Somatic mutations from exome and genome sequencing (WXS, WGS)

Exome sequencing selects and sequences the protein-coding regions of all genes, about one to two percent of the genome (Wikipedia), and whole genome sequencing determines the entire DNA sequence at once. TCGA relied mainly on exomes, so its mutation data (distributed as MAF files) covers coding changes; whole genomes add non-coding and structural variants. Mutation data is sparse (most genes unmutated in most tumours), which is why it adds little to expression in many prediction tasks.