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LaFramboise WA, Petrosko P, Krill-Burger JM, Morris DR, McCoy AR, Scalise D, Malehorn DE, Guthrie RD, Becich MJ, Dhir R. Proteins secreted by embryonic stem cells activate cardiomyocytes through ligand binding pathways. J Proteomics 2010; 73:992-1003. [PMID: 20045494 DOI: 10.1016/j.jprot.2009.12.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/13/2009] [Accepted: 12/19/2009] [Indexed: 12/12/2022]
Abstract
Human embryonic stem cells (hESC) underlie embryogenesis but paracrine signals associated with the process are unknown. This study was designed to 1) profile native proteins secreted by undifferentiated hESC and 2) determine their biological effects on primary neonatal cardiomyocytes. We utilized multi-analyte, immunochemical assays to characterize media conditioned by undifferentiated hESC versus unconditioned media. Expression profiling was performed on cardiomyocytes subjected to these different media conditions and altered transcripts were mapped to critical pathways. Thirty-two of 109 proteins were significantly elevated in conditioned media ranging in concentration from thrombospondin (57.2+/-5.0 ng/ml) to nerve growth factor (7.4+/-1.2pg/ml) and comprising chemokines, cytokines, growth factors, and proteins involved in cell adhesion and extracellular matrix remodeling. Conditioned media induced karyokinesis, cytokinesis and proliferation in mono- and binucleate cardiomyocytes. Pathway analysis revealed comprehensive activation of the ROCK 1 and 2 G-protein coupled receptor (GPCR) pathway associated with cytokinesis, and the RAS/RAF/MEK/ERK receptor tyrosine kinase (RTK) and JAK/STAT-cytokine pathway involved in cell cycle progression. These results provide a partial database of proteins secreted by pluripotent hESC that potentiate cell division in cardiomyocytes via a paracrine mechanism suggesting a potential role for these stem cell factors in cardiogenesis and cardiac repair.
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Affiliation(s)
- W A LaFramboise
- Department of Pathology, University of Pittsburgh School of Medicine, Shadyside Hospital, 5230 Centre Avenue, Pittsburgh, PA 15232, United States.
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Bernstam EV, Hersh WR, Johnson SB, Chute CG, Nguyen H, Sim I, Nahm M, Weiner MG, Miller P, DiLaura RP, Overcash M, Lehmann HP, Eichmann D, Athey BD, Scheuermann RH, Anderson N, Starren J, Harris PA, Smith JW, Barbour E, Silverstein JC, Krusch DA, Nagarajan R, Becich MJ. Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs. Acad Med 2009; 84:964-70. [PMID: 19550198 PMCID: PMC2884382 DOI: 10.1097/acm.0b013e3181a8144d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Clinical and translational research increasingly requires computation. Projects may involve multiple computationally oriented groups including information technology (IT) professionals, computer scientists, and biomedical informaticians. However, many biomedical researchers are not aware of the distinctions among these complementary groups, leading to confusion, delays, and suboptimal results. Although written from the perspective of Clinical and Translational Science Award (CTSA) programs within academic medical centers, this article addresses issues that extend beyond clinical and translational research. The authors describe the complementary but distinct roles of operational IT, research IT, computer science, and biomedical informatics using a clinical data warehouse as a running example. In general, IT professionals focus on technology. The authors distinguish between two types of IT groups within academic medical centers: central or administrative IT (supporting the administrative computing needs of large organizations) and research IT (supporting the computing needs of researchers). Computer scientists focus on general issues of computation such as designing faster computers or more efficient algorithms, rather than specific applications. In contrast, informaticians are concerned with data, information, and knowledge. Biomedical informaticians draw on a variety of tools, including but not limited to computers, to solve information problems in health care and biomedicine. The paper concludes with recommendations regarding administrative structures that can help to maximize the benefit of computation to biomedical research within academic health centers.
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Affiliation(s)
- Elmer V Bernstam
- University of Texas Health Science Center at Houston, Texas 77030, USA.
