@olszewskip if there’s no email around let me know and i’ll look through my archives and find it
and fixed :)
Hi! I'm new here and not an expert on genetics but if you look at the page for SNP rs187238 it says the genotype frequency for CC is 54%, CG is 39% and GG is 7%. However the article this info is based on here seems to say that GG has frequency 54% and CC has frequency 7%. Am I misinterpreting something or is it the wrong way around on the website? Thanks!
hey @Amborella! That’s well spotted. This is most likely the result of how 23andMe reports their SNPs. 23andMe and most other genotyping companies report the variations all based on the +/forward strand of the DNA. But dbSNP and many publications etc. give variants based on the orientation of the gene.
In the case you highlight the IL18 gene is on the -/reverse strand of the DNA (see https://www.snpedia.com/index.php/Rs187238), so one needs to take the complement of the reported 23andMe allele to be in line with that notation, which flips the Gs & Cs around in this case.
Hope that makes sense! :)
Also according to what it says on openSNP 7% of the population (those with genotype GG by the notation on the page) have increased risk for SCD due to hypertension while according to the original paper 54% of people had this risk (those with genotype GG going by the notation in the original paper). Should the complement be taken somewhere here as well?
So if you are CC in 23andme (and by extension in openSNP), then this translates to being GG in the paper you are looking at
and then i think all the numberes make sense, no? 7% CC in openSNP means we have 7% GG in the notation of the paper?
From your reply I get the impression that it is not possible to just go from the genotype frequency on openSNP to the Links to SNPedia to work out what percentage of population is susceptible to the increased risk without checking if the variant is on the negative strand. Can you confirm if that is correct?
so for rs187238 SNPedia says that GG on the minus strand gives the elevated risk, which the paper says is found in 54% of the population. As it’s on the minus strand we have to look at the CC in openSNP and can see that 54% of openSNP members have that variant too, no?
Also as an aside how do you tell if a SNP is on the negative strand from SNPedia? Is it the - in -137G or something else?
done!
the current cert expires Sunday, 22 November 2020. if it works right then next thursday (tomrorow) we'll have a later cert.
Is it because something needs to be run as
app instead of root for the containers?