So HC, Kwan JSH, Cherny SS, Sham PC (2011) Risk prediction of complex diseases from family history and known susceptibility loci, with applications to cancer screening. Am J Hum Genet. 88(5):548-65.
FamGenePred Program
R code (beta version)
For prediction of lifetime disease risk for a genotyped individual, given any family history and any number of genotyped relatives; also allows for age-conditional risk estimates
sample ped file
sample incidence file