Pan-cancer insights from The Cancer Genome Atlas: the pathologist's perspective

ABSTRACT

The Cancer Genome Atlas (TCGA) represents one of several international consortia dedicated to performing comprehensive genomic and epigenomic analyses of selected tumor types to advance understanding of disease and provide an open-access resource for worldwide cancer research. Thirty-three tumor types (selected by histology or tissue of origin, to include both common and rare diseases), comprising over 11,000 specimens were subjected to DNA sequencing, copy number and methylation analysis, and transcriptomic, proteomic, and histologic evaluation. Each cancer type was analyzed individually to identify tissue-specific alterations, and make correlations across different molecular platforms. The final data set was then normalized and combined for the PanCancer Initiative which seeks to identify commonalities across different cancer types or cells of origin/lineage, or within anatomically or morphologically-related groups. An important resource generated along with the rich molecular studies is an extensive digital pathology slide archive, comprised of frozen section tissue directly related to the tissues analyzed as part of TCGA, and representative formalin-fixed paraffin-embedded, hematoxylin and eosin (H&E) stained diagnostic slides. These H&E image resources have primarily been used to verify diagnoses and histologic subtypes with some limited extraction of standard pathologic variables such as mitotic activity, grade, and lymphocytic infiltrates. Largely overlooked is the richness of these scanned images for more sophisticated feature extraction approaches coupled with machine learning, and ultimately correlation with molecular features and clinical endpoints. Here we document initial attempts to exploit TCGA imaging archives, describe some of the tools, and the rapidly evolving image analysis / feature extraction landscape. Our hope is to inform, and ultimately inspire and challenge the pathology and cancer research communities to exploit these imaging resources so that the full potential of this integral platform of TCGA can complement and enhance the insightful integrated analyses from the genomic and epigenomic platforms.

from #ORL-AlexandrosSfakianakis via ola Kala on Inoreader http://ift.tt/2Ecs0K6