Urgent - opportunity to help our community project cheaply

General Discussion
#4

The analysis steps will be:

  1. See if we can find an association between all (PFS+PAS+PSSD+etc) cases and controls

  2. Check if each group shows an association by itself. At this point, if neither 1 nor 2 show anything significant, there is no point in looking further. Reasons for this outcome could be a) insufficient number of genomes combined with b) too many snp’s involved, or c) 23andMe array doesn’t cover snp’s relavant to our disease or d) P-etc. has no genetic component (highly unlikely).

  3. Assuming 2 turns out positive, and if we have sufficient genomes, the next step will be to see if we can find a difference between “mild” cases and ones which have vast and strong symptoms. PFS etc. is what is called a continuous trait in genetics, meaning that the phenotype (presentation of the disease in our case) varies strongly between cases. The results of the survey will help us define some categories along the severity scale, and it would be extremely interesting to see if we can find alleles which predict those categories. Currently, however, it is extremely unlikely that we can get to this stage with the number of genomes we have. What you are suggesting would require even more.

At this stage, I would already be thrilled out of my mind if we could find an overall association, and perhaps demonstrate that the genotype is the same between PFS, PAS, PSSD and P-etc. groups. This would be huge beyond imagination, and help catapult us into NIH funding territory.

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#5

Makes sense - but for your association to be statistically significant you will need to find something common between what, 50 percent of folks? 100 percent is obviously not going to be the case because presumably some folks who submitted their data may not even have pfs. Also if pfs is simply a trigger for many different diseases (like autism), then you may not find commonality between us all. BUT, maybe there a few diseases that are affecting us (triggered by fin), and folks with only mental sides have one issue, folks with physical sides have another issue, and folks with sexual sides have a another issue. What’s statstically insignificant with a large sample size maybe be significant with a smaller, more precise one. I find it hard to believe that me, with my visual and neurological sides only, and someone with only sexual sides, will have the same genetic predisposition. If that was the case I would assume would we react more similarly. Anyways just thoughts. I hope there is some commonality between us all and this disease isn’t like autism.

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#6

Where do I submit my 23 and me results when I get them? Accutane sufferer going to order now

#7

How many genomes do you have and how many do you need?

#8

We need as many as possible.

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#9

The upload links are there @Rmoney96 :slight_smile:

#10

I understand. I just don’t think that this is the most motivating thing to propose. Having a clear goal and seeing the number of datasets that still needs to be contributed to reach that goal might lead to a higher engagement of the community…

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#11

Which kit exactly is needed? What’s bare minimum, the ancestry ?

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#12

Yes, @Rmoney96, the ancestry option is sufficient.

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#13

The clear goal is to rid us of this terrible condition. The plan with the 23&me testing is to build our evidence base, enable us to seek governmental funding that could well lead to a treatment that will give you your life back.

I can understand your reluctance to spend what is today - Black Friday - the equivalent of the cost of a pair of shoes on saving your life, but it is what it is and nobody is telling you that you must do it.

Sorry if that sounds flippant, I’m not trying to be rude, but if we say we need 250 samples and say we have 10, what’s your motivation level? Is it higher or lower? If we say we have 100 and we need 101, are you gonna do it or leave it to someone else.

The gist is more samples is better.

Update - I just sent Tonster an apology for this post, not my finest hour.

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#14

No need to feel offended. I submitted my data long ago. It’s just a suggestion that might lead to a higher engagement of the community, cause sadly it seems that you haven’t received enough datasets yet. I leave it with that. That said: Thank you guys so much for your efforts!

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#15

Hi UKguy82,

Is this the product you are talking about ?

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#16

We currently have 33 genomes from mainly PFS patients, and another 14 from PSSD patients. I will attempt a first run at around 50 PFS genomes. As we all know, PFS is a very variable disease, both in scope and intensity. As written earlier, PFS is what is called a variable trait disease. From a genetics point of view, this indicates that a number of genes are likely involved. The more genes that are involved, the more samples we will need to cut through the statistical noise. The following picture shows a “Manhattan Plot”, which is a common way of representing GWAS results:

image
image946×433 62.2 KB

One can clearly see the noise I am talking about in this sample. Incidentally, this was from a study which looked at 1.1 million cases. I am not suggesting we need a million cases, but I hope that this example allows one to appreciated that even with 50 genomes, we will need a lot of luck to find something useful. It may be that we’ll need at least a few hundred genomes before we start to see something.

This work won’t produce an instant cure, but it will for sure contribute to better understanding our disease and hopefully provide some direction for future investigation. One of the key things we need to achieve is an animal model of PFS (rat, mouse). That will only be possible if we understand the genetic drivers of PFS, i.e. what makes US different from those many other guys, who apparently can take these substances without a problem. If we know those drivers, it should be possible to genetically engineer an animal so it develops PFS. Ideally, we would want it to get PFS quickly, and not have to wait 5 years. That means, we need to figure out which genes predict a quick onset of strong PFS, which further limits the available genomes.

Notice that I interchangeably am talking about genes, even though the data we have are snp’s. These represent locations on our chromosomes. Those locations will help find the underlying genes, but also here additional work is involved. Please appreciate that these kind of studies typically are run by a team of full time scientists. I am not a scientist, and doing this in my spare time. I have a rough understanding of what I am doing, but may run into limitations due to time and/or knowledge. If I reach that point, I am intending to get scientists involved to help. This will likely require further funding. If you are interested in this work and it’s objectives, you may want to save your donation money for this. If we get to the point where we need help, the funding will be collected through the Foundation, specifically ear marked for this study.

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#17

Thanks, Awor!

Guys, there you have it, straight from the horse’s mouth, what we need and why it is important. Unfortunately, we are faced with a very complex problem that we will not be able to solve on our own and which is expensive to investigate. Awor and others have done a great job so far on a small budget putting this problem on the map in the scientific community, creating the Foundation and funding studies that so far have shown that we are looking in the right direction and that our basic idea about the drivers of this condition are correct.

To drill deeper and to move faster, we will need much more money. This project is an attempt to potentially be in a position to receive grants from federal institutions. It’s obvious why this is highly important. The resources of our small community are limited.

Ukguy82 has spotted an excellent opportunity for people to get this test done on the cheap. Now it’s up to each and everyone of you here to do your part. We all need to work together here, we will need the support of everyone. We have only ourselves to blame if we do not support the incredible research initiatives that people from this community have started.

Personally, this is my 11th year of PFS. A lot of people get better initially, but after a certain period many are stuck in this condition or even getting worse. This problem won’t go away on it’s own and it’s unlikely that we will solve it by accident trialing supplements or meds without having a clear target. That’s why we need this research to hopefully one day treat this mess. The clock is ticking. Let’s do something about it!

Please everyone check out this thread and participate in the project. The process is simple and fairly cheap.

Thank you!

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#18

Well this offer is still on! It runs until 5am on the 26th. This is a top chance to join the others here who’ve already dug in.

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#19

@Rmoney96 - it’d be brill if you could get involved in the project! Expires 5am on 26th. So - time running down, but still chance to get it at the low price.

#20

What about ancestry then putting it into another paid site to get the health stuff from 23 and me? (Ends up being cheaper)

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#21

You only need the ancestry test for our study.

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#22

But I mean from ancestry.ca

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#23

Huh, I don’t know.

Does anyone else know?

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