Dr Ron Davis - Updates on ME/CFS research - September 2019 onwards

Barry said:
So would this rephrasing from your example also be correct?

If there truly is no correlation between [Chemical A] and [Condition X], there would be a 1% probability that due to random chance alone, we would see a big enough difference between patients and controls to erroneously suggest there is a correlation. i.e. 1% chance of a false positive.
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Kind of. The p-value is derived from the measurements we have already taken. So I would rephrase your rephrasing as:

If there truly is no correlation between [Chemical A] and [Condition X], there would be a 1% probability that due to random chance alone, we would see a difference between patients and controls at least as large as we've measured in our current experiment
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Taking a simpler example:
  • I have a coin in my pocket that I think is biased towards coming up heads.
  • The null hypothesis is that it is fair and has an equal probability of coming up heads or tails.
  • I toss the coin six times. It comes up heads five times.
  • My p-value is the probability that, if the null hypothesis is correct, I got the result I did - i.e. if the coin is fair, what is the probability of getting at least five heads upon six coin tosses.
 
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Does anyone know how the 50 people that weren’t in the severe study were screened/selected? I know a little while back Dr. Phair was looking for whole genome sequences of anyone who suspected they had ME/CFS. Were those people used as the additional 50 people tested for the IDO2 mutation or were they pulled from somewhere else?
 
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I've seen discussions of p-values where, in trying to define it, it's referred to as the probability that a finding is a "fluke" or is the result of chance. That description is dismissed, however, on the basis that all findings are "flukes" and the result of chance.

If you run a typical study again, with a different set of people (or even with the same set of people) you are unlikely to get the to exact same result. The idea, though, is that the more people you test, the more likely it is that the result will be similar to other groups of that size (I think).

The IDO2 test seems a bit different, though, because it is kind of a coin toss. Unlike other studies where the individual results can have a considerable range, the range of the IDO2 test is binary - either it's broken, or it's not.*

Assuming that the tests are reliable, the IDO2 results should be repeatable within the same group. It's like counting how many people are missing a thumb, as opposed to measuring everyone's temperature.

I don't know if statistics are calculated differently in a coin toss vs. a variable with a wider range. And the IDO2 test really isn't a coin toss anyway because each individual subject should not give a random result. Each subject should give a consistent result on the IDO2 test.


But I think I've probably said enough by this point to prove that I might well not know what I'm talking about.:)


[*Actually, I think there are something like 5 different ways IDO2 can be broken. It only takes one, but I think one could have up to 5 different concurrent faults, any of which would render it broken.]
 
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Feel free to edit title to better reflect the topic—I don’t know how to edit titles. Thanks.
 
Mij said:
Umm, my information tells me that the lab was pretty deserted a few years ago.
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I'm down at the lab every few months donating blood. A few years ago when I was first involved it was deserted. When they bring you in and downstairs you really can't tell how many people are there working
unless they bring you into the different departments. I look at the parking lot and at 10:00 Am there are a lot of cars.
 
Mij said:
Umm, my information tells me that the lab was pretty deserted a few years ago.
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My understanding is that a few years ago they weren't getting the patients they needed from local clinics, so in 2017 the researchers decided to recruit study participants themselves and bring people into the heart of their lab for blood draws, or go to homes of the most severely affected. (They use local patients as they require very quick processing of the blood and a two hour or in some cases overnight fast, to reduce collection and processing variations).

This had the added benefit that researchers doing the work get to meet patients and hear their stories. The side effect is that it forms great motivation and purpose for what they are doing.
 
wigglethemouse said:
My understanding is that a few years ago they weren't getting the patients they needed from local clinics, so in 2017 the researchers decided to recruit study participants themselves and bring people into the heart of their lab for blood draws, or go to homes of the most severely affected. (They use local patients as they require very quick processing of the blood and a two hour or in some cases overnight fast, to reduce collection and processing variations).

This had the added benefit that researchers doing the work get to meet patients and hear their stories. The side effect is that it forms great motivation and purpose for what they are doing.
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Although, this is likely not the place to post this, I am certain many of us would like to have an update about what the researchers are able to do or not to do in this frightful and perilous period. Dr Davis gave an update. So, that is one so far. If anyone knows what other researchers are doing, please post. What is Dr. Scheibenbogen doing, for instance? Does anyone in Germany know? And Dr. Prusty? etc.
 
email from Linda Tannenbaum
In a world seemly upended, Open Medicine Foundation can offer you the assurance that this crisis will not divert us from our search for a cure for ME/CFS.

