown significance on this gene/UQCRQ, on chromosome 5)

    @BeautifulDay

    upload_2017-9-6_20-58-15.png
     

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    Last edited: Sep 7, 2017
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  2. BeautifulDay

    BeautifulDay Senior Member

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    First day of school here. I'm about to go pick up a child. I will definitely get back to you on this with a few screen shots to help out. :)
     
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  3. pattismith

    pattismith Senior Member

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    Yes I understand how busy you are. Don't worry, my mtDNA will wait :)

    You are so generous by sharing your experience, you gave to us more energy to find more answers to our questions!

    I also have three rare variants in the mtDNA on MT-ND1 (missense mutations of unknown signification)

    "MT-ND1 mutations are a rare cause of mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS). Most cases of MELAS are caused by mutations in other mitochondrial genes, but a small number of cases resulting from mutations in the MT-ND1 gene have been reported. Fewer than five mutations, each of which alters a single DNA building block (nucleotide) in the gene, have been identified in affected individuals. These genetic changes reduce the activity of complex I, which disrupts energy production within mitochondria. Although these abnormalities have the greatest impact on tissues that require a lot of energy (such as the brain and muscles), researchers have not determined how changes in the MT-ND1 gene lead to the specific signs and symptoms of MELAS."

    and I also carry another missense rare mutation (unknown significance) of the mtDNA on MT-CYB...(some mitoD are associated with known mutations on this gene)
     

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    Last edited: Sep 7, 2017
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  4. Valentijn

    Valentijn Senior Member

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    My rare one is on MT-ND1 as well, at position 3796. It's been implicated in causing mitochondrial disease, though the strength of the evidence isn't very good.
     
  5. BeautifulDay

    BeautifulDay Senior Member

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    There are many different ways to sort the data. The first one is to see if you have any rare pathogenic mutations pop up in Enlis' already defined mutations.

    After you've gone through the process to upload your data into the system, you'll see a screen like this. Next to the word genome, will be the names of the people in your system. Here, I've whited some family members names out.

    Enlis upload genome in program.png

    If the above 1 genome was me, I'd click on the little button next to my name that looks like this:
    Enlis button.png

    Now it should look like this:
    Enlis Variation Summary.png

    This is my version using my 23andme raw data. Whole exome data provides many times more variations than this. It's not unusual for a person to have this many.

    I'd then click on the 627,912 in the above report to filter and sort those variations.

    You should be on the Variation Filter Page. On the top right side, click on "Load Filter Set" and go down and click on "All Clinically Significant".

    Enlis All Clinically Significant.png

    Then right under the tan box, there are buttons, at the top of the fifth column of buttons is "+ Allele Frequency". Click on that. I then slide it over 10% of the population having this variance allele. I use 10% as a starting point because sometimes fairly rare mutations (like 10%) combined with another rare mutation on the same gene can be the issue. Multiple issues on same gene can be the culprit. In addition, 10% in this sort is only going to leave you with a few dozen mutations that are pathogenic or a disease risk factor that you carry that are also rare.

    Then push the little grey button on the left that says "Go".

    This should bring up your variances. A word of caution here. Some of the issues will look like major issues, and then with some research into the mutation in the medical literature you'll find out the the mutation only causes a 4% chance of increased risk for a disease. Then off the wall mutations might pop up that say you carry a mutation where everyone dies by age 3. Well that one is clearly wrong. Then keep in mind that 23andme and even medical labs have been found to be wrong in the mutations they report people as having. No hyperventilating over anything, until everything has been fully vetted and checked and double checked and lab results confirmed by a medical lab.

    Most things will be noted as interesting, yet, put in the back of your mind as something to be remembered.

    Enlis Clinical Significance.png

    If you click on the arrow next to "Pathogenic" or "Risk Factor" up will pop up the trait name. This one above comes up Becker Muscular Dystrophy. So then of course, off I go Googling "Becker Muscular Dystrophy" and it states --
    "Becker muscular dystrophy is an X-linked recessive inherited disorder characterized by slowly progressive muscle weakness of the legs and pelvis. It is a type of dystrophinopathy. This is caused by mutations in the dystrophin gene, which encodes the protein dystrophin."

