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Updated: Feb 15, 2026

Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing
Published on: October 10, 2025
Protocol for quantifying interaction patterns among genomic alterations in cancer
Adrián Maqueda-Real1, Seokjin Ham1, Laia Ollé-Monràs2
1Cancer Genomics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain.
None:
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.
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