A Network Medicine Approach to Investigating ME/CFS Pathogenesis in Severely Ill Patients: A Pilot Study, 2024, Hung, Davis, Xiao

Maybe the statistics aren't that complicated, since we're just looking at a single variant and not collapsing multiple variants in a gene.

For this one specific variant, a Fisher's exact test comparing allele count in this study (7/40) to total allele count in gnomAD (94/1613706) gives an odds ratio of 3641.3 and a p-value of 5.66e-23.

As far as the number of variants they looked at, from methods:
High-confidence variants were derived by applying a series of filters as follows:
  • Variants had to be supported by reads from both strands.
  • Conflicting variants (i.e., multiple types of variants were called at the same position) were excluded.
  • Variants located within repetitive regions were excluded.
  • Variants in the proximity of miscalls were removed to eliminate sequencing errors in specific regions.
  • To reduce miscalls resulting from in-vitro contaminations or other systematic errors, a reasonable variant must have at least one homozygous sample in which both alleles are consistent with the reference.
In total, 2,798,019 high-confidence variants passed these five filters and were subsequently used in the following variant analysis.
Click to expand...

I think we can do multiple test correction based on 2,298,019 tests. But I don't think the specific number matters much here because of how significant the finding is. Wikipedia says there are around 324 million known human variants. Even if we assume they tested every human variant and we did Bonferroni correction on the above p-value for 324 million tests, that would still leave the corrected p-value extremely significant: Bonferroni p=1.83e-14

(I'm not sure if any of the 7 individuals with the variant are related. That'd make the finding less significant, though it could still be impressive depending on how many individuals are related.)

I think we need to allow for the possibility of genotyping error at this variant, because of how big of a deal this would be if it was real. It'd be a cause identified in a significant proportion of people with severe ME/CFS.

I would think it'd be relatively easy and a major priority to validate this specific variant in other cohorts. Considering how rare the variant is in the general population, I think if even 1 out of 50 other people with severe ME/CFS had this variant (and we were sure the sequencing result in the follow-up wasn't an error), that'd be good evidence of this being real.
 
Last edited:
forestglip said:
From looking at the supplementary table, the seven patients with an MFRP variant share one specific pathogenic variant in this gene: rs730882143
Click to expand...
Here is what Genome Explorer (the very limited free version) reports for this snip for me. No idea how to interpret it, never seen a snp reported in this way before (but I hardly know anything about this sort of thing). According to the website’s guide:

“D - Represents a deletion of one or more letters. Click on the D to view the sequence of the deletion.” [in my case it shows D=G]

“I - Represents an insertion of one or more letters. Click on the I to view the sequence of the insertion.” [in my case it shows I=GA for the I below ‘Alt’, and I=A I=A for the double I below ‘Your Data’]

It doesn’t say anywhere what the superscript 0 and 1 beside the I under ‘Alt’ and ‘Your Data’ mean. I don’t know either why some snps, like this one, are repeated on multiple lines

Anyway, just putting it here in case someone else can figure out if this strengthens the suggestion that this snp could be overrepresented in ME/CFS, or otherwise
Screenshot rs730882143.png
 
forestglip said:
Potentially very important if around 35% of severe ME/CFS patients really share one specific ultra-rare variant. But I don't really know how the statistics work with these studies, such as with multiple test correction. Maybe they looked at a large enough number of variants that something like this would be expected to come up by chance?
Click to expand...

It raises the possibility that severe ME/CFS involves a quantum step further in mechanism from most ME/CFS, involving susceptibility of certain neurological target pathways such as retinal signalling. I think it is quite likely that this gene is involved in other parts of brain (the eye is part of the brain) like auditory routes, for instance. There are other inherited defects that can affect both retina and hearing. The functions found so far may be very incomplete.

The sort of severe patients recruited here might be rare or absent in the DecodeME cohort?

I am a bit surprised we did not home in on this more at the time.
It is a pity that the paper's discussion seems to raise old tropes rather than focus in on detail.
 
Andy said:
12.4% of participants were severe, 0.4% were very severe (NICE severity levels).
Click to expand...

Yes, I should clarify. Since this study was just 20 cases my guess is that they may have been in the NICE very severe grouping. I guess that it is also conceivable that this particular variant gene has appeared relatively recently and so specific to a geographic area. Hopefully, none of these 20 patients were closely related, which would screw things up too.
 
Jonathan Edwards said:
It raises the possibility that severe ME/CFS involves a quantum step further in mechanism from most ME/CFS, involving susceptibility of certain neurological target pathways such as retinal signalling. I think it is quite likely that this gene is involved in other parts of brain (the eye is part of the brain) like auditory routes, for instance. There are other inherited defects that can affect both retina and hearing.
Click to expand...


This would make sense to me. When I deterioated to severe, light sensitivity and eye pain were two of the things that immediately became most prominent and intense, as well as sensitivity to sound.

I did have a leser degree of sound and light sensitivity as a mild pwME, and as a moderate these things became worse. I even had some during my prodromal phase- gigs became less pleasant experiences and people always said that I kept the lights in my room low - but severe was absolutely a quantum leap in sensory sensitivity. Maybe this gene is why? That would be vital would it not?

Also, It's reassuring to note that people who improve or go into remission do not report still having severe level sound and light sensitivity (which would be impossible to ignore). Which suggests it's probably reversible.

