ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine.

Abstract

Background: Single-sample pathway enrichment analysis is an effective approach for identifying cancer subtypes and pathway biomarkers, facilitating the development of precision medicine. However, the existing approaches focused on investigating the changes in gene expression levels but neglected somatic mutations, which play a crucial role in cancer development.

Findings: In this study, we proposed a novel single-sample mutation-based pathway analysis approach (ssMutPA) to infer individualized pathway activities by integrating somatic mutation data and the protein-protein interaction network. For each sample, ssMutPA first uses local and global weighted strategies to evaluate the effects of genes from mutations according to the network topology and then calculates a single-sample mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. To illustrate the performance of ssMutPA, we applied it to 33 cancer cohorts from The Cancer Genome Atlas database and revealed patient stratification with significantly different prognosis in each cancer type based on the ssMutPES profiles. We also found that the identified characteristic pathways with high overlap across different cancers could be used as potential prognosis biomarkers. Moreover, we applied ssMutPA to 2 melanoma cohorts with immunotherapy and identified a subgroup of patients who may benefit from therapy.

Conclusions: We provided evidence that ssMutPA could infer mutation-based individualized pathway activity profiles and complement the current individualized pathway analysis approaches focused on gene expression data, which may offer the potential for the development of precision medicine. ssMutPA is available at https://CRAN.R-project.org/package=ssMutPA.