I thought I would take a moment to let you in on how we work and why we are so
Linda%20Working%203-30-20.jpg
confident about our collective ability to stay on task. Our models of work for both our OMF staff and the Collaborative Research Centers are streamlined and adaptable. We are distributed worldwide and are experts at using remote communication and data-sharing tools.

But I have another source of hope: The OMF staff and research teams are called to this work based on a personal connection to ME/CFS patients and families.

Choosing to work on ME/CFS by definition requires embracing challenges and finding creative solutions. And OMF will see this work through until patients have the answers they need.

We are working to free many millions of patients from the cruel restraints of this disease and to shield millions more who could someday have it from the suffering it inflicts.

Each of us faces many added fears and worries today, so I invite you to set aside your concerns about the continuity of ME/CFS research. It will go on, and so will we.

Stay safe, and take care of each other,
With hope for all,
linda%20signature%20001.jpg

Linda Tannenbaum
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Perrier said:
Although, this is likely not the place to post this, I am certain many of us would like to have an update about what the researchers are able to do or not to do in this frightful and perilous period. Dr Davis gave an update. So, that is one so far. If anyone knows what other researchers are doing, please post. What is Dr. Scheibenbogen doing, for instance? Does anyone in Germany know? And Dr. Prusty? etc.
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To be honest, if they are like the researchers I'm in touch with, they will be all trying to find ways to continue doing what they were before this crisis - unless of course if they are called into the efforts to directly address the situation i.e. research COVID-19, provide testing etc

As frustrating as it is for us I think the best thing to do is to try and have as much patience as we can with them as they are probably rushed off their feet (and they probably didn't have enough time to do what they wanted at the best of times).
 
Sly Saint said:
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'one [NIH] reviewer rejecting 1 for a diagnostic test: “because there’s no cure for ME/CFS – why would we want to diagnose it better?” '
The very act of stating something so crass in a review comment, should flag up their total unsuitability as a reviewer.

Why would we want to diagnose it better? Better and safer illness management? Better understanding of prevalence, demographics, etc? Better chances for those misdiagnosed with ME/CFS? And many more reasons no doubt.
 
From the livestream of ME Action (US) for ME Awareness Day, 34:00 to 42:00


- Nanoneedle: the assay shows a signal for 50 ME/CFS patients but none of the healthy controls. Rahim Esfandyapour contacted 2 labs, one in the US and the other in China, for developing a prototype of the nanoneedle chip but that is on hold due to the COVID19 lockdown of labs.

- Metabolic trap theory: all 77 patients tested have a mutation in the IDO2 gene, this is "unusual". They are now using cultured cells for experiments, which makes testing easier, faster and cheaper because it provides "an abundance of material": they don't need a mass spectrometer anymore. They have the equipment available at Stanford with someone who knows how to use it, so they can run tests on a daily basis.

- Post-COVID19 study: the plan is to spot when the conversion from viral infection to ME/CFS occurs by gathering a massive amount of data from biological samples over time. Ron Davis thinks this conversion occurs very early on after the infection.
 
cassava7 said:
From the livestream of ME Action (US) for ME Awareness Day, 34:00 to 42:00


- Nanoneedle: the assay shows a signal for 50 ME/CFS patients but none of the healthy controls. Rahim Esfandyapour contacted 2 labs, one in the US and the other in China, for developing a prototype of the nanoneedle chip but that is on hold due to the COVID19 lockdown of labs.

- Metabolic trap theory: all 77 patients tested have a mutation in the IDO2 gene, this is "unusual". They are now using cultured cells for experiments, which makes testing easier, faster and cheaper because it provides "an abundance of material": they don't need a mass spectrometer anymore. They have the equipment available at Stanford with someone who knows how to use it, so they can run tests on a daily basis.

- Post-COVID19 study: the plan is to spot when the conversion from viral infection to ME/CFS occurs by gathering a massive amount of data from biological samples over time. Ron Davis thinks this conversion occurs very early on after the infection.[
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