Amatica Patient-centred chronic disease research

I hope that you won't mind me commenting on your results. The first screenshot suggests that Amatica is reporting that your mast cell results are unusual. But, your summary of gene expression only has a single supposedly mast cell-related gene where the expression is barely outside the 95% confidence range. I don't know how many mast cell related genes they tested, but it's hard to see how they decided you have a mast cell issue.

Did you understand the point that if you are sampling thousands of genes supposedly related to these areas of interest, everyone will have something that looks a bit odd. Maybe there is some valid information here, but you need to see what the controls' data looks like n order to work out which bit might be useful. It is likely that each control individual also has some gene expression that is unusual. There could be lots of reasons for the variations, and plenty of them aren't related to ME/CFS pathology, especially with such a low number of controls.
 
Hutan said:
I hope that you won't mind me commenting on your results. The first screenshot suggests that Amatica is reporting that your mast cell results are unusual. But, your summary of gene expression only has a single supposedly mast cell-related gene where the expression is barely outside the 95% confidence range. I don't know how many mast cell related genes they tested, but it's hard to see how they decided you have a mast cell issue.

Did you understand the point that if you are sampling thousands of genes supposedly related to these areas of interest, everyone will have something that looks a bit odd. Maybe there is some valid information here, but you need to see what the controls' data looks like n order to work out which bit might be useful. It is likely that each control individual also has some gene expression that is unusual. There could be lots of reasons for the variations, and plenty of them aren't related to ME/CFS pathology, especially with such a low number of controls.
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Of course, no problem...
Amatica just sent us all the genes to analyze on AI.
We had a panel, a selection... we have the complete analysis now...
interferon 1 problem for me. I don't understand any of it... haha
In two months they'll do a detailed report for each patient.
Anyway, that's their work, interesting for beginners.
 
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Hutan said:
Honestly @neophyte32, I think their product is misleading for beginners, and will lead to people incorrectly thinking they have all sorts of answers for their health issues. I'm concerned that it will lead to people taking drugs that won't help them and may harm them.
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Yes, I see what you mean. But their project is only just beginning. When we have 500 patients and the same number in the control group, it might be more useful.

But finding certain aberrant values that perfectly match the symptoms doesn't reveal anything, does it?
One might find that it has no scientific value, of course, but at some point, when you've been bedridden for a year, you want to know what's happening in your body.
The fact, for example, that my angiotensin II level in a blood protein test is at the 99th percentile (50 healthy individuals and hundreds of patients) could be useful to me. But where does this compensatory mechanism come from? I don't know. What to do? Sartans? I have no idea.
But I need answers.
The more I learn, the more I think I'm not even sure there's just one disease, but several, because the symptoms vary enormously from one person to another. There must be subgroups.
These studies, considered too amateurish, still give us some data.
 
neophyte32 said:
Yes, I see what you mean. But their project is only just beginning. When we have 500 patients and the same number in the control group, it might be more useful.
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Yes, fair enough. I understand the need for information. And, I guess if they do things well for long enough, it could be useful.

It's just a shame if people are spending money they don't have for something of questionable validity and uncertain utility. In particular, the 'doing things well' can be very difficult. Upthread there have been questions asked about the care and processing of the samples for example.

If there is a robustly healthy person with some spare cash, It would be interesting to have them sign up, fill out the questionnaire as a person with ME/CFS. And then publish their results. (They presumably could later withdraw their data from the database, so as not to contaminate it. Or update their details to become a healthy control). It could give people a bit of a lead on how useful the reports are right now for drawing conclusions.
 
ChronicallyOverIt said:
A bit ironic Amatica is now going with there is no such thing as healthy control when they let anyone that pays $1000 into the sick testing cohort. Been largely ignoring this but it feels opportunistic to make people pay $1000 for these tests.

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this is highly speculative on my part, but I feel like this could be a lead up or a cop out for why their test cannot differentiate between healthy controls. Historically, anyways, they’ve used a minimal amount of controls and their studies are incredibly underpowered so they’re probably seeing that noise quite a bit.
 
neophyte32 said:
What do u mean ? My liver enzyme are a bit high. Juste a bit. I think it s low dose abilify
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Thanks Jack, have you checked your enzymes before taking abilify or only after? Also, I am sure you are aware of the Chris Ponting study mentioning liver dysfunction in patients who were not taking -I assume- abilify so it would be great for all of us to know what happened and what is the reason behind your elevated liver enzymes. I am aware that the discussion is for one person but nevertheless it would be good to know.

Perhaps the solution is much simpler than we all think, at least for some patients
 
mariovitali said:
Merci Jack. As-tu fait contrôler tes enzymes avant ou après avoir pris de l'Abilify ? Par ailleurs, je suis certain que tu as entendu parler de l' étude de Chris Ponting mentionnant des dysfonctionnements hépatiques chez des patients qui ne prenaient pas d'Abilify (je suppose). Ce serait donc intéressant pour nous tous de savoir ce qui s'est passé et la cause de ton élévation des enzymes hépatiques. Je sais que cette discussion concerne une seule personne, mais il serait tout de même utile de le savoir.

