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  • Jul 26 09:20

    tsujigiri on genomeprep

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    add genomeprep link (#538) (compare)

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  • Jul 25 06:31
    philippbayer commented #538
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    gedankenstuecke on genomeprep

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Mark Glasgow
@glasgowm148
so I can get the dataset
but what data tool would you use to compare
suppose I could figure out how to do it in R
think this does what I need :: https://github.com/HajkD/orthologr
Bastian Greshake Tzovaras
@gedankenstuecke
ah, i don’t think you want to do anything with orthologs. What you rather would need to do is running statistical tests for comparing whether the changes in frequency are significant or not. I think @philippbayer has done some work like that. maybe he has an idea for how to do it
Mark Glasgow
@glasgowm148
maybe VCFtools? I'm surprised it's not available in an executable app though. Figured none-cs people would be daft for comparing files with their relatives
Philipp Bayer
@philippbayer
isn't that an FSt test between the 'healthy' and the 'afflicted' population groups, using vcftools?
you could also make for each snp a contingency table:
              healthy    sick
alleleA    1233         5
alleleB       10        1233
and then run a million chi squares, one for each SNP, and then use something like p.adjust() to get FDR adjusted p-values
Philipp Bayer
@philippbayer
if it's a bunch of SNPs right next to each other, running something like FarmCPU via rMVP should also work
or something like https://www.pnas.org/content/116/4/1195
Mark Glasgow
@glasgowm148
Hmm, I'll have a look into that thanks. Maybe I'm misunderstanding the terminology but I don't care about the healthy group
Just want frequency in the dataset provided
Theres only a small amount of 'risk' genes I'm looking for so doing that bit manually is easier
I'm making a auto-updating spreadsheet people can select their genes from too : https://docs.google.com/spreadsheets/d/1g7f-0DT2_XYcTdjzYwE0V30LenynAL05zsQJkYXqITM/edit?usp=sharing
Bastian Greshake Tzovaras
@gedankenstuecke
The thing is that you need to compare the frequencies of the non-healthy group to something in order to know whether the change in frequency is meaningful. That’s why you need to have this one too
Mark Glasgow
@glasgowm148
I believe this affects 30-50% of the population and such comparisons are why it's missed
30% have adrenal issues/mutations (CAH) - 60% have methylation issues (MTHFR/etc) - chronic illness is a Venn diagram of those two sets
  • C4 / CYP mutations
  • +
Mark Glasgow
@glasgowm148
Ok, think I've figured it out. I think you're right in the end - I need to compare manifested diseases in those with RCCX mutations to those without and see if immunological diseases appear above expected
Is there an easy way to export everyone who has a specific mutation?
Philipp Bayer
@philippbayer
sadly not right now! you can export all specific phenotypes, but not specific snps
you could download the entire dataset and use grep to find the right files
philiprhoades
@philiprhoades
People,
I signed up here some time ago but never got around to doing anything interesting with my (and my parents and two siblings) 23andMe stuff past doing a Promethease report as well. Now one sibling wants to extend the testing to her children and some in-laws. There seems to be some hassle with people ordering on 23andMe from Australia now so I went looking at the alternatives - overall, MyHeritage appears to be the best combo of Genetics and Genealogy choice - do people here have preferences / suggestions? It would be nice if openSNP had grown to the scale of some of the commercial ops DBs . . but I guess that is not the way of the world . .
Thanks,
Phil.
Philipp Bayer
@philippbayer
I think here in Australia, ancestry.com is the biggest provider? at least the one that advertises the most :) they give you your raw data too: https://support.ancestry.com.au/s/article/Downloading-AncestryDNA-Raw-Data
'professional' projects like dna.land and others who have proper staff etc. have grown relatively large, and I'm happy with them :) I think we'd struggle a lot (computationally) if we'd work on that scale
Bastian Greshake Tzovaras
@gedankenstuecke
yep, if we’d grow to the size of those companies we’d be in real trouble in terms of scaling our system :D
philiprhoades
@philiprhoades
Philipp and Bastian,
Right - thanks for that.
Bastian Greshake Tzovaras
@gedankenstuecke
MyHeritage is pretty big these days too and my best guess is that it doesn’t really make a big difference which provider you go with as the data is pretty similar across all of them
philiprhoades
@philiprhoades
Right - good to know.
Bastian Greshake Tzovaras
@gedankenstuecke
I know that MyHeritage allows the upload of data from other providers
I’m not sure whether Ancestry allows that too
Philipp Bayer
@philippbayer
probably not from looking through their faq, no mentinos
philiprhoades
@philiprhoades
Yes, I just tested that as an exercise with MyHeritage - it took them a few days to process the 23andMe file and I got a bit of info back but to get all of the info they want to charge another AUS$48 . .
It looks like we might stick with 23andMe just for the convenience of most of the family already being there . .
Bastian Greshake Tzovaras
@gedankenstuecke
yeah, that certainly makes things easier if you already have many people on 23andme
Philipp Bayer
@philippbayer
makes sense to me!
Bastian Greshake Tzovaras
@gedankenstuecke
and i just uploaded my own 23andme data to myheritage just for fun, to see what they offer :)
philiprhoades
@philiprhoades

I know what you mean about scaling and processing but for some years I have been following:

https://safenetwork.org

which could potentially offer a distributed store of data and possibly processing . . it would be great to have an inexpensive store and comparison of nearly ALL the data from the commercials . .

Philipp Bayer
@philippbayer
currently we're still ok (thanks to patreon!!) but it could be a thing for the future!
philiprhoades
@philiprhoades
There is a bunch of stuff I want to put there once they go live - I will keep this stuff in mind and bring it up again in the future . .
Bastian Greshake Tzovaras
@gedankenstuecke
thanks!
Philipp Bayer
@philippbayer
Bastian Greshake Tzovaras
@gedankenstuecke
wow!
Bastian Greshake Tzovaras
@gedankenstuecke
420 and me! :D
Philipp Bayer
@philippbayer
I didn't see that dna.land is closing down/relaunching as a commercial service? https://medium.com/@dl1dl1/dna-land-is-relaunching-34f5a505504f
Philipp Bayer
@philippbayer
I like this: 'Please note that because DNA.Land is closing as a research project, all accounts and data will be permanently deleted and erased from the DNA.Land servers on September 30th, 2019. You will be able to recreate an account on DNA.Land 2.0 and upload your data just as you did when you signed up to join DNA.Land.'
Bastian Greshake Tzovaras
@gedankenstuecke
@philippbayer yeah, that’s cool. I had missed that somehow!
Philipp Bayer
@philippbayer
updating ssl certificate right now, server seems to have trouble coming back
oh. the harddrive is full\