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Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 07, 2018 4:07 pm
by Ghost
DrugsAreBad wrote:It seems there set of rsid:s in the pssd and control datasets are quite different. Any idea why this is? It seems more often than not that its the pssd datset that lacks information on rsids.


The data has some weird trends. If you look at the SNP data I have on my site you may see it. There are a few common numbers you'll see a lot:

1: The newest chip I believe. There is one person who has WAY more SNPs than the rest. This is why I asked Cipro to update the program for me. This would lead to SNPs having 100%, and would trigger false results - about 20 false for every good one. This meant that I had to do things by hand or use a piece of code that I hacked together to do some of this work for me.

3: Another common one. Idk why this was bc mine was alway one of these three, and my test a bit dated. I've cut these and the n=1 samples from the results online.

12,13,14: also common numbers for sample size. Odd because they usually don't include myself (and my older test), but the n=3 ones do...

16: This is the full number of SNPs in the dataset in Build 2.0. This is when EVERY person in the PSSD group is sampled.

Of course, Cipro's new version fixes this problem. As noted above, we're really glad that they were pointed out to us.

The control are all from OpenSNP project. IDK on how old they are. In Build 3.0 and above I'm going to get a much better control dataset.


There's also a tentative Build 2.1 where I take all the 2.0 SNPs and run them with the new genomes that I've received since I started 2.0 (A LOT). This will put these new genomes to use this fall instead of when I finish Build 3.0 (likely winter/spring 2019).

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 07, 2018 4:24 pm
by Ghost
DrugsAreBad wrote:I've done some more digging around in the dataset. Here is a list of the top 25 rsids I've found that are different between the groups. What now?

rs4871622
rs1467809
rs11994900
rs6887352
rs7113273
rs9294483
rs231023
rs231024
rs2894113
rs4552410
rs7173365
rs10884674
rs2253372
rs2939402
rs588765
rs6555885
rs680244
rs12138053
rs1264704
rs1927393
rs4728731
rs6419647
rs6677662
i6058149
rs10449236


Here is the output using the Build 2.0 numbers (n=16, n=30). Soon I'll update those databases so i can use more PSSD genomes if wanted.
Difference == 0

GREAT work on these though... I'll have to add them to my site soon.

### rs4871622 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %21.05
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %20.0 -- CONTROL CT: %78.95
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %80.0 -- CONTROL TT: %0.0


### rs1467809 ###
PSSD AA: %93.33 -- CONTROL AA: %15.79
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %6.67 -- CONTROL AG: %63.16
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %21.05
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs11994900 ###
PSSD AA: %0.0 -- CONTROL AA: %5.26
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %80.0 -- CONTROL AG: %10.53
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %20.0 -- CONTROL GG: %84.21
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs6887352 ###
PSSD AA: %6.67 -- CONTROL AA: %57.89
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %93.33 -- CONTROL AG: %21.05
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %21.05
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs7113273 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %13.33
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %100.0 -- CONTROL CT: %33.33
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %53.33


### rs9294483 ###
PSSD AA: %20.0 -- CONTROL AA: %5.26
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %26.67 -- CONTROL AG: %94.74
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %53.33 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 07, 2018 4:32 pm
by Ghost
@ Cipro

These are the ones with n >= 10, which was the case for the ones I just posted above too:


### rs2606345 ###
PSSD AA: %56.25 -- CONTROL AA: %53.33
PSSD AC: %43.75 -- CONTROL AC: %43.33
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %3.33
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs2228099 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %53.33 -- CONTROL CC: %33.33
PSSD CG: %40.0 -- CONTROL CG: %50.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %6.67 -- CONTROL GG: %16.67
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs1051740 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %6.25 -- CONTROL CC: %10.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %31.25 -- CONTROL CT: %53.33
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %62.5 -- CONTROL TT: %36.67


### rs1056836 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %12.5 -- CONTROL CC: %30.0
PSSD CG: %56.25 -- CONTROL CG: %53.33
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %31.25 -- CONTROL GG: %16.67
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs1799814 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %87.5 -- CONTROL GG: %100.0
PSSD GT: %12.5 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs2234922 ###
PSSD AA: %56.25 -- CONTROL AA: %73.33
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %43.75 -- CONTROL AG: %23.33
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %3.33
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs2260863 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %37.5 -- CONTROL CC: %63.33
PSSD CG: %43.75 -- CONTROL CG: %33.33
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %18.75 -- CONTROL GG: %3.33
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 07, 2018 4:33 pm
by Ghost
General update: I put a lot of time into the SNP list today. A lot more SNPs have some substance now.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Mon Sep 10, 2018 6:28 am
by DrugsAreBad
Ghost: Have you looked at plink? Looks like it might be useful. Links below.

Also, could you publish a list of all the snp files?

https://www.cog-genomics.org/plink/1.9/
http://zzz.bwh.harvard.edu/plink/dist/plink-doc-1.07.pdf

Re: PSSD Genome Project [Megathread]

Unread postPosted: Wed Sep 12, 2018 8:36 pm
by Ghost
Yes I've looked at plink. It's probably what I'll be doing in the future. It's just a lot of setup that I don't understand yet. it's what the PFS guys and I are going to do.

As for the SNP list. it's on my site:

https://pssdlab.wordpress.com/snps/

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 14, 2018 9:42 am
by fema4psyciatrists
You may have found a common altered gene in us? It was altered or activated or when we were born with it? It is a problem with taking in sunshine? Has that got anything to do with Serotonin's relationship with melatonin?

Do you need more people to put their interest in getting a 23andme spit test here? Maybe we can help them pay for it with donations if they do not have the money but are interested?

Re: PSSD Genome Project [Megathread]

Unread postPosted: Fri Sep 14, 2018 11:28 am
by DrugsAreBad
I meant the files containing snp:s, not just the list of specific snp:s. :)

Re: PSSD Genome Project [Megathread]

Unread postPosted: Sat Sep 29, 2018 11:33 am
by Ciprofloxacin
@Ghost
Please check these:

Code: Select all
https://drive.google.com/open?id=10cNlGrph93tboQZ69KTdNA8gKTcCzTBI

Code: Select all
https://drive.google.com/open?id=1gqOeyLavAmLyFh8T_w6OIR4HJ_oYy26k



Also, I just saw this. Looks like the tool we need.

https://blast.ncbi.nlm.nih.gov/Blast.cg ... =blasthome

There is a video about that.

https://www.youtube.com/watch?v=gKRDe7-l42M

What a coincidence, on the video, I saw these :d

https://drive.google.com/open?id=14WpNp ... Z_ReyNb6hS

Anyway. Maybe it saves time.

Re: PSSD Genome Project [Megathread]

Unread postPosted: Sun Sep 30, 2018 10:34 am
by Ghost
@Cipro, will run those tonight and look at those links today.

Note to everyone: There are a lot of new results posted on my site: https://pssdlab.wordpress.com/logging/