In general, the absolute difference in accuracy was only ~0.01 between the averages after five and 10 replicates for all scenarios using the base model and QTL with a moderately low average MAF, very low average MAF or extremely low average MAF.
In each simulation, 100 or 1000 QTL were sampled assuming that they followed one of the three QTL MAF patterns i.e. moderately low average MAF, very low average MAF, or extremely low average MAF.
When genotypes for the imputed variants representing QTL were included in the dataset used to calculate G a and G w, genotypes of all imputed variants in the three classes were used i.e. 80 515 variants with a moderately low average MAF, 97 296 with a very low average MAF and 4064 with an extremely low average MAF.
All variants that segregated in the entire dataset, consisting of 3000 Holstein-Friesian and 3000 Jersey individuals, were considered as potential QTL, which resulted in 65 920 potential QTL with a moderately low average MAF, 67 097 with a very low average MAF, and 2142 with an extremely low average MAF.
Table 1 shows the demographic and baseline characteristics of the ITT population, without differences between groups and well representative of the common knee osteoarthritis outpatient population: mostly women (63%), mean age approximately 67 years, moderately overweight (average body mass index approximately 28) and with Kellgren and Lawrence radiological grades II and III evenly distributed.
Five patients (4.6%) with no adverse side effects were classified as highly radioresistant; 36 (33.3%), 44 (40.7%), and 10 patients (9.3%) with mild to moderate skin reactions were classified as, respectively, moderately radioresistant, average, and moderately radiosensitive; and 13 patients (12%) with pronounced signs of radiation acute sensitivity were considered highly radiosensitive (Fig. 1).
In general, accuracies were greatest for QTL with a moderately low average MAF and smallest for QTL with an extremely low average MAF.
For the multi-breed reference populations, the proportion of variance explained by the within-breed animal component was equal to ~27% and ~52% for the RANDOM and VAR scenarios, respectively, when QTL had a moderately low average MAF, ~33% and ~53% when QTL had a very low average MAF, and ~40% and ~63% when QTL had an extremely low average MAF.
Contrarily, Indianapolis and Columbus are much more measured with ample amounts of rain and snow, and a moderately cold average temperature.
The mathematics subtests were moderately heritable – average heritability of 44%.
