51 research outputs found
Understanding the immune landscape and tumor microenvironment of pancreatic cancer to improve immunotherapy
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Circulating tumor cells as a biomarker of response to treatment in patient derived xenograft mouse models of pancreatic adenocarcinoma
No full textMultifocal Branch Duct Intraductal Papillary Mucinous Neoplasm with 3 cm Lesion in Head of Pancreas
No full textAbstract B80: Stroma in pancreatic cancer: Automated quantification and its prognostic significance
No full textDe novo compartment deconvolution and weight estimation of tumor samples using DECODER
No full textTumors are mixtures of different compartments. While global gene expression analysis profiles the average expression of all compartments in a sample, identifying the specific contribution of each compartment remains a challenge. With the increasing recognition of the importance of non-neoplastic components, the ability to breakdown the gene expression contribution of each is critical. Here, we develop DECODER, an integrated framework which performs de novo deconvolution and single-sample compartment weight estimation. We use DECODER to deconvolve 33 TCGA tumor RNA-seq data sets and show that it may be applied to other data types including ATAC-seq. We demonstrate that it can be utilized to reproducibly estimate cellular compartment weights in pancreatic cancer that are clinically meaningful. Application of DECODER across cancer types advances the capability of identifying cellular compartments in an unknown sample and may have implications for identifying the tumor of origin for cancers of unknown primary
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