    Well that's interesting. It falls under Mitochondrial Disease and fits some family symptoms. Definitely something I'd want to bring up with the Mito Doctor.

    So I do that for each one. And it's time consuming and something I have to keep coming back to over time. I put the printout of the list in a folder and then for each one that pops up, I put why I discarded it or why it's interesting.

    Please note above, that one of them is listed as "SNP x2". That's important. Only 5.17% of the population has one of those mutations and I have two of those mutations. Being homozygous (two of them) for a rare mutation can be more concerning for disease causing mutations. Spend extra time ruling those one's out. The mutation above with x2 is for an increased risk of inflammatory bowel disease.

    Then for all the interesting mutations that I noted, I then look to see if they are on any genes noted by the doctors to cause Mitochondrial Disease. For example, for the Becker's Muscular Dystrophy mutation, I'm looking for the gene MT-ND1. For the Inflammatory Bowel Disease, I'm looking for NOD2. So I go to:
    https://mseqdr.org/ and I click around until I get to the genes list (or I go directly by clicking on)
    https://mseqdr.org/mb.php?url=index.php

    I enter MT-ND1 in the spot for "Symbol" and I push enter. Up pops this.
    Mito Database - MT-ND1.png
    What this says is that Mutations on the MT-ND1 gene have been reported by Mitochondrial Disease experts as causing Mitochondrial Disease. Under the columns for variants, it states that experts have entered 87 variants -- so a lot of Mito has been found due to variants on this gene. The column for Associated Diseases include LHON, MELAS.....

    So then click on the "87" and up pops this page.
    MT-ND1 Homepage.png

    Where it says "Total Number of Public Variances Reported" click on the number. In this case it's click on 87. Then up pops the 87 variants that are currently entered into the database. You'll need to do it yourself to see all 87.
    MT-ND1 Variants.png

    Next I want to see if my MT-ND1 mutation has been entered in the database. If it's not, it might mean they just haven't come across it yet, or it's not entered yet, or it's on a list at some university still waiting to be studied.

    To find the DNA change name I have for my mutation, I have to go back to that Enlis page (above), where it has Becker's Muscular Dystrophy. At the beginning of that line it says it's Chromosome Position "M: 3,394". So I click on M: 3,394 on that Enlis page and up pops the name.

    Continued.....
     
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  6. BeautifulDay

    BeautifulDay Senior Member

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    ..... Continued

    variation detail at 3394.png
    I then look up the protein Tyr30His (from above) in the NIH database and come up with this below.

    TYR30HIS.png

    So here are some names that I want to see if they are on the MitoD database. And I go down the list of names see if any of them are on that list from MitoD and look, yes, the one called 88T>C has been entered by a MitoD expert into the database.

    88T greater than sign C.png

    Next I click on the 88T>C in the database and up pops this.
    88T greater than C clicked on.png

    So what I do with this one is make a folder of into for the mito doctor's genetics doctor with the Enlis page showing I've got it, a printout of the page showing it in the MitoD database, and this page above, and all the other relevant studies I find on it. Then when my Mito appointment comes up, the geneticist agrees to fight to have it tested for via Medical Lab. She goes and does her own research to make sure my research flows through (i'm not perfect and there can be errors), and the Mito Geneticists are not familiar with every mutation. They have to research too. So it's a lot of work to get this far in finding one Mito Mutation.

    This mutation is in mtDNA so I would have passed this one onto each child. Then it gets into heteroplasmy for this one. The work never ends.

    And yes, multiple Mito mutations in mtDNA and nDNA do happen in families like mine.
     
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  7. BeautifulDay

    BeautifulDay Senior Member

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    I then go back and see if there are any mutations in the MitoD database for "Inflammatory Bowel Disease NOD2 from the Enlis findings. I enter NOD2 into the gene symbol and nothing comes up. It can just mean none have been entered. Every year the doctors find new genes impacting Mito.

