I do neuroimaging research, and am interested in dabbling in genetics. I am trying to create an anxiety risk profile score from several SNPs shown to correlate with measures of anxiety in past GWAS studies. However, many of the GWAS studies, such as this one (https://www.biorxiv.org/content/10.1101/540245v1) don't seem to explicitly state which allele was the risk allele (i.e. which allele was positively correlated with anxiety). It's likely that in most cases the minor allele is the risk allele, but I don't want to assume this. Am I missing something in the text of the example manuscript, or would I need to contact the author to find this out?
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I suggest you contact the authors, because they do not show the direction of effect. They should share this information, otherwise you will never be able to tell which one is the allele that gives risk and which one is protective. And, as you said, it is better if you do not assume that the risk allele is the minor allele. There is no reason to be like this. – Fabio Marroni Aug 30 '19 at 13:18