PSSD Genome Project [Megathread]

This is a place to post research you have done on the topic along with your conclusions.
sovietxrobot
Posts: 283
Joined: Tue Oct 03, 2017 12:04 pm
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by sovietxrobot »

It would be nice to summarize the results with p-values and a Manhattan plot. You can do a simple test of proportions against the control group.

Do you have any phenotype information on the PSSD subjects?

I am a statistical geneticist I would be happy to help with this.
User avatar
Ghost
Posts: 1746
Joined: Wed Jan 21, 2015 11:16 pm
Location: USA
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by Ghost »

sovietxrobot wrote: Mon Oct 11, 2021 2:10 pm It would be nice to summarize the results with p-values and a Manhattan plot. You can do a simple test of proportions against the control group.

Do you have any phenotype information on the PSSD subjects?

I am a statistical geneticist I would be happy to help with this.
YES! I'll shoot you a PM and we can go from there. I'm sure you have way more knowledge than me - no need for me to re-invent the wheel.
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it :)
Flo
Posts: 20
Joined: Thu Jul 07, 2022 12:20 pm
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by Flo »

Hi, what stage are you at with this? Are you still looking for data?
Thanks
Flo
User avatar
anacleta
Posts: 658
Joined: Fri Jan 23, 2015 5:47 am
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by anacleta »

Ghost, I wrote to you but you didn't answer me

how many 23andme tests have you collected?

can you take stock of the research you've done, what were the interesting things, what were the biggest limitations of those tests?

is it possible to ask you to check specific things in comparing the data?
Darman
Posts: 101
Joined: Thu Jul 01, 2021 3:23 am
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by Darman »

sovietxrobot wrote: Tue Oct 22, 2019 11:11 am Paper on the genetic effects of citalopram: Kanherkar et al. 2018. The effect of citalopram on genome-wide DNA methylation of human cells. International Journal of Genomics.

In short: Human cell culture exposed to citalopram for a month. OXT gene downregulated, inhibition of dopa pathway. Coincides with findings of negative effects of SSRIs on dopaminergic signaling.
sorry I'm very late with this reply but isn't this finding significant? If these are know effects are there any drugs which reverse these changes?
Brain food
Posts: 348
Joined: Sat Aug 15, 2020 9:54 am
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by Brain food »

Darman wrote: Tue Aug 02, 2022 6:11 am
sovietxrobot wrote: Tue Oct 22, 2019 11:11 am Paper on the genetic effects of citalopram: Kanherkar et al. 2018. The effect of citalopram on genome-wide DNA methylation of human cells. International Journal of Genomics.

In short: Human cell culture exposed to citalopram for a month. OXT gene downregulated, inhibition of dopa pathway. Coincides with findings of negative effects of SSRIs on dopaminergic signaling.
sorry I'm very late with this reply but isn't this finding significant? If these are know effects are there any drugs which reverse these changes?

These are findings in a lab. They are not even findings in adult psychiatric patients. HEK-293 cells are a specific immortalised cell line derived from a spontaneously miscarried or aborted fetus or human embryonic kidney cells grown in tissue culture taken from a female fetus in 1973. This study is supposed to be a first step to encourage more research. It’s a very long way before there are treatments.
Darman
Posts: 101
Joined: Thu Jul 01, 2021 3:23 am
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by Darman »

Hi. Thanks for your reply. To be honest I would still be prepared to offer up myself as a test subject even at this early stage...
User avatar
Ghost
Posts: 1746
Joined: Wed Jan 21, 2015 11:16 pm
Location: USA
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by Ghost »

anacleta wrote: Mon Aug 01, 2022 5:26 am Ghost, I wrote to you but you didn't answer me

how many 23andme tests have you collected?

can you take stock of the research you've done, what were the interesting things, what were the biggest limitations of those tests?

is it possible to ask you to check specific things in comparing the data?
Thanks for your interest in the genome project!

30 Genomes - a lot of info housed here: https://pssdlab.wordpress.com/raw-data- ... e-project/
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it :)
thepineapple
Posts: 15
Joined: Tue Aug 16, 2022 8:27 am
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by thepineapple »

Ghost wrote: Thu Aug 25, 2022 11:15 pm
anacleta wrote: Mon Aug 01, 2022 5:26 am Ghost, I wrote to you but you didn't answer me

how many 23andme tests have you collected?

can you take stock of the research you've done, what were the interesting things, what were the biggest limitations of those tests?

is it possible to ask you to check specific things in comparing the data?
Thanks for your interest in the genome project!

30 Genomes - a lot of info housed here: https://pssdlab.wordpress.com/raw-data- ... e-project/
When I look at the 20 genomes you posted on google sheets I can't find cyp2d6, why is it?
User avatar
Ghost
Posts: 1746
Joined: Wed Jan 21, 2015 11:16 pm
Location: USA
Contact:

Re: PSSD Genome Project [Megathread]

Unread post by Ghost »

thepineapple wrote: Wed Sep 07, 2022 9:46 pm
Ghost wrote: Thu Aug 25, 2022 11:15 pm
anacleta wrote: Mon Aug 01, 2022 5:26 am Ghost, I wrote to you but you didn't answer me

how many 23andme tests have you collected?

can you take stock of the research you've done, what were the interesting things, what were the biggest limitations of those tests?

is it possible to ask you to check specific things in comparing the data?
Thanks for your interest in the genome project!

30 Genomes - a lot of info housed here: https://pssdlab.wordpress.com/raw-data- ... e-project/
When I look at the 20 genomes you posted on google sheets I can't find cyp2d6, why is it?
not sure of the exact reason. Maybe it wasn't tested, or maybe it didn't have enough samples for me to put it in there. I set a threshold for number of samples (i think it's documented on the site) so that we could minimize the risk of 1 or 2 samples looking more significant than they actually are.

I've gotten a lot better at programming since I wrote the code for the .csv data a few years ago.
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it :)
Post Reply

Who is online

Users browsing this forum: No registered users and 2 guests