    So next I do a search on Google Scholar for NOD2 and Mitochondrial Disease and up pops a paper titled "Mitochondrial DNA mutations in human neoplasia". Neoplasmia is abnormal growths or tissue. https://s3.amazonaws.com/academia.e...=Mitochondrial_DNA_mutations_in_human_neo.pdf

    That paper states that: "The genetics of breast cancer has been widely studied for the last 20 years. Many pathways and genes have been implicated in the process of breast cancer development. These include BRCA1, BRCA2, CHEK2, CDKN2A (p16), NOD2, and NBS1 (Lubinski et al. 2004; Debniak et al. 2005; Gorski et al. 2005; Huzarski et al. 2005).

    So there is NOD2. It doesn't say it's Mitochondrial Disease. But in addition to Inflammatory Bowel, breast cancer has happened in our family (as well as colon cancer). There are theories among Mito Doctors that with low energy, the cells and systems that clear out cancer from our bodies don't work as well. Couple that with mutations that increase cancer and maybe I shouldn't skip my mammo appointment again.

    So this goes in the interesting information and again backs up the idea that I should eat well and exercise (to my ability) to help my system stay working to the best of it's ability under the circumstances.
     
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  8. pattismith

    pattismith Senior Member

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    So much to read! Thank you for the special Enlis training @BeautifulDay :)

    it's already a stronger evidence than my three "unknown" :lol:
     
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  9. pattismith

    pattismith Senior Member

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    It's very interesting, I can see that for my 4 rare missense mtDNA mutations, the allele frequency is 0.00%...I don't think I will ever know their real significance!
    docgenes4.jpg
     
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  10. raghav

    raghav Senior Member

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    India
    Dear Friends,
    I want to find out my mitochondrial gene defects. What is the name of the test that I should order ? Please help. A company called xcode www.xcode.in is offering genetic tests in India and the cost seems affordable.
     
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  11. pattismith

    pattismith Senior Member

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    I wish we could find a reliable test for mito gene defects. Unfortunatly, the mito genetic is more complicated than nuclear DNA genetic for several reasons...
    One of those is that your mito genes maybe different from a tissu/organ to another, another reason would be that there are less scientific studies for mito genes than nuclear DNA genes (it will probably improve soon hopefully)...So even though some very bad mutations have already been found, some susceptibility genes (increased risk) may not have been identifyed.
    The fact that mito genes are more prone to mutations than nuclear DNA genes can complexify more the situation.
     
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  12. Valentijn

    Valentijn Senior Member

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    @pattismith - There's no data for MTND1 3377, but it looks like your mutation there would substitute a glutamate with a glycine. That change is rated as -2 on the BLOSUM62 scale, meaning that's a big change in the type of amino acid being substituted, so that can affect how well the MTND1 enzyme holds together and behaves. The BLOSUM62 scale runs from -3 to +3 for substitutions, with -3 being the most different and +3 being the most similar substitutions.

    The allele right before it at 3376 (not one you have listed there), which is part of the same codon and accordingly also codes for the same glutamate, is labeled pathogenic, despite it being a milder substitution (+1). Due to your mutation at 3377 being for the same amino acid, but even more dissimilar than the listed mutation at 3376, it seems likely that your mutation would cause at least as much of a problem, if not more so. The evidence for 3376 being pathogenic is based on a single case study, but the chemical and genetic analysis they did was extremely thorough and pretty definitively pinpointed 3376 as a heteroplasmic mutation present in nearly all muscle cells but much less so in blood and urine.

    dbSNP (your mutation is to the right of this one, and unlabeled) - https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=397515612
    Case study for 3376 - https://www.nature.com/ejhg/journal/v13/n5/full/5201363a.html

    So it seems like a very suspicious mutation. I haven't looked at the others yet.
     
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  13. Valentijn

    Valentijn Senior Member

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    @pattismith - You have exactly the same type of mutation at 3734, where a GAA codon coding for glutamate is changed into a GGA to make glycine. And again, the SNP right in front of it at 3733 has a flagged pathogenic mutation from a milder substution (GAA -> AAA, glutamate -> Lysine). The evidence for the 3733 mutation is also fairly strong - it was only found in two families, but they did a lot of chemical investigations to see how much the mutation impacted enzyme function.

