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Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Mar 22, 2019 5:50 pm
by GIXXER
I did some DNA pharmacogenomic testing with a company here in Canada. It basically takes out the trail and error process of these meds based on our genotypes. Today I received my results. Its very in depth for my genotype and recognized that my genes don't react well with SNRI/SSRI. Some recommendations were made on what will work for me. Im not sure if I will follow them yet as all these meds terrify me.

Also a med called Brexpiprazole came up in my report.

Brexpiprazole, sold under the brand name Rexulti, is an atypical antipsychotic. It is a dopamine D2 receptor partial agonist and has been described as a "serotonin–dopamine activity modulator" (SDAM).

Re: PSSD Genome Project [Megathread]

Unread postPosted: Wed Apr 17, 2019 2:50 pm
by Ghost
@Mesolimbo
When using the charts remember that:
C = RED
G = GREEN
A = BLUE
T = BLACK
Heterozygotes will be combinations of the above colors.


5HTTPLR allele
- rs25531 (irrelevant on 23+Me apparently - all are called C/C)
- rs25532:
-- 4 SNPs for rs25532 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 50.0
AA: 0.0
AT: 0.0
TT: 0.0
CT: 0.0
AG: 50.0
AC: 0.0
GT: 0.0
CHART (Click to open):
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0

- rs2129785:
-- 28 SNPs for rs2129785 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 85.71428571428571
CT: 14.285714285714285
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0

- rs11867581:
-- 29 SNPs for rs11867581 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 13.793103448275861
AA: 37.93103448275862
AT: 0.0
TT: 0.0
CT: 0.0
AG: 48.275862068965516
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
--------------------------------------------------------------------------------------------------------
COMT-Met
- rs4680:
-- 29 SNPs for rs4680 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 27.586206896551722
AA: 20.689655172413794
AT: 0.0
TT: 0.0
CT: 0.0
AG: 51.724137931034484
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0

- rs4633:
-- 28 SNPs for rs4633 analyzed for frequency --
CC: 25.0
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 21.428571428571427
CT: 53.57142857142857
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0

- rs165599:
-- 29 SNPs for rs165599 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 6.896551724137931
AA: 31.03448275862069
AT: 0.0
TT: 0.0
CT: 0.0
AG: 62.06896551724138
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
--------------------------------------------------------------------------------------------------------
FKBP5:
- rs1360780
-- 28 SNPs for rs1360780 analyzed for frequency --
CC: 57.14285714285714
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 14.285714285714285
CT: 28.57142857142857
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0

Re: PSSD Genome Project [Megathread]

Unread postPosted: Mon Jul 15, 2019 12:52 am
by Ghost
I will be starting another iteration of the genome project in the coming weeks.

My computer suddenly crashed this spring and with it I lost a lot of the organization I had with the genome project. I still have copies of all of the genomes, but I either need to find a way to recover some of my scripts and reorganize the data, or do it again - which would take a lot of time.

I'm building a new computer this week and after that will give some updates on how the project is progressing.

Stay tuned.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Mon Sep 16, 2019 7:45 pm
by Ghost
I have the new computer built and it's running a modified version of the old python code to analyze genomes. I'm still re-downloading the genomes that everyone sent me so that I get a big enough database for the next iteration of the analysis.

Expect another update in a few weeks. Things are moving forward again.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Tue Sep 17, 2019 2:21 am
by AnhedonicApe
Ghost wrote:I have the new computer built and it's running a modified version of the old python code to analyze genomes. I'm still re-downloading the genomes that everyone sent me so that I get a big enough database for the next iteration of the analysis.

Expect another update in a few weeks. Things are moving forward again.


Hey, do you have any data on methylation levels?

Re: PSSD Genome Project [Megathread]

Unread postPosted: Tue Sep 17, 2019 2:24 am
by AnhedonicApe
AnhedonicApe wrote:
Ghost wrote:I have the new computer built and it's running a modified version of the old python code to analyze genomes. I'm still re-downloading the genomes that everyone sent me so that I get a big enough database for the next iteration of the analysis.

Expect another update in a few weeks. Things are moving forward again.


Hey, do you have any data on methylation levels?
I was thinking about it, probably not

Re: PSSD Genome Project [Megathread]

Unread postPosted: Tue Sep 17, 2019 9:26 pm
by Ghost
Only data I have is on genotype, not expression :(

Re: PSSD Genome Project [Megathread]

Unread postPosted: Wed Sep 18, 2019 8:37 pm
by Ghost
Attention all programmers/coders: I NEED YOUR HELP!!!

Current program is good but it needs to reference a set number of control files to compare with PSSD patients, this is slow and gives a small sample size prone to error
I'd rather compare it to a bigger sample like the ones on SNPedia
I know I'm being vague but I'd help anyone who had ideas...

https://www.snpedia.com/index.php/Bulk - this is the best documentation that I can find.

I want a database of all of the SNPs from SNPedia that have frequency data...

https://www.snpedia.com/index.php/Help_ ... _diversity)- Scroll down here and look at the population diversity box. This contains the information I think. But where? How can I use this to turn it into a frequency that I can use for my program?

Someone might also be able to figure this out with hapmap: https://www.genome.gov/10001688/interna ... ap-project

Any help would be GREAT!

Re: PSSD Genome Project [Megathread]

Unread postPosted: Thu Sep 19, 2019 6:34 am
by sovietxrobot
what are you trying to do- compare allele frequencies of PSSD cases with controls?

Re: PSSD Genome Project [Megathread]

Unread postPosted: Thu Sep 19, 2019 9:40 am
by TalkingAntColony
Can you start a GitHub repo to make it easier to review and contribute code?