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Shirts BH, Perera S, Hanlon JT, Roumani YF, Studenski SA, Nace DA, Becich MJ, Handler SM. Provider management of and satisfaction with laboratory testing in the nursing home setting: results of a national internet-based survey. J Am Med Dir Assoc 2009; 10:161-166.e3. [PMID: 19233055 DOI: 10.1016/j.jamda.2008.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 08/25/2008] [Accepted: 08/27/2008] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To describe the management of and satisfaction with laboratory testing, and desirability of laboratory health information technology in the nursing home setting. DESIGN Cross-sectional study using an Internet-based survey. PARTICIPANTS AND SETTING National sample of 426 nurse practitioners and 308 physicians who practice in the nursing home setting. MEASUREMENTS Systems and processes available for ordering and reviewing laboratory tests, laboratory test result management satisfaction, self-reported delays in laboratory test result review, and desirability of computerized laboratory test result management features in the nursing home setting. RESULTS A total of 96 participants (48 physicians and 48 nurse practitioners) completed the survey, for an overall response rate of 13.1% (96/734). Of the survey participants, 77.1% had worked in the nursing home setting for more than 5 years. Over half of clinicians (52.1%) reported 3 or more recent delays in receiving laboratory test results. Only 43.8% were satisfied with their laboratory test results management. Satisfaction was associated with keeping a list of laboratory orders and availability of computerized laboratory test order entry. In the nursing home, 35.4% of participants reported the ability to electronically review laboratory test results, 12.5% and 10.4% respectively had computerized ordering of chemistry/hematology and microbiology/pathology tests. The following 3 features were rated most desirable in a computerized laboratory test result management system: showing abnormal results first, warning if a test result was missed, and allowing electronic acknowledgment of test results. CONCLUSION Delays in receiving laboratory test results and dissatisfaction with the management of laboratory test result information are commonly reported among physicians and nurse practitioners working in nursing homes. Test result management satisfaction was associated with computerized order entry and keeping track of ordered laboratory tests, suggesting that implementation of certain health information technology could potentially improve quality of care.
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Affiliation(s)
- Brian H Shirts
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Handler SM, Hanlon JT, Perera S, Saul MI, Fridsma DB, Visweswaran S, Studenski SA, Roumani YF, Castle NG, Nace DA, Becich MJ. Assessing the performance characteristics of signals used by a clinical event monitor to detect adverse drug reactions in the nursing home. AMIA Annu Symp Proc 2008; 2008:278-282. [PMID: 18998853 PMCID: PMC2656060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 06/30/2008] [Indexed: 05/27/2023]
Abstract
Adverse drug reactions (ADRs) are a common cause of morbidity and mortality in the nursing home (NH) setting. Traditional non-automated mechanisms for ADR detection are time-consuming, costly, and fail to detect the majority of ADRs. We describe the implementation and pharmacist evaluation of a clinical event monitor using signals previously developed by our research team to detect potential ADRs in the NH. The overall positive predictive value (PPV) for all signals combined was 81% (54/67), with individual signal PPVs ranging from 0-100%. The PPVs were 53% (10/19) for the antidote signals category and 96% (44/46) for the laboratory/ medication combination signals category. The majority 75% (12/16) of the preventable ADRs were laboratory/medication combination signals. The results suggest that ADRs can be detected in the NH setting with a high degree of accuracy using a clinical event monitor that employs a set of signals derived by expert consensus.
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Affiliation(s)
- Steven M Handler
- Division of Geriatric Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Dhir R, Patel AA, Winters S, Bisceglia M, Swanson D, Aamodt R, Becich MJ. A multidisciplinary approach to honest broker services for tissue banks and clinical data: a pragmatic and practical model. Cancer 2008; 113:1705-15. [PMID: 18683217 PMCID: PMC2745185 DOI: 10.1002/cncr.23768] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Honest broker services are essential for tissue- and data-based research. The honest broker provides a firewall between clinical and research activities. Clinical information is stripped of Health Insurance Portability and Accountability Act-denoted personal health identifiers. Research material may have linkage codes, precluding the identification of patients to researchers. The honest broker provides data derived from clinical and research sources. These data are for research use only, and there are rules in place that prohibit reidentification. Very rarely, the institutional review board (IRB) may allow recontact and develop a recontact plan with the honest broker. Certain databases are structured to serve a clinical and research function and incorporate 'real-time' updating of information. This complex process needs resolution of a variety of issues regarding the precise role of the HB and their interaction with data. There also is an obvious need for software solutions to make the task of deidentification easier. METHODS The University of Pittsburgh has implemented a novel, IRB-approved mechanism to address honest broker functions to meet the specimen and data needs of researchers. The Tissue Bank stores biologic specimens. The Cancer Registry culls data and annotating information as part of state- and federal-mandated functions and collects data on the clinical progression, treatment, and outcomes of cancer patients. The Cancer Registry also has additional IRB approval to collect data elements only for research purposes. The Clinical Outcomes Group is involved in patient safety and health services research. Radiation Oncology and Medical Oncology provide critical treatment related information. Pathology and Oncology Informatics have designed software tools for querying availability of specimens, extracting data, and deidentifying specimens and annotating data for clinical and translational research. These entities partnered and submitted a joint IRB proposal to create an institutional honest broker facility. The employees of this conglomerate have honest broker agreements with the University of Pittsburgh and the Medical Center. This provides a large group of honest brokers, ensuring availability for projects without any conflict of interest. RESULTS The honest broker system has been an IRB-approved institutional entity at the University of Pittsburgh since 2003. The honest broker system currently includes 33 certified honest brokers encompassing the multiple partners of this system. The honest broker system has handled >1600 requests over the past 4 years with a 25% increase in volume each year. CONCLUSIONS The current results indicate that the collaborative honest broker model described herein is robust and provides a highly functional solution to the specimen and data needs for critical clinical and translational research activities.
