Work

Protocol for quantifying interaction patterns among genomic alterations in cancer

Year: 2026

Type: article

Abstract: 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

Source: STAR Protocols

DOI: 10.1016/j.xpro.2026.104364

Authors: Adrián Maqueda-Real, Seokjin Ham, Laia Ollé-Monràs, Solip Park

Institutions: Spanish National Cancer Research Centre, Vall d'Hebron Institute of Oncology

Language: English

Topic: Cancer Genomics and Diagnostics

Subfield: Cancer Research

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $1,550