Protocol for quantifying interaction patterns among genomic alterations in cancer

Publicly available large-scale cancer datasets allow for the systematic analysis of complex genomic alteration associations in tumorigenesis. Here, we present a protocol to quantify diverse interaction patterns between genomic alterations. We describe steps to prepare a binarized alteration matrix and analyze mutation-copy number alteration (CNA) associations, including pairwise, high-order, and context-dependent associations. This protocol enables the analysis of context-specific genetic interactions. For complete details on the use and execution of this protocol, please refer to Maqueda-Real et al. 1 1. Maqueda-Real, A. ∙ Ollé-Monràs, L. ∙ Park, S. Mapping cancer gene dynamics through state-specific interactions Cell Rep. 2025; 44 , 115872 Google Scholar