# What is the cause of “imbalanced” linkage disequilibrium?

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With perfect linkage disequilibrium ($$D' = 1, R^2 = 1$$), you might have the following table of counts for the alleles:

``B b A 100 0 a 0 100``

With "partial" linkage disequilibrium ($$D' < 1, R^2 < 1$$), you'll see something like this:

``B b A 100 25 a 25 100``

But I've sometimes seen the following "imbalanced" linkage disequilibrium ($$D' = 1, R^2 < 1$$):

``B b A 100 0 a 50 100``

What gives rise to this sort of situation, where aB occurs, but Ab never does? Is there a name for this phenomenon? Which is a better measure of linkage disequilibrium in this case, the normalized LD coefficient $$D'$$, or the squared-correlation $$R^2$$?

This can occur if the Ab genotype is lethal, i.e. you won't observe individuals with a Ab genotype.

Allele lethality is a common mechanisms that can explain non-mendelian inheritance of a trait.

For the question of which LD metric to use, this is tricky. Under the assumption that allele lethality is indeed at play, you observed perfect haplotypes, so D'=1 wouldn't be incorrect. Yet the correlation coefficient is also correct in the sense that SNP A is not a perfect proxy for SNP B.

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