Beta coefficient is positive, but potential SNP effect size is negative
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23 months ago
BobN ▴ 20

I'm new to genetics so maybe my question will be very basic, but I can't find answer by myself for a long time.

I've seen some visualisations of SNP contribution to phenotype like that: enter image description here

I noted that "potential" effect maybe positive or negative. But how is it possible when we usually have effect size only for risk allele? So i assumed that SNP effect size may be only equal to risk allele beta coefficient in case of 1 risk allele in genotype, or x2 in case of 2 risk alleles in genotype.

For example: risk allele: T, beta coefficient: +0.3

Case 1: Genotype: AT, effect size: +0.3

Case 2: Genotype: TT, effect size: +0.6

How is it possible that potential effect size maybe lower than 0 in that example?

I assume that it is something to do with risk allele frequency but I can't find information on how exactly does it work.


PS: I found formula 2β^2 * f(1 − f), where f is the allele frequency for either of the two SNP alleles, but I'm not sure that it is the answer for my question.

PPS: here are one more example: enter image description here

SNP • 1.9k views
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The effect size is negative if the allele that is called "effect allele" confers a decrease in the measuread phenotype, and positive if it confers an increase. It is possible that in the regression the effect is calculated for allele A and then in the results the effect size is reported for allele B by simply changing the sign.

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But how is it possible that SNP simultaneously have possible positive and negative effect ? Does it mean that minor allele gives positive effect and major allele gives negative?

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That is a possible scenario, yes.

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From where are you taking this information in your question?

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From here: https://dna.land/traits-info#effect_hist

As I understood it is something to do with ancestry group, but I still don't get what calculations should I make to get charts like this even if I have ancestry group and allele frequencies for this ancestry group.

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