ArticleCancer control : journal of the Moffitt Cancer Center
Assessing the Impact of Patient Selection and Analytical Methods on mRNA Biomarker Identification in Ovarian Cancer Using TCGA Data.
Article in Cancer control : journal of the Moffitt Cancer Center. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
IntroductionThe Cancer Genome Atlas (TCGA) data has been extensively used for differentially expressed genes (DEGs) discovery and validation in high-grade serous ovarian cancer (HGSOC), however platinum-sensitivity biomarkers have not yet reached clinical application. We aimed to propose a robust analytical framework for TCGA platinum sensitivity studies and systematically demonstrate how patient characteristics influence DEG analyses between platinum-sensitive and resistant groups, while also considering experimental platforms and analysis pipelines, as their impact is recognized but not comprehensively evaluated.MethodsThis retrospective TCGA cohort study used publicly available microarray and RNA-seq gene expression data. TCGA-derived datasets were identified through a literature review, including only studies enabling unambiguous patient identification. Three TCGA-based cohorts were assembled-two directly from published studies and one curated through own selection-differing in patient numbers (230, 201 and 142 patients, respectively) and stage distribution. Data were analyzed using
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