Sambit K. Mohanty

The CAP cancer protocols – a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid

BackgroundThe Cancer Biomedical Informatics Grid (caBIG™) is a network of individuals and institutions, creating a world wide web of cancer research. An important aspect of this informatics effort is the development of consistent practices for data standards development, using a multi-tier approach that facilitates semantic interoperability of systems. The semantic tiers include (1) information models, (2) common data elements, and (3) controlled terminologies and ontologies. The College of American Pathologists (CAP) cancer protocols and checklists are an important reporting standard in pathology, for which no complete electronic data standard is currently available.MethodsIn this manuscript, we provide a case study of Cancer Common Ontologic Representation Environment (caCORE) data standard implementation of the CAP cancer protocols and checklists model – an existing and complex paper based standard. We illustrate the basic principles, goals and methodology for developing caBIG™ models.ResultsUsing this example, we describe the process required to develop the model, the technologies and data standards on which the process and models are based, and the results of the modeling effort. We address difficulties we encountered and modifications to caCORE that will address these problems. In addition, we describe four ongoing development projects that will use the emerging CAP data standards to achieve integration of tissue banking and laboratory information systems.ConclusionThe CAP cancer checklists can be used as the basis for an electronic data standard in pathology using the caBIG™ semantic modeling methodology.

The development and deployment of Common Data Elements for tissue banks for translational research in cancer – An emerging standard based approach for the Mesothelioma Virtual Tissue Bank

BackgroundRecent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) – compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC).MethodsThe purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML).ResultsCommon Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, clinical history, pathology data including block level annotation, and follow-up data including treatment, recurrence and vital status. The end result of such an effort would eventually provide an increased sample set to the researchers, and makes the system interoperable between institutions.ConclusionThe CAP, ADASP and the NAACCR elements represent widely established data elements that are utilized in many cancer centers. Herein, we have shown these representations can be combined and formalized to create a core set of annotations for banked mesothelioma specimens. Because these data elements are collected as part of the normal workflow of a medical center, data sets developed on the basis of these elements can be easily implemented and maintained.

Mixed Epithelial and Stromal Tumors of the Kidney: An Overview

Mixed epithelial and stromal tumor of the kidney is a recently recognized distinct neoplasm that should be distinguished from other renal neoplasms. These tumors are relatively rare with a female preponderance. Imaging studies are not diagnostic but reveal a solid or solid and cystic mass in most cases. Histopathologically, these tumors reveal biphasic growth pattern comprising mesenchymal and epithelial elements with characteristic estrogen and progesterone receptor immunoreactive mesenchyme reminiscent of ovarian stroma. Malignant transformation, recurrence, and metastasis are rare; however, recently a few cases of malignant mixed epithelial and stromal tumors have been reported in the literature. Recently a case with translocation t(1;19) has been described. This article provides a brief overview of the current knowledge of mixed epithelial and stromal tumor of the kidney.

The importance of pathology informatics in translational research.

Pathology informatics involves management and analysis of large complex data sets derived from various tests performed in clinical and anatomic pathology laboratories, annotated biorepositories, image analysis, telepathology, and large scale experiments, including gene expression analysis, proteomics, and tissue array studies. It facilitates intelligent use of computing technologies to improve patient care and understand the natural history of disease. Herein, we describe the various bioinformatics tools used to support translational research at the University of Pittsburgh Medical Center.

Uterine Angioleiomyoma: A Rare Variant of Uterine Leiomyoma

Uterine angioleiomyoma is an extremely rare and unique variant of leiomyoma. It usually occurs in middle-aged women, who commonly present with menorrhagia, abdominal pain, or abdominal mass. The lesions are either single or multiple and manifest as submucosal, intramural, or subserosal whorled nodules. Microscopy of the individual nodule shows interlacing fascicles of spindle cells swirling around thick-walled blood vessels. Angioleiomyoma usually lacks mitotic figures, pleomorphism, or necrosis, although cases with marked nuclear atypia and multinucleated giant cells have been reported. The tumor cells are immunoreactive for smooth muscle actin, desmin, h-caldesmon, and progesterone receptor, with a low Ki-67 labeling index. Because these lesions are vascular, they may undergo spontaneous rupture and pose a life-threatening emergency, especially in pregnancy. There are no specific imaging findings; therefore, a preoperative diagnosis is extremely difficult. It is important to recognize this entity and differentiate it from a malignancy, particularly when angioleiomyoma shows significant cytologic atypia or raised cancer antigen 125 levels by thorough sampling. When required, a proper immunohistochemical panel should be used to arrive at a correct diagnosis. In this review, we discuss the current knowledge on uterine angioleiomyoma and its clinical relevance.