The study was planned for 200 patients. Exploratory analysis was done for all patients and for subgroups of patients receiving valganciclovir prophylaxis or preemptive treatment. Statistical analyses were performed using R version 3.3.2 [20] or SAS 9.4. Tests were two-sided and statistical significance was defined as p<0.05, but results should be interpreted descriptively. Pearson’s Chi-squared test was used to analyze associations between valganciclovir prophylaxis or preemptive treatment and the occurrence of CMV infection, CMV disease, graft loss or death, rejection, infections (viral, bacterial, fungal and other non-CMV infections), and leukopenia. CMV infection was defined as CMV-PCR ≥400 CMV copies/mL from visit 2 (day 7) until follow-up visit 27, excluding unscheduled visits.

Associations between SNPs and the occurrence of CMV infection, CMV disease, graft loss or death, rejection, infections, and leukopenia were examined using an asymptotic independence test (Cochran-Armitage trend test). The trend tests were envisaged for n = 30 genetic variants and 6 endpoints in the overall cohort and two subgroups (prophylaxis and preemptive treatment). For two variants (IFN-γ rs2069723 and IL10 rs3024489), no nucleotide changes were observed in our cohort. Only two events occurred for CMV disease in the prophylaxis group. The effective number of tests was therefore determined as n = 476 (= 28*17), and the corresponding Bonferroni corrected significance level consequently as α* = 0.05/476 ≈ 0.00011. Odds-Ratios (OR) and 95% confidence intervals (95% CI) were calculated using a logistic regression model as an association between genotypes and endpoints. Patients with missing data were excluded. Lower OR correspond to lower odds of seeing an event in the largest genotype group.

Haplotype analyses were performed with R-library haplo.stats [21]. Haplotypes were estimated separately for each gene, using all studied variants. Associations between haplotypes and the occurrence of CMV infection, CMV disease, graft loss or death, rejection, infections, and leukopenia were investigated using logistic regression and an additive genetic model. The minimal haplotype frequency for a haplotype to be included as a separate term in the regression model was set to 5%. Results with unusually large coefficients from the logistic regression fit (occurring for dependent variables with less than 15 events or haplotype frequencies close to 5% in treatment subgroup analyses) were considered as unreliable and therefore disregarded.

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