Genome (hg19) using TopHat36 (v2.0.10) and Bowtie37 (v2.1.0). Resulting sequence alignment files were analysed using RSeQC package for quality control38. Reads covering gene coding regions were counted with BED Tools and count data were analysed for differential expression using edgeR39 (v2.15.0). For Gene Ontology analysis, gene lists were obtained for disease enrichment from PharmGKB, KEGG pathways from the Encyclopedia of Genes and Genomes and gene ontology (GO) from AmiGO. IDs for each gene list are provided in Supplementary Table 2. P values were calculated from a cumulative hypergeometric distribution, calculated at (http://www.geneprof.org/GeneProf/tools/hypergeometric.jsp). The total population size was set to 20,687. Additional gene ontology analysis was performed with WebGestalt40.
