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    Created in 2008, Phoenix Rising is the largest and oldest forum dedicated to furthering the understanding of and finding treatments for complex chronic illnesses such as chronic fatigue syndrome (ME/CFS), fibromyalgia (FM), long COVID, postural orthostatic tachycardia syndrome (POTS), mast cell activation syndrome (MCAS), and allied diseases.

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  1. K

    Anxiety/panic attacks before coming down with CFS

    I vote that anxiety, panic disorder, and GAD should be added to the diagnostic criteria as a co-morbidity rather than be listed as a differential diagnosis.
  2. K

    Anxiety/panic attacks before coming down with CFS

    I believe GAD is probably more often a result than a risk factor. Chicken vs egg.
  3. K

    Anxiety/panic attacks before coming down with CFS

    At least for my ME, anxiety and panic were big symptoms. I think shouldn't be surprising as I believe that many have symptoms of chemical sensitivity and neurotoxicity. And a neurotoxic chemical exposure (such as pesticides, etc) can put the sympathetic or parasympathetic into overdrive...
  4. K

    Olfactory-Related Quality of Life in Multiple Chemical Sensitivity: A Genetic-Acquired Factors Model

    A new and relevant study out of Italy relating to Olfactory, Phase I and Phase II detoxification, glutathione polymorphisms, MTHFR, etc in MCS. https://www.mdpi.com/1422-0067/21/1/156/htm
  5. K

    Big Data App to Explore Genomes for Clinical Relevance, Rare Variants, Drug Response, etc (Free)

    I can't edit the original post. So I thought I'd mention that a couple weeks ago, I put the project on a permanent domain and named it GenVue Discovery. It's the first GenVue product but I'm working on new things. https://genvue.geneticgenie.org
  6. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    I made a new spreadsheet with 30 genomes. 23andMe, Ancestry, and FT-DNA, which should add a little more statistical relevance. I haven't update the spreadsheet with the new information yet as it's a bit tricky. Interesting, in both spreadheets, there is variant that is 16x more prevalent than...
  7. K

    Big Data App to Explore Genomes for Clinical Relevance, Rare Variants, Drug Response, etc (Free)

    Strange. If you PM me I can take a look at this and fix the issue if you are ok with sharing your data. It should work with Genos files though. How long ago were you sequenced?
  8. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    I found this about olfactory receptor pseudogenes. Please read my post about the increase in frequency of these pseudogenes and MMP26 on page 1. I wonder if these increases in frequency could be causing the hyperosmia and Idiopathic Environmental Intolerance (IEI/MCS) in ME/CFS. What if these...
  9. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    Factoring in processing time, I could make a table like this in probably an hour or two if I had the data.... I just have to dump those genomes in a database and run a query. It would actually be pretty simple. That said, I know 25 (or less) is a small sample size. But I do believe I have...
  10. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    Bug fixed. @Moof you might want to take a look at those 3 variants again.
  11. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    The spreadsheet ignores and does not tally no calls, so that's not the case. :) edit: Spoke too soon. It is tallying the no calls. Argh! I thought I got that right! I'll have to correct.
  12. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    OpenSNP makes rs1951708 falsely look like a miscall. But it most definitely is not when looking at all the data! rs196912 and rs196939 are real too. But it looks like they may have what's called linkage disequilibrium, Meaning they are SNPs that are inherited together rather than randomly...
  13. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    An excerpt from the abstract of a study titled Matrix metalloproteinase-26, a novel MMP, is constitutively expressed in the human intervertebral disc in vivo and in vitro. https://www.ncbi.nlm.nih.gov/pubmed/21945733
  14. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    So I've done more research on what's going on. And the variants I am finding are actually not MMP26 variants. BUT, they were within olfactory pseudogenes within first intron for MMP26. So basically, there are a whole bunch of olfactory genes/SNPs embedded within an MMP26 intron! I'm a bit over...
  15. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    It means that there is a difference in ME/CFS vs the normal population. Could be good, could be bad. Depending on how many genomes, that seems significant if it's not a miscall. I would add a comment for that SNP on the RS# cell with the comment button on the spreadsheet like I do. It's hard to...
  16. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    Big addition/addendum to the post above. There is strong linkage disequilibrium (LD) in MMP26. So factoring in LD, I'd give a more conservative number of 5 for the amount of variants with a relevance score over 2 (which is still significant). And there are a couple more SNPs that are 1.75x...
  17. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    Looking through the data and doing my own queries, I have preliminarily determined that the gene MMP26 is one of the most "mutated" genes in the ME/CFS 23andMe coding region. Followed by OR51F1, and ADAMTS13. ME/CFS patients have 9 (!) MMP26 SNPs with a relevance score greater than 2. This...
  18. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    I followed many suggestions you made. No frequencies in percentages yet. I think what I might add miscalls to a second spreadsheet? And leave checkboxes for others to indicate other miscalls. Should make the spreadsheet more clean. I don't know how much others can edit the sheet as I have most...
  19. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    @Moof I've noticed the multiple variant bug. Sometimes it's because there are multiple gene names, others it's because the database is off. And I think sometimes it's because ne It's not that big of a deal if you can just ignore it. ;) But maybe I should allow people to edit the gene name...
  20. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    All those very rare ones at the top are probably miscalls. Instead of comparing it to your own data, it would help to compare it to OpenSNP data. If 100% of ME/CFS patients have something that 1 out of 10,000 have, it's a miscall and the "bad?" checkbox should be checked. Remember to multiple...
  21. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    I locked the sheet and left two columns for anonymous people to edit in. I also realized that I slightly miscalculated frequencies (who would have thought calculating frequencies would be so hard?). Unfortunately, this fix makes the IDO2 SNPs (and others) not very statistical significant in...
  22. K

