Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD 21204, USA. Electronic address: [Email]
Large-scale cancer sequencing studies of patient cohorts have statistically implicated many genes driving cancer growth and progression, and their identification has yielded substantial translational impact. However, a remaining challenge is to increase the resolution of driver prediction from the level of genes to mutations because mutation-level predictions are more closely aligned with the goal of precision cancer medicine. Here, we present CHASMplus, a computational method that is uniquely capable of identifying driver missense mutations, including those specific to a cancer type, as evidenced by significantly superior performance on diverse benchmarks. Applied to 8,657 tumor samples across 32 cancer types in The Cancer Genome Atlas (TCGA), CHASMplus identifies over 4,000 unique driver missense mutations in 240 genes, supporting a prominent role for rare driver mutations. We show which TCGA cancer types are likely to yield discovery of new driver missense mutations by additional sequencing, which has important implications for public policy.