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Affiliation(s)
- Rajiv Dhir
- Department of Pathology, University of Pittsburgh, UPMC Shadyside-Presbyterian Hospital, Pittsburgh, Pennsylvania 15232, USA.
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Abstract
Rebecca Crowley and colleagues propose that academic health centers can and should lead the transition towards a culture of biomedical data sharing.
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Amin W, Parwani AV, Schmandt L, Mohanty SK, Farhat G, Pople AK, Winters SB, Whelan NB, Schneider AM, Milnes JT, Valdivieso FA, Feldman M, Pass HI, Dhir R, Melamed J, Becich MJ. National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research. BMC Cancer 2008; 8:236. [PMID: 18700971 PMCID: PMC2533341 DOI: 10.1186/1471-2407-8-236] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2008] [Accepted: 08/13/2008] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Advances in translational research have led to the need for well characterized biospecimens for research. The National Mesothelioma Virtual Bank is an initiative which collects annotated datasets relevant to human mesothelioma to develop an enterprising biospecimen resource to fulfill researchers' need. METHODS The National Mesothelioma Virtual Bank architecture is based on three major components: (a) common data elements (based on College of American Pathologists protocol and National North American Association of Central Cancer Registries standards), (b) clinical and epidemiologic data annotation, and (c) data query tools. These tools work interoperably to standardize the entire process of annotation. The National Mesothelioma Virtual Bank tool is based upon the caTISSUE Clinical Annotation Engine, developed by the University of Pittsburgh in cooperation with the Cancer Biomedical Informatics Grid (caBIG, see http://cabig.nci.nih.gov). This application provides a web-based system for annotating, importing and searching mesothelioma cases. The underlying information model is constructed utilizing Unified Modeling Language class diagrams, hierarchical relationships and Enterprise Architect software. RESULT The database provides researchers real-time access to richly annotated specimens and integral information related to mesothelioma. The data disclosed is tightly regulated depending upon users' authorization and depending on the participating institute that is amenable to the local Institutional Review Board and regulation committee reviews. CONCLUSION The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. Furthermore, it protects patient privacy by disclosing only de-identified datasets to assure that biospecimens can be made accessible to researchers.
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Affiliation(s)
- Waqas Amin
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Anil V Parwani
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, PA, USA
| | - Linda Schmandt
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Sambit K Mohanty
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Ghada Farhat
- Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andrew K Pople
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Sharon B Winters
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Nancy B Whelan
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Althea M Schneider
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - John T Milnes
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Federico A Valdivieso
- Department of Pathology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Michael Feldman
- Department of Pathology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, Division of Thoracic Surgery and Thoracic Oncology, New York University School of Medicine, New York, NY, USA
| | - Rajiv Dhir
- Department of Pathology, University of Pittsburgh School of Medicine, PA, USA
| | - Jonathan Melamed
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michael J Becich
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, PA, USA
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Handler SM, Shirts BH, Perera S, Becich MJ, Castle NG, Hanlon JT. Frequency of laboratory monitoring of chronic medications administered to nursing facility residents: results of a national Internet-based study. Consult Pharm 2008; 23:387-95. [PMID: 18540792 PMCID: PMC2597281 DOI: 10.4140/tcp.n.2008.387] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To determine the minimal frequency of laboratory monitoring of 30 types of chronic medications or classes that are administered to nursing facility residents and are either listed under pharmacy services tag F329 (the tag for unnecessary medications), or have a narrow therapeutic index. DESIGN AND SETTING Cross-sectional, Internet-based survey. PARTICIPANTS National sample of 500 pharmacists, 500 nurse practitioners, and 327 physicians. MAIN OUTCOME MEASURE Minimal frequency of monitoring, recorded as an interval of 1, 3, 6, 9, or 12 months, for each of 35 laboratory parameters (e.g., serum drug level, complete blood count, liver function tests) for the 30 types of chronic medications or classes. Agreement was defined as having two or more of the three professional groups select the same minimal monitoring interval. RESULTS Overall, 116 professionals (20 pharmacists, 48 physicians, and 48 nurse practitioners) completed the survey. Most respondents were women (58.6% [68/116]), and most had worked in nursing facilities for > 5 years (66.4% [77/116]). Regarding minimal laboratory monitoring intervals, respondents reached agreement concerning 33 of 35 parameters. They selected three or six months as the minimum interval for 30 of 35 parameters (85.7%), one month as the minimum for two parameters, and 12 months as the minimum for one parameter. CONCLUSION The multidisciplinary panel agreed that most medications that were listed under the F329 tag or have a narrow therapeutic index should have laboratory monitoring every three or six months. The results can be used by nursing facility professionals to establish minimal laboratory monitoring parameters for chronic medications, which may potentially reduce the occurrence of adverse drug reactions.
