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I'm trying to figure out how to map 23andMe genetic data to a paper but having trouble. I'm able to find the gene here (https://www.ncbi.nlm.nih.gov/gene/1813) but the paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6128289/) mentions an "A1 Allele" while the 23andMe data says it is "AG".

How can I reconcile this data? Or in other words, how can I see which alleles are present in 23andMe data?

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    $\begingroup$ I'd be cautious about overinterpreting your genetic results without consulting an expert in genetic counselling. I'm not sure whether your question should be closed as personal medical advice but I don't think I'd feel good about giving an answer here, I think there can be some risk in giving people some Dunning-Kruger style expertise. $\endgroup$
    – Bryan Krause ♦
    Jul 26, 2022 at 23:57
  • $\begingroup$ @BryanKrause this is purely for research purposes and would absolutely not constitute medical advice to anybody. $\endgroup$
    – Rob
    Jul 27, 2022 at 4:01
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    $\begingroup$ @user438383 A researcher involved in genetics? I kind of highly doubt it... $\endgroup$
    – Bryan Krause ♦
    Jul 27, 2022 at 17:18
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    $\begingroup$ Honestly, I'm just interested if my father (who died from alcoholism) and I have the same genetics related to addiction. I'd like to better understand the causes behind his death and if there's some way that I could help people in the future $\endgroup$
    – Rob
    Jul 27, 2022 at 19:04
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    $\begingroup$ @Rob That is exactly the sort of thing I was warning about interpreting without expert guidance. $\endgroup$
    – Bryan Krause ♦
    Jul 27, 2022 at 23:14

2 Answers 2

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As answered in your other question, you should use the rs ID for the allele. This is a systematic method (rather than the informal "A1" terminology) of being very precise about the variant. This ID will be shared / mappable across a dizzying variety of genetic resources, including 23andme.

For this specific variant, the rs ID is rs1800497.

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  • $\begingroup$ This is very helpful! Thank you! $\endgroup$
    – Rob
    Jul 28, 2022 at 3:22
  • $\begingroup$ @Rob — Please take the time to take the tour and then consult the help center starting with How to Ask. You have asked what appears to be essentially the same question twice and are now asking a followup question in the comments. Both of these actions are frowned upon on this site — doing this makes it harder (if not impossible) for other users to find material, which is a primary aim of the site. Please see above links for details. ——— In addition, your posts suggest you have a limited understanding of the basics of molecular genetics. If this is true, you would be best to address that ... $\endgroup$
    – tyersome
    Jul 28, 2022 at 4:51
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    $\begingroup$ @Rob: I can't evaluate the AG issue since I'm not sure what it's referring to at 23andme. I'll note that AG would be the reverse complement of CT. In other words, there are C and T alleles, which if you turn them around are A and G alleles. Just a guess, not sure. $\endgroup$
    – Maximilian Press
    Jul 28, 2022 at 5:13
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    $\begingroup$ @tyersome I do think that this and the other question are distinct (and potentially useful to answer independent questions)- obviously or I wouldn't have answered both. This question is more about "how do I figure out what to do with 23andme data" and the other one is more along the lines of "how do I look up stuff about a variant". I agree they're closely related, and the answers happen to converge. But knowing about that convergence is pretty specific domain knowledge about human variant databases (IMO). $\endgroup$
    – Maximilian Press
    Jul 28, 2022 at 5:17
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Just in case anyone finds this useful:

The data from 23andMe contains information about SNPs (single nucleotide polymorphisms), which are basically single base pairs in your DNA, eg. AT, AG, TT, etc.

However, in many academic papers, the authors usually write about entire genes, which are many SNPs that come together to form a trait. Alleles are simply different configurations of these SNPs for the gene that encodes for something.

Eg.

  1. A gene could be the color of your eyes
  2. Some Alleles for the eye color gene could be ones that encode blue, green, or brown eyes
  3. The SNPs inside each Allele would be different, for example, green eyes could be AA, TT, GG whereas blue eyes could be AG, GG, TT

Therefore, since 23andMe contains information about individual SNPs, there's still work required to understand the SNPs for each Allele. I'm currently trying to figure out where I can find this information.

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