RNA-seq data were processed using a pipeline built with molgenis-compute76. FASTQ files were aligned against the GRCh38.p13 primary assembly using the GENCODE77 v32 annotation with STAR78 (v2.6.1c), while excluding patch sequences (Supplementary Note) with the following parameter settings: outFilterMultimapNmax = 1, twopassMode Basic and outFilterMismatchNmax = 8 for paired-end sequences; and outFilterMismatchNmax = 4 for single-end sequences. Gene quantification was performed using STAR, similar to gene quantification using HTSeq79, with default settings. The gene counts were then TMM-normalized80 per cohort using edgeR81 (v3.20.9) with R82 (v3.5.1). Quantification for the GeneNetwork was done using Kallisto83 v0.43.1 (Supplementary Note).
