I have finished paper on use of genotype probabilities in selection on PrP genotype in sheep. PrP genotype is one of the main factors for susceptibility to scrapie in sheep. Here is the link to the last version of the paper. And the abstract:
PrP genotype probabilities for ungenotyped animals of Jezersko-Solcava sheep breed were calculated. Data consisted of 10,429 animals among which 3,669 had PrP genotype data. There were 2,673 live ungenotyped animals. Five PrP haplotypes were present with the following frequencies: ARR 0.174, AHQ 0.074, ARH 0.083, ARQ 0.632, and VRQ 0.037. All 15 PrP genotypes were found. Iterative allelic peeling with incomplete penetrance model as implemented in GenoProb program was used for calculation of PrP genotype probabilities. There were only some additional PrP genotype and NSP type identifications with high probability. Main reasons for a low number of additional identifications can be attributed to large number of haplotypes with moderate frequencies, incomplete penetrance model, uniform prior, and inherently pedigree and genotype data structure. Incomplete penetrance model caused inflation of small probabilities but has proved to be very useful for field data where conflicting data rise due to pedigree of genotype errors. Novel parameters (maximal NSP type, average NSP type and its variance and accuracy) are proposed that make use of PrP genotype probabilities and can facilitate selection for scrapie resistance. Parameters were derived with emphasis on practical implementation of selection schemes based on NSP types. Maximal NSP type can be used to infer maximal potential scrapie susceptibility of individual ungenotyped animals as well as for whole flocks. Average NSP type makes full use of all PrP genotype probabilities and is the most useful and practical parameter for selection on NSP type and therefore PrP genotype. In addition, accuracy of average NSP type should also be used as selection criteria in order to assess the variability of average NSP type.