Friday, January 29, 2016

Linking a SNP (rs1234567) to your own 23andMe variant

You read about a new genetic discovery - some allele has some effect - and you wonder about yourself. Your genome (or at least the subset they sequenced) is catalogued in the 23andMe database and some sites let you check your own allele variant (SNP - 'snip') in just one click. How do they do that?

They use a link like this.
Gene variants for schizophrenia are just in the news. Now in the current report the relevant risk factor is number of copies of the C4 gene, something which is not assessed by 23andMe at present. But SNPs do have some predictive power for schizophrenia and other mental conditions - for example this (at Genetic Lifehacks):
rs4570625T is the minor allele and has been studied in reference to a number of psychiatric conditions. A recent study found that those carrying the T allele were more susceptible to major depression even when not exposed to “high-negative life events”.  A Chinese study in 2014 found that those with the T allele were more susceptible to paranoid schizophrenia.
When you click on the rs4570625 link above, you're taken to the 23andMe login page. After logging in, this is what you see (click on image to make larger):

I seem to be OK as regards that particular allele (one SNP is not going to make that much difference in what is a polygenic condition) - here's what SNPedia has to say about rs4570625 (for what it's worth).

Incidentally, I'm GG and my mother was GT. What can we say about my father? Well, I received one of those Gs from my mother, so I must have got the other from my father, so he was either GG or GT. Now, I didn't actually need my mother's sequence to deduce my father's options, but knowing she was GT means that the odds favour my father being GG.


In case you're wondering: what's with these rs1234567 things ...?
"A reference SNP ID number, or “rs” ID, is an identification tag assigned by NCBI to a group (or cluster) of SNPs that map to an identical location."

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