Question

23andme files uses GRCh37 or GRCh38 ?

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8.4 years ago

ahm3dhany ▴ 20

Does anyone know if 23andme switched to GRCh38 or they are still using GRCh37?

23andme orientation reference genome genome • 2.9k views

ADD COMMENT • link updated 8.4 years ago by Devon Ryan 104k • written 8.4 years ago by ahm3dhany ▴ 20

score 5 · Accepted Answer · 2016-06-13

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8.4 years ago

Denise CS ★ 5.2k

According to Which reference genome does 23andMe use?, it's GRCh37.

ADD COMMENT • link 8.4 years ago by Denise CS ★ 5.2k

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I can confirm this is currently the case by cross-referencing the coordinates in my raw 23andme data with dbSNP. (e.g. rs13096 is at coordinate 25359841, not 25206907)

ADD REPLY • link 8.4 years ago by Keith Callenberg ▴ 960

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Another 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:

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on snpedia (for rs4988235):

enter image description here

on snpedia (for rs9939609):

enter image description here

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

enter image description here

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.