    ME/CFS Variant Spreadsheet with Frequencies, CADD scores, Variant Effect Prediction, etc (Citizen Science)

    I'm wondering if anyone is willing to contribute to citizen science. I created a Spreadsheet of Exomic variants from 25 ME/CFS 23andMe genomes hosted on OpenSNP. There are relevance rankings, RS#'s, Ref/Alt allele, ME/CFS frequencies, gnomAD population frequencies, type of mutation, as well as...
  23. K

    Studies find HHV-7 active in ME, yet ME Drs often don't test for it & Valcyte doesn't work for HHV-7

    Yeah, not RNA viruses unfortunately (I knew that but forgot for a second when I wrote the above post). But there are ways to get that testing. The test for Coxsackievirus was through LabCorp.
  24. K

    Studies find HHV-7 active in ME, yet ME Drs often don't test for it & Valcyte doesn't work for HHV-7

    I did shotgun analysis of my saliva myself (from unmapped WGS reads) and I noticed that I have HHV-7 DNA in my saliva. I was surprised that I never hear anything about HHV-7 and knew nothing about it. Not that I necessarily believe this means a whole lot, but it's interesting because my titers...
  25. K

    Big Data App to Explore Genomes for Clinical Relevance, Rare Variants, Drug Response, etc (Free)

    Fixed a lot of bugs and made some important fixes so 23andMe and Ancestry data a lot more accurate the past week or so. I haven't fixed some of the bugs mentioned above or lower priority bugs yet. But those are next! I also noticed some people have Genos data, and realized my app was not...
  26. K

    Big Data App to Explore Genomes for Clinical Relevance, Rare Variants, Drug Response, etc (Free)

    That appears to be a common miscall in 23andMe. I should probably filter that variant. Has almost no frequencies about around 20% on 23andMe are AG. This is not a real variant. https://www.opensnp.org/snps/i5008699
  27. K

    Big Data App to Explore Genomes for Clinical Relevance, Rare Variants, Drug Response, etc (Free)

    For some reason, medical likes to ignore the mitochondrial variants. Surprisingly, there isn't a well curated frequency databases. A lot of variants are just part of your haplogroup/subclade. And some variants are risks for disease that exist within that haplogroup or sublclade. I plan on...
  28. K

    NOD2: A Common pathway that may be disrupted in ME/CFS

    Thank you @J.G and @Nine lives for sharing information about your variants!
  29. K

    NOD2: A Common pathway that may be disrupted in ME/CFS

    It should, yes. There may have been some corrections to the app since you used it. And there's a button now to save your results as an HTML archive. It will miss the very rare NOD2 predicted pathogenic variants that are currently not classified. And it seems that some may have extraordinarily...
  30. K

    NOD2: A Common pathway that may be disrupted in ME/CFS

    That variant is in about 33% of the population and is benign. Where is shows 0.33 for frequency, you take this number and multiply by 100 for frequency in percentage. 0.33 * 100 = 33 So 33% of the population has this variant. If you click on the "ClinVar" link on that same link. You can see...