Paper "Calculation of PrP genotype and NSP type probabilities in Slovenian sheep" is finnaly finnished. I will send it to the journal today. This is a sort of a companion paper to the previous one where the methods were derived and tested, while in this paper we used those methods on all sheep breed in the Slovenian breeding programme for sheep. Here is the abstract:
PrP genotype probabilities in ungenotyped Slovenian sheep were calculated. Altogether 36,083 ewes and rams of various breeds were included into the analysis. PrP genotype was known for 10,504 animals. Five different PrP alleles were present in the data. Pedigree and genotype data structure differed between breeds. Iterative allelic peeling with incomplete penetrance model was used for the calculation of genotype probabilities for each animal given the genotype data of relatives. Analyses were performed for each breed separately. Additionally, NSP (National Scrapie Plan) type probabilities and the average NSP type were calculated from the genotype probabilities. Results were presented for live animals only. There were no animals with additionally identified PrP genotype or NSP type with certainty. With 95 % probability PrP genotype was additionally identified for 0.0 to 5.7 % animals of different breeds. NSP type was additionally identified with the same probability for 0.0 to 34.9 % animals of different breeds. We maintain that the low number of additional identifications was due to: a large number of alleles, intermediate allele frequencies, data structure, a uniform prior, and the use of incomplete penetrance model. Additional identifications provided some cost savings, but did not prove useful in the selection for scrapie resistance of the entire populations. The average NSP type should be used instead, since it can be calculated for all animals and encompasses all information from genotype probabilities.