Differential gene expression analysis model
Since this study focused on protein‐coding transcripts, all non‐coding RNAs were excluded. Also excluded were RNAs with read count = 0, in 50% or more samples in any of the study subgroups (baseline, 12‐, 24‐month) of CR or AL (For expression results, we also incorporated additional information using similar LMM models but replaced the linear time terms with visit indicator functions (non‐linear time) to estimate differentially expressed transcripts at the specific 12‐ and 24‐month visits between the CR and AL groups (Equation We used a threshold of 