IDO2 gene mutations - SNPs

What alleles do you have for rs10109853? (just for people with ME/CFS)

  • TT

    Votes: 6 46.2%

  • CT

    Votes: 6 46.2%

  • CC

    Votes: 1 7.7%
  • Total voters
    13
dreampop said:
Sorry if I'm not too bright, but the process for checking these would be going to 23andme, going to id02 and just searchign for the snp#s?
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If you open up your 23andMe raw data as a text file, you can just search for an rs number.

A relative decided to do ours a few years ago. The rest of us hadn't a clue what the point was, to be honest! – but I thought I'd open it up to take a screenshot for you:


Screenshot 2021-05-17 at 09.27.26.png
 
I have a v4 23andme chip data file and it reports my rs10109853 IDO2 variants.
 

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I can only find two of the relevant snps (from 23andme) but on those I would fit the compound heterozygous situation. Interesting. My diagnosis is mod-severe CFS postviral onset (?Norovirus), chronic Mycoplasma, more recently Tick-Borne Illness & Ross River Virus. 61B950E1-DAB8-48F9-BF69-B90EB3102446.jpegE6BAE292-5F06-42C9-8457-626ED9CD8394.jpeg
 
Milo said:
How trustful are you guys about your 23 &ME results? Has it come to your mind that there might be errors in your results?
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I’m pretty sure I had a thread about this a year or two ago on this forum. Mine came up with a few results for severe genetic illnesses, including one which causes cancer all over the body - despite none of my family having a history of cancer. I then went searching for articles from the Guardian & the Independent etc and came across quite a few articles where it said 40% of 23andME data are false positives. I also remember seeing on one of the articles that it said the tests were designed to be used only for the results it had on the dashboard (like I think curly hair, or one of the iron related things) not the other background data. which is why I’m surprised that people may be taking this data as accurate.
 
lunarainbows said:
I’m pretty sure I had a thread about this a year or two ago on this forum. Mine came up with a few results for severe genetic illnesses, including one which causes cancer all over the body - despite none of my family having a history of cancer. I then went searching for articles from the Guardian & the Independent etc and came across quite a few articles where it said 40% of 23andME data are false positives. I also remember seeing on one of the articles that it said the tests were designed to be used only for the results it had on the dashboard (like I think curly hair, or one of the iron related things) not the other background data. which is why I’m surprised that people may be taking this data as accurate.
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Remember Ubiome? The site was closed down and the owner was facing legal challenges.
 
Thanks everyone, I have the v5 as well for 23andme.

wigglethemouse said:
I have v5 23andMe and my rs10109853 IDO2 variants don't show on that platform - not measured.
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@Milo I'm not overly trustworthy, but it felt like getting it a plugging it into a data to see it there was an very clear pathogenic mutation was something I wanted to look to try. Ideally a geneticist and lab would get it. I'm not really qualified to look at and interpret the results and use a program called promethease to do it for me, which certainly doesn't cover everything. And most mutations are a very small part of the picture.
 
Milo said:
Some, but not all? And what does WSG stand for?
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WGS = whole genome sequencing.
23&me only tests a subset of gene locations whereas WGS tests (almost) the lot.
The exact subsets 23&me chooses to test vary from test chip version to test chip version. That's why some people can find a snp on their results and others can't.
 
Milo said:
Some, but not all? And what does WSG stand for?
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Sorry, Whole Genome Sequencing (WGS). No I haven’t looked at every snp to compare my 23andme results with the WGS results, just some significant results eg carrier for Hemochromatosis.
 
23andMe does clean up some of their data over time. I went down the rabbit hole of thinking I had a significant mitochondrial variants but when I posted about it others had it as well. A few years later I downloaded the results file again from 23andMe and the erroneous variant had been corrected.

Perez et Al (Klimas team) refused to listen to all the errors in their ME/CFS 23andME paper which were obvious. Another group reanalysed their data and found almost all their conclusions were invalid.
https://www.s4me.info/threads/re-an...few-remain-bedford-et-al-2020-preprint.17526/

I've not heard about errors with these IDO2 variants in 23andMe data. The biggest issues is that their v5 array does not capture the most common variant (the one for the poll in this thread).
 
Not strictly IDO2, but this 2008 paper https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-2-95 identifies TPH2 as a gene of interest

The genetic marker data consisted of 36 autosomal SNPs located near or within a set of eight genes that were considered biologically relevant for CFS (see Methods section for details) [38]. We chose to focus on SNP rs10784941 located within the TPH2 tryptophan hydroxylase 2 gene because it had previously been shown to be associated with chronic fatigue, and it was associated with CFS severity in our data set [38, 39]. Table 1 reports the average severity correlations for each of the eight genes and its most correlated SNP. The TPH2 SNP was associated with severity (p-value = 0.010) and moderately associated with the blue module gene expressions (p-value = 0.077). The TPH2 gene functions in serotonin synthesis which is part of the hypothalamic-pituitary-adrenal (HPA) feedback system that has been consistently implicated in CFS [53, 54].
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TPH2 is responsible for breaking down tryptophan. I have a couple very uncommon snps there (one is 0% but I think that must be a mistake).
 
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