    Basically the 3733 mutation doesn't have an impact unless something happens to inhibit MTND1, and then it's a fairly mild effect compared to other mutations when faced with similar inhibition. So that one might not have an impact unless subject to some source of biological stress, if I'm understanding it correctly. And there's no indication that it's been involved in anything except LHON (mitochondrial eye disease), perhaps due to it being such a mild mutation and eyes being the most sensitive to such things.

    Study - http://sci-hub.io/10.1002/ana.20236
    OMIM - https://www.omim.org/entry/516000#0015
    dbSNP - https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=199476125
    (Again, these are all for the SNP in front of your mutation, which is part of the same codon.)
     
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  14. Valentijn

    Valentijn Senior Member

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    And exactly the same situation at 3947. It changes glutamate to glycine, and the mutation right in front of it at 3946 on the same codon is confirmed to be pathogenic via chemical and enzyme analysis in a case study. The patient in that study had MELAS.

    Case Study - http://jmg.bmj.com/content/41/10/784.long
    OMIM - https://www.omim.org/entry/516000#0013
    dbSNP - https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=199476123
    (Yet again, these are all for the SNP in front of your mutation, which is part of the same codon.)
     
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  15. Valentijn

    Valentijn Senior Member

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    15,198 is another interesting one. No data for it, but the preceding SNP on the same codon at 15,197 is flagged pathogenic. The known mutation at 15,197 is rated -1 for the degree of difference on the BLOSUM62 chart, whereas your mutation at 15,198 rates -2, so would be even more of a difference. The evidence for the mutation at 15,197 is a single case study involving exercise intolerance. Again, they did a pretty thorough investigation of the chemistry and genetics to confirm that the mutation wasn't a coincidence.

    Case study - https://www.nature.com/ejhg/journal/v9/n7/pdf/5200678a.pdf
    OMIM - https://www.omim.org/entry/516020#0009
    dbSNP - https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=207460001
    (Again, these are all for the SNP in front of your mutation, which is part of the same codon.)
     
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  16. pattismith

    pattismith Senior Member

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    :wide-eyed: all this is crazy interesting!
    Okay, 23andme may be wrong, maybe I don't have these mutations at all...

    It may be also that mutations found in saliva are not in my muscles/gut/brain...

    I was exposed to formaldehyde and organoP when I was younger (spray and gaz), they are known to damage mito, so maybe they produced local mutations?

    But, if you are right, I may change my mind. I had convinced myself I won't go to a mito specialist because I have no time to loose (I live 850 km far from Paris)....But It may be that the travel and the expenses are worth it...:)

    My lactates today did a peak to 4.8 mmol/l (I have done some changes in my supplements that may not be good), so I'm going to have a rest first and then think about all this.

    Thank you so much for your help valentijn, my poor brain is no more able to dig so much, I'm afraid.o_O
     
    Last edited: Sep 8, 2017
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  17. anni66

    anni66 mum to ME daughter

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    Amazing work Valentijn and Beautiful day, almost makes me wish i had done biochemistry and not architecture !
    I really need to get my head around this stuff for both my aunt and my daughter: very different routes to illness but no doubt some mito genetics/ epigenetics in common.
    Many thanks for the explanations
     
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  18. Valentijn

    Valentijn Senior Member

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    Never too late to learn ... I avoided biology as much as possible before getting sick. Nearly failed it in high school even :p
     
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  19. anni66

    anni66 mum to ME daughter

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    My knowledge is improving- mainly thanks to this forum and YouTube! Necessity is a great motivator .
    I' m currently trying to link up EBV/ chickenpox and liver function as my daughter had issues with benzoates after chickenpox, ( age 4), elimination and reintroduction in small amounts worked well. Now EBV seems to have reinstigated benzoate and salicylate issues, potentially hormonal and thyroid ( i didn' t realise what liver did before). My aunt has significant detox issues so lots to look at.....
     
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  20. TrixieStix

    TrixieStix Senior Member

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    the Genetic Medicine Specialist I saw at a large univeristy teaching hospital told me that I could assume my 23andme mutation information is correct. But that saod I do know that there are a few known flukes in 23andme's reading of specific genes. A few are reported on snpedia.com as likely being misreported/flipped or something like that.
     

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