23andme vs SNPedia confusion

Question

[ahm3dhany]

Question to clear up the confusion.. I am comparing the genotypes of rsIDs from the 23andme files versus the genotypes from snpedia.

23andme file for individual X:

on snpedia (for rs4988235):

on snpedia (for rs9939609):

after making some comparisons the results (i.e. the results i deduced):

if you noticed, in case of rs4988235 i flipped (i.e. converted) the genotype AA to TT because SNPedia shows that the orientation is minus, whereas i didn't flip the genotype for the rs9939609 because the orientation is plus.

So my question is, am I doing it the right way? I apologize if my question is naive, my background is in computer science not genomics.

Answer 1

[finswimmer]

Hello,

yes you're right. 23andme describes the genotype based on the reference genome, which is always the plus strand. In SNPedia the genotype is described based on the gene to which the SNP belongs. If the gene encode on the minus strand you will get the reverse complement genotype.

fin swimmer

Answer 2

[cjohnweb]

Hello ahm3dhany,

I have been seeking the answer to this for a long time and this post is the first time I have found anything what-so-ever on the topic. Thank you for posting this.

What you are saying makes sense to me, and if I had to guess I'd say you are doing it right.

I would love for someone who knows for sure to confirm if this is in fact the correct way to process this data.

Thank you