![]() ![]() The method is publicly available as an R package ( ), and as an interactive web application ( ). TumorComparer compares tumors and cell lines on the basis of multiple datum types, such as mutations, DNA CNAs, and mRNA gene expression, by using weights to emphasize events relevant to the specific biological question at hand, e.g., the more frequent and/or known oncogenic events ( Figure 1A). TumorComparer is a generally applicable method suitable for pre-clinical cancer research and personalized medicine applications where sets of samples need to be assessed for similarity. We apply TumorComparer to the comparison of ∼8,000 tumors and ∼600 cell lines across 24 cancer types as an initial application to provide a general, pan-cancer resource based on knowledge of oncogenic alterations gained from The Cancer Genome Atlas program (TCGA). We present TumorComparer, a computational comparison method based on weighted features to allow expert- and knowledge-driven comparison of tumors and experimental models, such as cell lines or organoids. This motivates the need for a flexible method of comparing tumors with potential cell line models by using researcher-selected properties. Furthermore, many research questions focus on particular genes and their activity (e.g., specific signaling pathways, drug targets, etc.). However, not all changes are functionally important-few genes can promote oncogenesis (also termed “cancer drivers”), whereas other altered genes have little effect on the phenotype (termed “passengers”). Cancer is a genetic disease, typically marked by widespread somatic alterations (e.g., mutations, copy-number alterations, and gene expression changes). ![]()
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January 2023
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