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The massive genomic data from The Cancer Genome Atlas (TCGA), including proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC), provides a unique opportunity to study cancer systematically. While most observations are made from a single type of genomics data, we apply big data analytics and systems biology approaches by simultaneously analyzing DNA amplification, mRNA and protein abundance. Using multiple genomic profiles, we have discovered widespread dosage compensation for the extensive aneuploidy observed in TCGA breast cancer samples. We do identify 11 genes that show strong correlation across all features (DNA/mRNA/protein) analogous to that of the well-known oncogene HER2 (ERBB2). These genes are generally less well-characterized regarding their role in cancer and we advocate their further study. We also discover that shRNA knockdown of these genes has an impact on cancer cell growth, suggesting a vulnerability that could be used for cancer therapy. Our study shows the advantages of systematic big data methodologies and also provides future research directions. [ABSTRACT FROM AUTHOR]

Clostridium difficile is the most common cause of nosocomial diarrhea in the United States and Europe, and is a cause of significant morbidity and mortality among hospitalized patients. A newly identified epidemic strain has been associated with many hospital outbreaks of C. difficile-associated disease (CDAD), raising the concern of an escalating burden of CDAD among at-risk patients. Hematopoietic SCT (HSCT) recipients are known to be at increased risk for a wide variety of infectious complications, including CDAD as a result of prolonged hospitalizations, exposure to broad-spectrum antibiotics, altered integrity of the intestinal mucosa and GVHD. The incidence of CDAD in the HSCT population has been reported as high as 20% in some large series. The frequency and seriousness of CDAD in this defined group as compared with the general hospital population, however, are not clearly delineated. We discuss the epidemiology and diagnosis of CDAD and review recent studies examining the risk factors and characteristics of CDAD in HSCT recipients. Finally, we provide a management algorithm for the diagnosis and treatment of CDAD at our institution.Bone Marrow Transplantation (2008) 42, 705–713; doi:10.1038/bmt.2008.317; published online 6 October 2008 [ABSTRACT FROM AUTHOR]