title: Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association.
abstract: Automated analysis of whole mount tissue sections can provide insights into tumor subtypes and the underlying molecular basis of neoplasm. However, since tumor sections are collected from different laboratories, inherent technical and biological variations impede analysis for very large datasets such as The Cancer Genome Atlas (TCGA). Our objective is to characterize tumor histopathology, through the delineation of the nuclear regions, from hematoxylin and eosin (H&E) stained tissue sections. Such a representation can then be mined for intrinsic subtypes across a large dataset for prediction and molecular association. Furthermore, nuclear segmentation is formulated within a multi-reference graph framework with geodesic constraints, which enables computation of multidimensional representations, on a cell-by-cell basis, for functional enrichment and bioinformatics analysis. Here, we present a novel method, multi-reference graph cut (MRGC), for nuclear segmentation that overcomes technical variations associated with sample preparation by incorporating prior knowledge from manually annotated reference images and local image features. The proposed approach has been validated on manually annotated samples and then applied to a dataset of 377 Glioblastoma Multiforme (GBM) whole slide images from 146 patients. For the GBM cohort, multidimensional representation of the nuclear features and their organization have identified 1) statistically significant subtypes based on several morphometric indexes, 2) whether each subtype can be predictive or not, and 3) that the molecular correlates of predictive subtypes are consistent with the literature. Data and intermediaries for a number of tumor types (GBM, low grade glial, and kidney renal clear carcinoma) are available at: http://tcga.lbl.gov for correlation with TCGA molecular data. The website also provides an interface for panning and zooming of whole mount tissue sections with/without overlaid segmentation results for quality control.
authors.affiliation: Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. hchang@lbl.gov
authors.forename: Hang
authors.initials: H
authors.lastname: Chang
authors.forename: Ju
authors.initials: J
authors.lastname: Han
authors.forename: Alexander
authors.initials: A
authors.lastname: Borowsky
authors.forename: Leandro
authors.initials: L
authors.lastname: Loss
authors.forename: Joe W
authors.initials: JW
authors.lastname: Gray
authors.forename: Paul T
authors.initials: PT
authors.lastname: Spellman
authors.forename: Bahram
authors.initials: B
authors.lastname: Parvin
mesh_terms: D000465:Algorithms; D001932:Brain Neoplasms / Q000737:chemistry / Q000473:pathology*; D002467:Cell Nucleus / Q000737:chemistry; D004396:Coloring Agents / Q000737:chemistry; D016208:Databases, Factual; D004801:Eosine Yellowish-(YS) / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry; D005909:Glioblastoma / Q000737:chemistry / Q000473:pathology*; D006416:Hematoxylin / Q000737:chemistry; D006651:Histocytochemistry / Q000379:methods; D006801:Humans; D013194:Staining and Labeling / Q000379:methods
chemical_list: D004396:Coloring Agents; D005456:Fluorescent Dyes; D004801:Eosine Yellowish-(YS); D006416:Hematoxylin