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Affiliation(s)
- Steven M Handler
- Department of Medicine, Division of Geriatric Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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Mohanty SK, Mistry AT, Amin W, Parwani AV, Pople AK, Schmandt L, Winters SB, Milliken E, Kim P, Whelan NB, Farhat G, Melamed J, Taioli E, Dhir R, Pass HI, Becich MJ. 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. BMC Cancer 2008; 8:91. [PMID: 18397527 PMCID: PMC2329649 DOI: 10.1186/1471-2407-8-91] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2007] [Accepted: 04/08/2008] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Recent 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). METHODS The 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). RESULTS Common 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. CONCLUSION The 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.
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Affiliation(s)
- Sambit K Mohanty
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amita T Mistry
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Waqas Amin
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anil V Parwani
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andrew K Pople
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Linda Schmandt
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sharon B Winters
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Paula Kim
- Translating Research Across Communities, USA
| | - Nancy B Whelan
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ghada Farhat
- Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jonathan Melamed
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Emanuela Taioli
- Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rajiv Dhir
- Translating Research Across Communities, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, Division of Thoracic Surgery and Thoracic Oncology, New York University School of Medicine, New York, NY, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Bartos CE, Fridsma DB, Butler BS, Penrod LE, Becich MJ, Crowley RS. Development of an instrument for measuring clinicians' power perceptions in the workplace. J Biomed Inform 2008; 41:1041-9. [PMID: 18375189 DOI: 10.1016/j.jbi.2008.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 02/18/2008] [Accepted: 02/20/2008] [Indexed: 10/22/2022]
Abstract
We report on the development of an instrument to measure clinicians' perceptions of their personal power in the workplace in relation to resistance to computerized physician order entry (CPOE). The instrument is based on French and Raven's six bases of social power and uses a semantic differential methodology. A measurement study was conducted to determine the reliability and validity of the survey. The survey was administered online and distributed via a URL by email to 19 physicians, nurses, and health unit coordinators from a university hospital. Acceptable reliability was achieved by removing or moving some semantic differential word pairs used to represent the six power bases (alpha range from 0.76 to 0.89). The Semantic Differential Power Perception (SDPP) survey validity was tested against an already validated instrument and found to be acceptable (correlation range from 0.51 to 0.81). The SDPP survey instrument was determined to be both reliable and valid.
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Affiliation(s)
- Christa E Bartos
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Abstract
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.
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Affiliation(s)
- Sambit K Mohanty
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
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Raab SS, Grzybicki DM, Condel JL, Stewart WR, Turcsanyi BD, Mahood LK, Becich MJ. Effect of Lean method implementation in the histopathology section of an anatomical pathology laboratory. J Clin Pathol 2007; 61:1193-9. [PMID: 17675533 DOI: 10.1136/jcp.2007.051326] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:In the USA, the lack of processes standardisation in histopathology laboratories leads to less than optimal quality, errors, inefficiency and increased costs. The effectiveness of large-scale quality improvement initiatives has been evaluated rarely.Aim:To measure the effect of implementation of a Lean quality improvement process on the efficiency and quality of a histopathology laboratory section.Methods:A non-concurrent interventional cohort study from 1 January 2003 to 31 December 2006 was performed, and the Lean process was implemented on 1 January 2004. Also compared was the productivity of the Lean histopathology section to a sister histopathology section that did not implement Lean processes. Pre- and post-Lean specimen turnaround time and productivity ratios (work units/full time equivalents) were measured. For 200 Lean interventions, a 5-part Likert scale was used to assess the impact on error, success and complexity.Results:In the Lean laboratory, the mean monthly productivity ratio increased from 3439 to 4074 work units/full time equivalents (p<0.001) as the mean daily histopathology section specimen turnaround time decreased from 9.7 to 9.0 h (p = 0.01). The Lean histopathology section had a higher productivity ratio compared with a sister histopathology section (1598 work units/full time equivalents, p<0.001) that did not implement Lean processes. The mean impact, success and complexity of interventions were 2.4, 2.7 and 2.5, respectively. The mean number of specific error causes affected by individual interventions was 2.6.Conclusion:It is concluded that Lean process implementation improved efficiency and quality in the histopathology section.
