= Homozygosity mapping
Homozygosity mapping searches for shared homozygous marker regions in individuals with a rare recessive condition, often in an <inbred> pedigree. Under a single ancestral disease copy, affected individuals inherit two copies identical by descent. Marker homozygosity alone gives <identity by state>, so founder haplotype frequencies matter. If a particular haplotype has founder frequency $p$ and $K$ distinct founder chromosome copies underlie all selected descendant copies, their marker-pattern probability is $E[p^K]$. For complete linkage and a single disease copy, the affected-only numerator is $p$, yielding a <LOD score> $\log_{10}(p/E[p^K])$ under linkage-equilibrium founder assumptions.
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