The Cancer Genome Atlas (TCGA) generates comprehensive genomic data for thousands of patients over more than 20 cancer types. TCGA data are typically whole-genome measurements of multiple genomic features, such as DNA copy numbers, DNA methylation, and gene expression, providing unique opportunities for investigating cancer mechanism from multiple molecular and regulatory layers. We propose a B...

BACKGROUND Six gene expression subtypes of invasive epithelial ovarian cancer were recently defined using microarrays by Tothill and colleagues. The Cancer Genome Atlas (TCGA) project subsequently replicated these subtypes and identified a signature predictive of survival in high-grade serous (HGS) cancers. We previously validated these signatures for use in formalin-fixed paraffin-embedded tis...

Objective To provide a review of emerging knowledge from genomics and related basic science, preclinical, and clinical precision medicine studies in head and neck squamous cell carcinoma (HNSCC). Data Sources The Cancer Genome Atlas Network (TCGA) publications, PubMed-based literature review, and ClinicalTrials.gov. Review Methods TCGA publications, PubMed, and ClinicalTrials.gov were queri...

Purpose: We aimed to identify DNA methylation biomarkers of progression-free survival (PFS) to platinum-based chemotherapy in high-grade serous ovarian cancer (HGSOC) within biologically relevant ovarian cancer-associated pathways. ExperimentalDesign:Associationwith PFS of CpG island (CGI) promoterDNAmethylation at genes in the pathways Akt/mTOR, p53, redox, and homologous recombination DNA rep...

Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian cancers profiled by microarray (p<0.01). We also identified 12 miRNAs that a...

Protein levels and function are poorly predicted by genomic and transcriptomic analysis of patient tumours. Therefore, direct study of the functional proteome has the potential to provide a wealth of information that complements and extends genomic, epigenomic and transcriptomic analysis in The Cancer Genome Atlas (TCGA) projects. Here we use reverse-phase protein arrays to analyse 3,467 patien...

Cancer results from a breakdown of normal gene expression control, so the study of gene regulation is critical to cancer research. To gain insight into the transcriptional and epigenetic factors regulating abnormal gene expression patterns in cancers, we developed the Cistrome Cancer web resource (http://cistrome.org/CistromeCancer/). We conducted the systematic integration and modeling of over...

Lung cancer is the most prevalent cancer worldwide, and histopathological assessment is indispensable for its diagnosis. However, human evaluation of pathology slides cannot accurately predict patients' prognoses. In this study, we obtain 2,186 haematoxylin and eosin stained histopathology whole-slide images of lung adenocarcinoma and squamous cell carcinoma patients from The Cancer Genome Atla...

MOTIVATION Genomic analyses of many solid cancers have demonstrated extensive genetic heterogeneity between as well as within individual tumors. However, statistical methods for classifying tumors by subtype based on genomic biomarkers generally entail an all-or-none decision, which may be misleading for clinical samples containing a mixture of subtypes and/or normal cell contamination. RESUL...