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Affiliation(s)
- S S Raab
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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63
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Mohanty SK, Piccoli AL, Devine LJ, Patel AA, William GC, Winters SB, Becich MJ, Parwani AV. Synoptic tool for reporting of hematological and lymphoid neoplasms based on World Health Organization classification and College of American Pathologists checklist. BMC Cancer 2007; 7:144. [PMID: 17672904 PMCID: PMC1950311 DOI: 10.1186/1471-2407-7-144] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 07/31/2007] [Indexed: 11/19/2022] Open
Abstract
Background Synoptic reporting, either as part of the pathology report or replacing some free text component incorporates standardized data elements in the form of checklists for pathology reporting. This ensures the pathologists make note of these findings in their reports, thereby improving the quality and uniformity of information in the pathology reports. Methods The purpose of this project is to develop the entire set of elements in the synoptic templates or "worksheets" for hematologic and lymphoid neoplasms using the World Health Organization (WHO) Classification and the College of American Pathologists (CAP) Cancer Checklists. The CAP checklists' content was supplemented with the most updated classification scheme (WHO classification), specimen details, staging as well as information on various ancillary techniques such as cytochemical studies, immunophenotyping, cytogenetics including Fluorescent In-situ Hybridization (FISH) studies and genotyping. We have used a digital synoptic reporting system as part of an existing laboratory information system (LIS), CoPathPlus, from Cerner DHT, Inc. The synoptic elements are presented as discrete data points, so that a data element such as tumor type is assigned from the synoptic value dictionary under the value of tumor type, allowing the user to search for just those cases that have that value point populated. Results These synoptic worksheets are implemented for use in our LIS. The data is stored as discrete data elements appear as an accession summary within the final pathology report. In addition, the synoptic data can be exported to research databases for linking pathological details on banked tissues. Conclusion Synoptic reporting provides a structured method for entering the diagnostic as well as prognostic information for a particular pathology specimen or sample, thereby reducing transcription services and reducing specimen turnaround time. Furthermore, it provides accurate and consistent diagnostic information dictated by pathologists as a basis for appropriate therapeutic modalities. Using synoptic reports, consistent data elements with minimized typographical and transcription errors can be generated and placed in the LIS relational database, enabling quicker access to desired information and improved communication for appropriate cancer management. The templates will also eventually serve as a conduit for capturing and storing data in the virtual biorepository for translational research. Such uniformity of data lends itself to subsequent ease of data viewing and extraction, as demonstrated by rapid production of standardized, high-quality data from the hemopoietic and lymphoid neoplasm specimens.
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Affiliation(s)
- Sambit K Mohanty
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anthony L Piccoli
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lisa J Devine
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ashokkumar A Patel
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gross C William
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sharon B Winters
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anil V Parwani
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Patel AA, Gilbertson JR, Showe LC, London JW, Ross E, Ochs MF, Carver J, Lazarus A, Parwani AV, Dhir R, Beck JR, Liebman M, Garcia FU, Prichard J, Wilkerson M, Herberman RB, Becich MJ. A novel cross-disciplinary multi-institute approach to translational cancer research: lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC). Cancer Inform 2007; 3:255-74. [PMID: 19455246 PMCID: PMC2675833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
BACKGROUND The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu) is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1) for bioinformatics and a repository of serum and tissue samples; (2) a data model for biomarker data storage; and (3) a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium's intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancer-specific biomarkers and encourage collaborative research efforts among the participating centers. METHODS The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission. The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual property/tech transfer agreements, and material transfer agreements that have been approved by each of the member institutions. This was the foundational work that has led to the development of a centralized data warehouse that has met each of the institutions' IRB/HIPAA standards. RESULTS Currently, this "virtual biorepository" has over 58,000 annotated samples from 11,467 cancer patients available for research purposes. The clinical annotation of tissue samples is either done manually over the internet or semi-automated batch modes through mapping of local data elements with PCABC common data elements. The database currently holds information on 7188 cases (associated with 9278 specimens and 46,666 annotated blocks and blood samples) of prostate cancer, 2736 cases (associated with 3796 specimens and 9336 annotated blocks and blood samples) of breast cancer and 1543 cases (including 1334 specimens and 2671 annotated blocks and blood samples) of melanoma. These numbers continue to grow, and plans to integrate new tumor sites are in progress. Furthermore, the group has also developed a central web-based tool that allows investigators to share their translational (genomics/proteomics) experiment data on research evaluating potential biomarkers via a central location on the Consortium's web site. CONCLUSIONS The technological achievements and the statewide informatics infrastructure that have been established by the Consortium will enable robust and efficient studies of biomarkers and their relevance to the clinical course of cancer. Studies resulting from the creation of the Consortium may allow for better classification of cancer types, more accurate assessment of disease prognosis, a better ability to identify the most appropriate individuals for clinical trial participation, and better surrogate markers of disease progression and/or response to therapy.
