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I'm trying to estimate the penetrance of a disease in a population given a rare spontaneous mutation that confers predisposition in an autosomal dominant manner. Given that the mutation is spontaneous, it wouldn't necessarily appear higher up in pedigrees, so estimates based on genealogy won't work. I have data on the frequency of the mutation (e.g. NHLBI's exome sequencing project etc.) as well as data on the expressivity of the disease in a cohort of individuals. Does anyone know of any reliable way (or program) to calculate this kind of penetrance, other than just crudely taking a ratio between the frequency of the symptomatic disease and the frequency of the mutant allele? I'm new to this kind of research so any other resources or references you might suggest are also greatly appreciated. Thank you.

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Isn't penetrance DEFINED as the ratio between expression and allelic frequency though? What I think you are looking for is an odds ratio, which is how penetrance, sort of, is reported for disease-associated SNPs: en.wikipedia.org/wiki/Genome-wide_association_study. –  Richard Rymer Jun 3 at 16:52