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Re: PSSD Genome Project [Megathread]

Posted: Sun Feb 07, 2021 5:46 pm
by sovietxrobot
Ghost wrote: Sun Feb 07, 2021 4:59 pm
DrugsAreBad wrote: Sat Feb 06, 2021 5:01 pm @Ghost

Are you sure you posted the raw data? I only see a Spreadsheet containing frequencies and a link to snpedia.
I should clarify, I posted the raw data the program generated. Some time in the near furure I'm going to run it against the frequencies posted on the NCBI website.

RE rs1042778: I don't see it in the list of snps snpedia listed on the v4 chip, so I didn't grab the frequencies from the data. I can go back and grab it later if you'd like.
whats the dataset on the NCBI website, 1000 genomes? you want to test against controls from the same chip, otherwise you have no way of knowing if a statistical difference is due to phenotype or due to chip effects. even from the same chip, you need to run some QC to account for batch effects.

how many snps were on the chip before qc? I take it this is unimputed data?

Re: PSSD Genome Project [Megathread]

Posted: Wed Feb 10, 2021 8:26 pm
by PsychoGenesis
Ghost wrote: Sun Feb 07, 2021 4:59 pm
DrugsAreBad wrote: Sat Feb 06, 2021 5:01 pm @Ghost

Are you sure you posted the raw data? I only see a Spreadsheet containing frequencies and a link to snpedia.
I should clarify, I posted the raw data the program generated. Some time in the near furure I'm going to run it against the frequencies posted on the NCBI website.

RE rs1042778: I don't see it in the list of snps snpedia listed on the v4 chip, so I didn't grab the frequencies from the data. I can go back and grab it later if you'd like.
but it's there as you can see here:


https://www.snpedia.com/index.php/23andMe


Thanks.

Re: PSSD Genome Project [Megathread]

Posted: Sat Feb 20, 2021 6:57 am
by capitalCK
Ghost. I came to this site via your blog. Thanks for great work you're doing. I don't have PSSD but rather PAS and PFS. Well, the PFS part is a combination of Finasteride+Minoxodil topical combo.

I do have 23andMe and happy to send it. I think the genes responsible for nNOS, eNOS, iNOS are probably silenced.

For example, my SNP: rs2070744 has value T/T. Good responders to pde5 inhibitors have C in the value. It seems to me that perhaps PFS/PAS/PSSD people are people that have non-C value. So, we're already susceptible to low nitric oxide and then genes got further silenced/methylated by drugs so now we're deficient in nNOS, eNOS etc and effects of that then cascades and show up as various symptoms from cognitive to sexual.

But I can't verify this hypothesis by looking at values of others. Since you're already compiling, I figured, I should let you know to perhaps look for correlation in nNOS, eNOS, Arginase genes.

See:
https://www.nature.com/articles/tpj201149
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172885/

Re: PSSD Genome Project [Megathread]

Posted: Wed Aug 04, 2021 8:41 pm
by FindGoodNickname
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Re: PSSD Genome Project [Megathread]

Posted: Thu Aug 05, 2021 1:24 am
by TalkingAnt
FindGoodNickname wrote: Wed Aug 04, 2021 8:41 pm I have donated a huge amount of money to pssdlab.
I didn't get any feedback, so I explicitely asked if he got my donation.
No reply.

I guess the website is dead.

I feel really bad, having sent this huge amount of money into the Nirvana.
Ghost does not take donations, so I'm not sure where you sent money?

Re: PSSD Genome Project [Megathread]

Posted: Thu Aug 05, 2021 6:07 pm
by FindGoodNickname
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Re: PSSD Genome Project [Megathread]

Posted: Tue Aug 10, 2021 7:37 pm
by FindGoodNickname
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Re: PSSD Genome Project [Megathread]

Posted: Mon Oct 11, 2021 1:42 pm
by Ghost
FindGoodNickname wrote: Wed Aug 04, 2021 8:41 pm I have donated a huge amount of money to pssdlab.
I didn't get any feedback, so I explicitely asked if he got my donation.
No reply.

I guess the website is dead.

I feel really bad, having sent this huge amount of money into the Nirvana.
Site is not dead! I REALLY appreciate the donation. I logged on today to share positive news from the project! Funds will be very helpful as I continue to work.

Re: PSSD Genome Project [Megathread]

Posted: Mon Oct 11, 2021 1:51 pm
by Ghost
Large update to the PSSD Genome project (https://pssdlab.wordpress.com/raw-data- ... e-project/)

A huge detractor from the research I was trying to do was finding a control group to compare us against. I used to do this with 20 sample genomes I found online. That control group was tiny and led to huge amounts of error. Not to mention I had to cycle through 40 .txt files with Python, a process with took DAYS to do even on my beast of a computer build.

I've spent some time playing around with Python machine learning and web scraping. For now I implemented Selenium in order to scrape information from the NCBI website in order to use their HUGE (18,500) snp allele frequency database. I was able to write this info into the same format as I did for the PSSD genome metadata, cutting all future processing by well over 40x, and letting me do a lot of initial analysis in Microsoft Excel instead. This should also MASSIVELY decrease noise in the data due to small control size. The noise in the PSSD data will only be reduced with more Genomes, so as always I encourage everyone to sumbit their results. Funding is available if you can demonstrate inability to afford a 23andme test thanks to our generous donors!!!

As always, my process, code, and full de-identified results are available on my site at the link above. I'm always open to receieve feedback or comments on my process for the PSSD community, PFS/Accutane community, and anyone else interested in DIY genetics research.

G

Re: PSSD Genome Project [Megathread]

Posted: Mon Oct 11, 2021 2:07 pm
by FindGoodNickname
OMG, how cool. I thought you were gone.
Thank you so much for your message.
Why have you been away for so many months?