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Affiliation(s)
- Ashokkumar A. Patel
- Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh Cancer Institute
| | - John R. Gilbertson
- Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh Cancer Institute
| | | | | | | | | | - Joseph Carver
- Abramson Cancer Center of the University of Pennsylvania
| | - Andrea Lazarus
- Pennsylvania State Cancer Institute at Milton S. Hershey Medical Center
| | - Anil V. Parwani
- Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh Cancer Institute
| | - Rajiv Dhir
- Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh Cancer Institute
| | | | | | | | | | | | - Ronald B. Herberman
- Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh Cancer Institute
| | - Michael J. Becich
- Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh Cancer Institute
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Kajdacsy-Balla A, Geynisman JM, Macias V, Setty S, Nanaji NM, Berman JJ, Dobbin K, Melamed J, Kong X, Bosland M, Orenstein J, Bayerl J, Becich MJ, Dhir R, Datta MW. Practical aspects of planning, building, and interpreting tissue microarrays: The Cooperative Prostate Cancer Tissue Resource experience. J Mol Histol 2007; 38:113-21. [PMID: 17318343 DOI: 10.1007/s10735-006-9054-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Accepted: 08/23/2006] [Indexed: 10/23/2022]
Abstract
This is a review of several new approaches developed at or adopted by the Cooperative Prostate Cancer Tissue Resource (CPCTR) to resolve issues involved in tissue microarray (TMA) construction and use. CPCTR developed the first needle biopsy TMA, allowing researchers to obtain 200 or more consecutive cancer sections from a single biopsy core. Using radiographs of original paraffin blocks to measure tissue thickness we developed a method to produce TMAs with a larger number of usable sections. The modular approach to plan TMA construction is also a novel concept wherein TMAs of different types, such as tumor grade TMAs, metastasis TMA and hormone refractory tumors TMA can be combined to form an ensemble of TMAs with expanded research utility, such as support for tumor progression studies. We also implemented an open access TMA Data Exchange Specification that allows TMA data to be organized in a self-describing XML document annotated with well-defined common data elements. It ensures inter-laboratory reproducibility because it offers information describing the preparation of TMA blocks and slides. There are many important aspects that may be missed by both beginners and experienced investigators in areas of TMA experimental design, human subjects protection, population sample size, selection of tumor areas to sample, strategies for saving tissues, choice of antibodies for immunohistochemistry, and TMA data management.
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Affiliation(s)
- A Kajdacsy-Balla
- Department of Pathology, University of Illinois Chicago, Chicago, IL 60607-7053, USA.
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LaFramboise WA, Scalise D, Stoodley P, Graner SR, Guthrie RD, Magovern JA, Becich MJ. Cardiac fibroblasts influence cardiomyocyte phenotype in vitro. Am J Physiol Cell Physiol 2007; 292:C1799-808. [PMID: 17229813 DOI: 10.1152/ajpcell.00166.2006] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cardiac fibroblasts impact myocardial development and remodeling through intercellular contact with cardiomyocytes, but less is known about noncontact, profibrotic signals whereby fibroblasts alter cardiomyocyte behavior. Fibroblasts and cardiomyocytes were harvested from newborn rat ventricles and separated by serial digestion and gradient centrifugation. Cardiomyocytes were cultured in 1) standard medium, 2) standard medium diluted 1:1 with PBS, or 3) standard medium diluted 1:1 with medium conditioned > or =72 h by cardiac fibroblasts. Serum concentrations were held constant under all media conditions, and complete medium exchanges were performed daily. Cardiomyocytes began contracting within 24 h at clonal or mass densities with <5% of cells expressing vimentin. Immunocytochemical analysis revealed progressive expression of alpha-smooth muscle actin in cardiomyocytes after 24 h in all conditions. Only cardiomyocytes in fibroblast-conditioned medium stopped contracting by 72 h. There was a significant, sustained increase in vimentin expression specific to these cultures (means +/- SD: conditioned 46.3 +/- 6.0 vs. control 5.3 +/- 2.9%, P < 0.00025) typically with cardiac myosin heavy chain coexpression. Proteomics assays revealed 10 cytokines (VEGF, GRO/KC, monocyte chemoattractant protein-1, leptin, macrophage inflammatory protein-1alpha, IL-6, IL-10, IL-12p70, IL-17, and tumor necrosis factor-alpha) at or below detection levels in unconditioned medium that were significantly elevated in fibroblast-conditioned medium. Latent transforming growth factor-beta and RANTES were present in unconditioned medium but rose to higher levels in conditioned medium. Only granulocyte-macrophage colony-stimulating factor was present above threshold levels in standard medium but decreased with fibroblast conditioning. These data indicated that under the influence of fibroblast-conditioned medium, cardiomyocytes exhibited marked hypertrophy, diminished contractile capacity, and phenotype plasticity distinct from the dedifferentiation program present under standard culture conditions.
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Affiliation(s)
- W A LaFramboise
- University of Pittsburgh School of Medicine, Shadyside Hospital, Department of Pathology, West Wing G Floor, Rm. WG21.3, 5230 Center Ave., Pittsburgh, PA 15232, USA.
