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Ongoing Chakra Check-In Class

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Ryan Gomez
Ryan Gomez

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The Cancer Genome Atlas (TCGA) uses genome analysis technologies, such as large-scale genome sequencing, to aid in the understanding of the molecular basis of cancer [23]. The mRNA (RNASeqV2) and clinical data were downloaded for 1085 patients with breast invasive carcinoma who had received pharmacological treatment (hormone therapy), chemotherapy, hormone and chemotherapy, an unknown treatment, or no treatment. Cases, which were either ER or PR or HER2 positive, were excluded such that 114 patients with TNBC remained.




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For classifier comparison, we downloaded gene expression raw data files (.cel) of seven data sets from NCBI GEO database (GSE5327, GSE5847, GSE12276, GSE16446, GSE18864, GSE19615, and GSE20194). The expression values were summarized and normalized by Robust multiarray analysis (RMA) [24]. The Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) is a joint Canada-UK project with the purpose of analyzing the molecular signatures of a large number of well-annotated breast tumors to further classify the tumors into subtypes [25]. The clinical traits and gene expression data were analyzed for ER, PR, and HER2 information resulting in the identification of 126 TNBC cases. In addition, two more sets (GSE58812, GSE25066) and cell line data (GSE10890) were used for prognostic signature validation. 041b061a72


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