Homozygous Variants in Homozygous Regions

Question

[TP]

Does a recessive homozygous SNP that is disease causing always have to be found within a region of homozygosity? And if so how long should that region be? Can there be a homozygous snp that is disease causing found within a regular region of the genome?

Answer 1

[WouterDeCoster]

This is not strictly bioinformatics so this can get closed. Since my coffee is too hot to drink:

In the case of consanguinous or closely related parents, you would indeed expect a region of homozygosity around the homozygous SNP. The mean length of such a region would mainly depend on how closely related those individuals are.

But if the homozygous SNP is from unrelated parents then the regions don't have to be homozygous at all. The same pathogenic mutation may also arise independently on two different haplotypes, in which case, again, the regions don't have to be homozygous.

[TP]

Whooo! good thing your coffee was hot! Thanks for the pleasant response.