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Ma C, Lyons-Weiler M, Liang W, LaFramboise W, Gilbertson JR, Becich MJ, Monzon FA. In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays. J Mol Diagn 2006; 8:183-92. [PMID: 16645204 PMCID: PMC1867595 DOI: 10.2353/jmoldx.2006.050077] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of different amplification and labeling methods on DNA microarray expression results has not been previously delineated. To analyze the variation associated with widely accepted T7-based RNA amplificationand labeling methods, aliquots of the Stratagene Human Universal Reference RNA were labeled using three eukaryotic target preparation methods followed by uniform replicate array hybridization (Affymetrix U95Av2). Method-dependent variability was observed in the yield and size distribution of labeled products, as well as in the gene expression results. A significant increase in short transcripts, when compared to unamplified mRNA, was observed in methods with long in vitro transcription reactions. Intramethod reproducibility showed correlation coefficients >0.99, whereas intermethod comparisons showed coefficients ranging from 0.94 to 0.98 and a nearly twofold increase in coefficient of variation. Fold amplification for each method positively correlated with the number of genes present. Our experiments uncovered two factors that introduced significant bias in gene expression data: the number of labeled nucleotides, which introduces sequence-dependent bias, and the length of the in vitro transcription reaction, which introduces transcript size-dependent bias. This study provides evidence that variability in expression data may be caused, in part, by differences in amplification and labeling protocols.
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Affiliation(s)
- Changqing Ma
- Department of Pathology, Center for Pathology Informatics, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15237, USA.
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68
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Patel AA, Gilbertson JR, Parwani AV, Dhir R, Datta MW, Gupta R, Berman JJ, Melamed J, Kajdacsy-Balla A, Orenstein J, Becich MJ. An informatics model for tissue banks--lessons learned from the Cooperative Prostate Cancer Tissue Resource. BMC Cancer 2006; 6:120. [PMID: 16677389 PMCID: PMC1484486 DOI: 10.1186/1471-2407-6-120] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2006] [Accepted: 05/05/2006] [Indexed: 11/16/2022] Open
Abstract
Background Advances in molecular biology and growing requirements from biomarker validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control. Methods Data managers review the medical records to collect and continuously update information for the 145 clinical, pathological and inventorial CDEs that the Resource maintains for each case. An Access-based data entry tool provides de-identification and a standard communication mechanism between each group and a central CPCTR database. Standardized automated quality control audits have been implemented. Centrally, an Oracle database has web interfaces allowing multiple user-types, including the general public, to mine de-identified information from all of the sites with three levels of specificity and granularity as well as to request tissues through a formal letter of intent. Results Since July 2003, CPCTR has offered over 6,000 cases (38,000 blocks) of highly characterized prostate cancer biospecimens, including several tissue microarrays (TMA). The Resource developed a website with interfaces for the general public as well as researchers and internal members. These user groups have utilized the web-tools for public query of summary data on the cases that were available, to prepare requests, and to receive tissues. As of December 2005, the Resource received over 130 tissue requests, of which 45 have been reviewed, approved and filled. Additionally, the Resource implemented the TMA Data Exchange Specification in its TMA program and created a computer program for calculating PSA recurrence. Conclusion Building a biorepository infrastructure that meets today's research needs involves time and input of many individuals from diverse disciplines. The CPCTR can provide large volumes of carefully annotated prostate tissue for research initiatives such as Specialized Programs of Research Excellence (SPOREs) and for biomarker validation studies and its experience can help development of collaborative, large scale, virtual tissue banks in other organ systems.
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Affiliation(s)
- Ashokkumar A Patel
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - John R Gilbertson
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anil V Parwani
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rajiv Dhir
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Milton W Datta
- Departments of Pathology and Urology, Emory University, Atlanta, GA, USA
| | - Rajnish Gupta
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jules J Berman
- Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Melamed
- Departments of Pathology, New York University, New York, NY, USA
| | | | - Jan Orenstein
- Departments of Pathology, George Washington University, Washington, DC, USA
| | - Michael J Becich
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
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Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell 2005; 8:393-406. [PMID: 16286247 DOI: 10.1016/j.ccr.2005.10.001] [Citation(s) in RCA: 598] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 07/25/2005] [Accepted: 10/05/2005] [Indexed: 10/25/2022]
Abstract
Molecular profiling of cancer at the transcript level has become routine. Large-scale analysis of proteomic alterations during cancer progression has been a more daunting task. Here, we employed high-throughput immunoblotting in order to interrogate tissue extracts derived from prostate cancer. We identified 64 proteins that were altered in prostate cancer relative to benign prostate and 156 additional proteins that were altered in metastatic disease. An integrative analysis of this compendium of proteomic alterations and transcriptomic data was performed, revealing only 48%-64% concordance between protein and transcript levels. Importantly, differential proteomic alterations between metastatic and clinically localized prostate cancer that mapped concordantly to gene transcripts served as predictors of clinical outcome in prostate cancer as well as other solid tumors.
