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A founder is an individual whose parents are outside the recorded pedigree. The standard pedigree likelihood assigns unrelated founders independent genotype distributions based on population allele or haplotype frequencies. If founders are related, their joint prior must instead account for that relationship.

Ascertainment in a genetic study specifies how individuals or families enter a genetic study. If $A$ is the event of inclusion, then $P(X\mid A)=P(X)P(A\mid X)/P(A)$. Selection on disease phenotype can change an unconditional pedigree likelihood. When comparing genetic marker probabilities conditional on a specified disease pattern, selection depending only on that pattern cancels from the linkage likelihood ratio.

Parametric linkage analysis forms a pedigree likelihood from a specified disease model, including penetrance, allele frequencies and recessive inheritance or another transmission model. It estimates or tests the recombination fraction between a disease locus and a genetic marker.

// Target: biology.bigb

A phenotype is an observable characteristic of an organism, arising from its genotype, environment and other influences. Seed shape is a phenotype; $Aa$ is a genotype. The distinction prevents appearance from being mistaken for a complete inherited description. See NHGRI: phenotype.

For a specified binary phenotype $T$, let its penetrance in genotype $g$ be $r_g=P(T\mid g)$. The law of total probability gives $P(T)={\sum }_g{r}_{g}P(g)$. Thus the ideal $Aa\times Aa$ example has $P(T)=r_{AA}/4+r_{Aa}/2+r_{aa}/4$: the familiar $3/4$ follows only when these penetrances are $1,1,0$. A pedigree likelihood keeps inheritance and the conditional phenotype model as separate factors.