In order to test the hypothesis of the linkage between PrP gene expression and PrP genotype-associated susceptibility, 22 Latxa sheep with different genotypes were analysed.
Genotypes were analysed as haplotypes.
Differences in TNF production between different genotypes was analysed by the Mann Whitney t test where only two genotypes were present, or the Kruskall Wallis ANOVA when all three genotypes were identified.
Identified variants between SL2.40 genome SM and RSV genotype were analysed using SnpEff version 2.1b (build 2012-04-20) [ 20] to predict their the effect on the genes in ITAG2.3 annotation.
Association between clinico-pathological variables and SNP genotype was analysed by the Armitage trend test or by logistic regression with sex as covariate, on the cases only.
The MDR1 genotype was analysed from 72 patients in whom antiretroviral therapy was initiated between 1998 and 2004.
Haplotypes and tag SNPs were predicted based on the estimated LD blocks according to the definition of Gabriel et al. Associations between genotypes and phenotypes were analysed using the mixed linear model (MLM) using the TASSEL program with the following parameters: MAF of ≥0.05.
For VT, genotype groups were analysed separately.
Only SNPs with genotyping >90% were analysed.
When the associations between genotype and efficacy outcomes were analysed, the patients with the UGT1A1*60 or CYP2A6 variant alleles had significantly poorer response rates (Table 4).