La solution est peut-être beaucoup plus simple que nous le pensons tous, du moins pour certains patients.
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??? Im not Jack
 
An ME group I’m involved with got this recently:

Subject Early Amatica RNA Sequencing Findings in ME/CFS and Long COVID

I hope you’re doing well.

My name is Jack Hadfield, and I’m reaching out on behalf of Amatica Health. I am the Research Lead and also an ME/CFS and Long COVID patient.

We are building a research database that combines advanced tests, including RNA sequencing, with detailed patient questionnaires to identify biomarkers linked to diagnosis, disease mechanisms, subgroups, and treatment response.

The database currently includes 211 patients and 85 healthy controls. Our analysis of 159 patients and 85 controls has identified thousands of altered genes, dozens of altered pathways, and early RNA signatures that may help distinguish patients from healthy controls.

We are now preparing to share initial insights from this work, including the performance of these early signatures.

You can see the initial presentation containing the findings and methods recently used for a video sharing our preliminary data:

https://www.amaticahealth.com/blog/first-findings-from-our-rna-sequencing-cohort/

Our model allows individuals to access information-only research testing and, with consent, contribute de-identified data to the wider database. More than half of the cohort is housebound, with participants joining from multiple countries.

Would you be interested in discussing or sharing our research findings with your audience? I would be happy to arrange a call or send further information by email.



Best,
Jack

Co-Founder & Research Lead
Amatica Health
 
ChronicallyOverIt said:
Out of curiosity did they ever send a detailed report? I haven’t heard a peep out of these guys in a while
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  • 1Amino acid-related191 genes · 18↑ · 15↓
  • 2Antiviral Response Related89 genes · 3↑ · 21↓
  • 3Autoimmunity Related Immune Signalling142 genes · 5↑ · 24↓
  • 4Autonomic & orthostatic response related127 genes · 9↑ · 12↓
  • 5B-cell-related126 genes · 4↑ · 17↓
  • 6Cellular danger and stress response-related113 genes · 6↑ · 20↓
  • 7Complement System Related48 genes · 1↑ · 6↓
  • 8Connective Tissue & Collagen Related39 genes · 3↑ · 2↓
  • 9DNA damage, replication stress and genome integrity-related230 genes · 39↑ · 16↓
  • 10Epigenetic memory, chromatin and cell-state regulation-related253 genes · 18↑ · 27↓
  • 11GABA & Glutamate Related74 genes · 7↑ · 3↓
  • 12Gut barrier and mucosal immunity-related145 genes · 4↑ · 16↓
  • 13HPA-Axis & Stress-Response44 genes · 5↑ · 3↓
  • 14Immune Regulation Related39 genes · 1↑ · 6↓
  • 15Integrated stress response-related81 genes · 8↑ · 18↓
  • 16Lipid and fatty acid-related208 genes · 14↑ · 33↓
  • 17Mast Cell Associated & Allergy Related95 genes · 3↑ · 20↓
  • 18Mitochondria (Cell Energy) Related284 genes · 29↑ · 46↓
  • 19Brain & Nervous System Related165 genes · 8↑ · 22↓
  • 20Neutrophil Related68 genes · 12↓
  • 21NK-Cell Related39 genes · 3↑ · 4↓
  • 22Oxygen sensing and hypoxia adaptation-related68 genes · 4↑ · 13↓
  • 23Red blood cell and iron metabolism-related142 genes · 8↑ · 25↓
  • 24T-Cell Related60 genes · 4↑ · 2↓
  • 25Tryptophan, kynurenine and monoamine-related63 genes · 7↑ · 4↓
  • 26Vascular-related131 genes · 6↑ · 10↓
Yes, we each received an individual report. For each category, hundreds of RNA transcripts were analyzed, with a detailed description of each one. It's incredibly comprehensive and, frankly, very well put together.

But what exactly are the criticisms? Personally, I think there's a huge problem with patient selection. They seemed to accept pretty much anyone, regardless of what illness they had. Even though we had to fill out a questionnaire beforehand, I don't see how you can draw solid conclusions from such a heterogeneous group of patients.

And then there's the question of what they'll actually do with all this data. I'm not convinced they'll manage to get anything meaningful out of it.

For me, the biggest rip-off was their proteomic analysis: 31 proteins analyzed for over €1,000! That was when I genuinely felt I'd been ripped off.
By the way, I'd like to make an offer to everyone on this forum: if anyone wants to look at my profile and results, I'm more than happy to give you access. That way, you can see exactly how the reports are structured, which categories are covered, and which RNA transcripts are analyzed.

However, there's one thing I find genuinely interesting. When we compared our results with other patients, we noticed that the profiles of severely ill patients often looked remarkably similar. On the graphs, there are lots of values below the median, with this strange circular chart looking completely distorted, almost shattered.

By contrast, in mild or moderate patients, the circle tends to be much more regular, almost perfectly shaped. And this difference showed up in most of the profiles we compared.

I find that pretty striking. Of course, these are just informal observations between patients, but seeing such a clear difference depending on disease severity is surely worth investigating.

So no, I find it hard to believe that the whole thing is just one big scam. There may well be something useful in all this data, even if I don't yet know what.
 

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