Edit: Could this gene have something to do with the common reports of visual snow syndrome in pwME?
 
Jonathan Edwards said:
Yes, I should clarify. Since this study was just 20 cases my guess is that they may have been in the NICE very severe grouping. I guess that it is also conceivable that this particular variant gene has appeared relatively recently and so specific to a geographic area. Hopefully, none of these 20 patients were closely related, which would screw things up too.
Click to expand...
Is that geographic issue and relatedness something that could be clarified with the authors?
 
A Comprehensive Examination of Severely Ill ME/CFS Patients, 2021

That's the paper that describes the SIPS cohort.

Karnofsky Performance status index (%)
ME/CFS
​
 30:  Severely disabled; hospital admission is indicated, although death is not imminent ....5.0%

 40:  Disabled; requires special care and assistance .....30.0%
​
 50:  Require considerable assistance and frequent medical care. ....15.0%

 60:  Require occasional assistance, but is able to care for most personal needs. ....50.0%
​

Notably, 100% of the patients (19/19) suffer from the presence of significant pain and 89% (17/19) had sensitivity to light, noise, vibration, odor, taste, and touch
Click to expand...
(The 20th patient was very severely affected and was not able to complete the surveys.)

The median daily steps taken by the SIPS patients was 912
Click to expand...
 
Ravn said:
Here is what Genome Explorer (the very limited free version) reports for this snip for me. No idea how to interpret it, never seen a snp reported in this way before (but I hardly know anything about this sort of thing). According to the website’s guide:

“D - Represents a deletion of one or more letters. Click on the D to view the sequence of the deletion.” [in my case it shows D=G]

“I - Represents an insertion of one or more letters. Click on the I to view the sequence of the insertion.” [in my case it shows I=GA for the I below ‘Alt’, and I=A I=A for the double I below ‘Your Data’]

It doesn’t say anywhere what the superscript 0 and 1 beside the I under ‘Alt’ and ‘Your Data’ mean. I don’t know either why some snps, like this one, are repeated on multiple lines

Anyway, just putting it here in case someone else can figure out if this strengthens the suggestion that this snp could be overrepresented in ME/CFS, or otherwise
Click to expand...
No, it doesn't look like you have the variant. The reference is G, the very rare variant is GA (insertion of an A after the G), as it shows under Alt, and you have A (substitution of the G with an A), as it shows under Your Data. The one you have is fairly common. The fourth line is showing this variant in a more straightforward way.

I'll be surprised if the paper's finding for the MFRP variant isn't an artifact. I wonder why they didn't discuss how extreme the result is in the paper.

Another one is the BRCA1 variant shared by 3 patients: rs397509200 (insertion of G). As far as I can tell, the frequency of this variant is virtually zero in the general population. dbSNP links to a paper that reports finding this variant in a single family (Reeves 2004), but apart from that it appears to be too rare to have been seen in the hundreds of thousands of people with data in gnomAD.
 
Kitty said:
It does, specially as the usual consequences of pathogenic mutations seem to be significant visual impairments that are unlikely to be missed even if they're not diagnosed as genetic.
Click to expand...
Skimming some of the literature on this, the studies tend to be focussed on the people with the obvious structural eye issues - I guess these are the people who get to the specialists who know about the problem. Some have tested family members, one paper I saw noted the wide variation in phenotype in family members with the variation. From what I have seen, it seems likely that having the variant is no guarantee of structural eye problems.

I agree with @forestglip that these incidences of pathogenic variants look a bit suspect. I was surprised to see the BRCA gene variant show up. Identifying the variants isn't completely straightforward as forestglip's response to Ravn illustrates. If someone is not well informed, they could easily make a mistake.

I do think that we need to get a response from the authors about this.
 
forestglip said:
No, it doesn't look like you have the variant.
Click to expand...
Thanks. I was hoping someone would say that - I’m rather fond of my eyesight!

Taking a closer look, it is all very perplexing though and maybe what all this really tells us is that this particular position is difficult to map and/or interpret? And that any hits here should be taken with more than a grain of salt?

So... confusingly, in the paper’s supplementary table 1 the Ref for rs730882143 is listed as a deletion and the Alt as A, whereas the NCBI mentions 2 alleles: insA and insGA, with the first one being the rare and presumably pathogenic one

Even more confusing is comparing the 4th line to the ones above (screenshot1). Same position but different rs number, different frequency, different impact & rated as (likely) benign by NCBI

But wait, there’s more. There’s actually another hit for that same position. Genome Explorer only gives an RCV link (NCBI) but it appears to be this snp: rs2497092562. It’s listed as being of ‘uncertain significance’, with alleles given as GG>CA without any frequency info. It didn’t fit into the first screenshot, so showing it here, it’s the last line on this second screenshot below. In this case the I&D stand for: Ref I=GG, Alt D=CA, Your Data I=GG I=GG

For now I think I agree with forestglip
forestglip said:
I'll be surprised if the paper's finding for the MFRP variant isn't an artifact. I wonder why they didn't discuss how extreme the result is in the paper.
Click to expand...
Reattaching the original screenshot again so everything is in one place (the I&D for rs730882143 were Ref D=G, Alt I=GA, Your Data I=A I=A)
Screenshot rs730882143.pngScreenshot rs730882143 part2.png
 
You must log in or register to reply here.
Back
Top Bottom