4.1. ADME Genes and TCGA Cancer Types

Roughly 300 genes are considered as ADME genes with slightly different lists among studies [8,9,10,11,87]. The present study assessed the 298 ADME genes defined by the PharmaADME Consortium (http://www.pharmaadme.org) as previously reported [8,9]. These 298 genes include 32 core ADME genes and 266 extended ADME genes (Table S1). Core ADME genes are the most important genes directly involved in drug metabolism and clearance; the extended ADME genes are other genes related to drug metabolism/clearance. ADME genes are categorized into three groups: 1) phase I and II enzymes; 2) transporters; 3) modifiers (modulating the expression or activity of other ADME genes). The full names for all 298 ADME genes are given in Table S1.

Table 1 lists the 21 TCGA cancer types (7983 patients in total) that were included in our analysis of ADME gene expression profiles. For 20 of these cancer types, only primary tumours were included in the analysis; the SKCM dataset included about 30% primary tumour and 70% metastatic tumours [35].

The drug regimens of TCGA cancer types (Table S2) were downloaded from the GDC (Genomic Data Commons) data portal (https://portal.gdc.cancer.gov) using an R/Bioconductor package TCGAbiolinks as previously reported [88,89].