Question: I am a student, what can i do with 23andme raw data?
1
gravatar for crawforc3
3 months ago by
crawforc330
crawforc330 wrote:

I'm a bioinformatics student and I've never worked with the raw SNP data that you can get from 23andMe. What do people do with data like this? I'm not really looking for an analysis, but I would like to learn more about what a bioinformatician can do with a raw data set like this.

Here is the metadata and the first few lines as an example:

# This file contains raw genotype data, including data that is not used in 23andMe reports.
# This data has undergone a general quality review however only a subset of markers have been 
# individually validated for accuracy. As such, this data is suitable only for research, 
# educational, and informational use and not for medical or other use.
# 
# Below is a text version of your data.  Fields are TAB-separated
# Each line corresponds to a single SNP.  For each SNP, we provide its identifier 
# (an rsid or an internal id), its location on the reference human genome, and the 
# genotype call oriented with respect to the plus strand on the human reference sequence.
# We are using reference human assembly build 37 (also known as Annotation Release 104).
# Note that it is possible that data downloaded at different times may be different due to ongoing 
# improvements in our ability to call genotypes. More information about these changes can be found at:
# https://www.23andme.com/you/download/revisions/
# 
# More information on reference human assembly build 37 (aka Annotation Release 104):
# http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606
#

rsid    chromosome  position    genotype
rs4477212   1   82154   AA
rs3094315   1   752566  AA
rs3131972   1   752721  GG
rs12124819  1   776546  AG
rna-seq snp 23andme • 306 views
ADD COMMENTlink modified 3 months ago by firatuyulur120 • written 3 months ago by crawforc330

What do people do with data like this? I'm not really looking for an analysis, but I would like to learn more about what a bioinformatician can do with a raw data set like this.

That would entirely depend on the biological question.

ADD REPLYlink written 3 months ago by WouterDeCoster19k

Sure, do you have any biological questions as an example?

ADD REPLYlink written 12 weeks ago by crawforc330

An example could be to predict the ethnicity of the individual. I'm not sure which SNPs are included in the analysis, but if you have disease associated SNPs you can try to predict if the individual has a higher risk to develop disease A and a lower risk to develop disease B.

ADD REPLYlink written 12 weeks ago by WouterDeCoster19k
0
gravatar for firatuyulur
3 months ago by
firatuyulur120
firatuyulur120 wrote:

You can check the meaning of each SNP, given with the rs code. There are plenty snp databases where you can detailly read about the effects of each snp.

ADD COMMENTlink written 3 months ago by firatuyulur120
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