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Grzybicki DM, Turcsanyi B, Becich MJ, Gupta D, Gilbertson JR, Raab SS. Database construction for improving patient safety by examining pathology errors. Am J Clin Pathol 2005; 124:500-9. [PMID: 16146808 DOI: 10.1309/xn25jg7k0jfjb10c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A critical component of improving patient safety is reducing medical errors. "Improving Patient Safety by Examining Pathology Errors" is a project designed to collect data about and analyze diagnostic errors voluntarily reported by 4 academic anatomic pathology laboratories and to develop and implement interventions to reduce errors and improve patient outcomes. The study database is Web-mediated and Oracle-based, and it houses de-identified error data detected by cytologic-histologic correlation and interdepartmental conference review. We describe the basic design of the database with a focus on challenges faced as a consequence of the absence of standardized and detailed laboratory workload and quality assurance data sets in widely used laboratory information systems and the lack of efficient and comprehensive electronic de-identification of unlinked institutional laboratory information systems and clinical data. Development of these electronic data abstraction capabilities is critical for efforts to improve patient safety through the examination of pathology diagnostic errors.
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Affiliation(s)
- Dana Marie Grzybicki
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15232, USA
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Patel AA, Kajdacsy-Balla A, Berman JJ, Bosland M, Datta MW, Dhir R, Gilbertson J, Melamed J, Orenstein J, Tai KF, Becich MJ. The development of common data elements for a multi-institute prostate cancer tissue bank: the Cooperative Prostate Cancer Tissue Resource (CPCTR) experience. BMC Cancer 2005; 5:108. [PMID: 16111498 PMCID: PMC1236914 DOI: 10.1186/1471-2407-5-108] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Accepted: 08/21/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Cooperative Prostate Cancer Tissue Resource (CPCTR) is a consortium of four geographically dispersed institutions that are funded by the U.S. National Cancer Institute (NCI) to provide clinically annotated prostate cancer tissue samples to researchers. To facilitate this effort, it was critical to arrive at agreed upon common data elements (CDEs) that could be used to collect demographic, pathologic, treatment and clinical outcome data. METHODS The CPCTR investigators convened a CDE curation subcommittee to develop and implement CDEs for the annotation of collected prostate tissues. The draft CDEs were refined and progressively annotated to make them ISO 11179 compliant. The CDEs were implemented in the CPCTR database and tested using software query tools developed by the investigators. RESULTS By collaborative consensus the CPCTR CDE subcommittee developed 145 data elements to annotate the tissue samples collected. These included for each case: 1) demographic data, 2) clinical history, 3) pathology specimen level elements to describe the staging, grading and other characteristics of individual surgical pathology cases, 4) tissue block level annotation critical to managing a virtual inventory of cases and facilitating case selection, and 5) clinical outcome data including treatment, recurrence and vital status. These elements have been used successfully to respond to over 60 requests by end-users for tissue, including paraffin blocks from cases with 5 to 10 years of follow up, tissue microarrays (TMAs), as well as frozen tissue collected prospectively for genomic profiling and genetic studies. The CPCTR CDEs have been fully implemented in two major tissue banks and have been shared with dozens of other tissue banking efforts. CONCLUSION The freely available CDEs developed by the CPCTR are robust, based on "best practices" for tissue resources, and are ISO 11179 compliant. The process for CDE development described in this manuscript provides a framework model for other organ sites and has been used as a model for breast and melanoma tissue banking efforts.
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Affiliation(s)
- Ashokkumar A Patel
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Jules J Berman
- Cancer Diagnosis Program, National Cancer Institute, Bethesda, MD, USA
| | - Maarten Bosland
- Departments of Environmental Medicine and Urology, New York University, New York, NY, USA
| | - Milton W Datta
- Departments of Pathology and Urology, Emory University, Atlanta, GA, USA
| | - Rajiv Dhir
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Gilbertson
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Jan Orenstein
- Department of Pathology, George Washington University, Washington, DC, USA
| | - Kuei-Fang Tai
- Bioinformatics Program, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael J Becich
- Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
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Cannon GM, Pound CR, Landsittel DP, Bastacky SI, Dhir R, Becich MJ, Nelson JB. Perineural invasion in prostate cancer biopsies is not associated with higher rates of positive surgical margins. Prostate 2005; 63:336-40. [PMID: 15602747 DOI: 10.1002/pros.20197] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
PURPOSE High rates of extracapsular tumor extension have been reported with biopsy perineural invasion (PNI), leading some to advocate routine resection of the ipsilateral neurovascular bundle (NVB) with radical retropubic prostatectomy (RRP) to assure negative surgical margins. The contemporary rates of extracapsular tumor extension (ECE) and margin status associated with biopsy PNI were investigated. MATERIALS AND METHODS The prostate needle biopsies, RRP specimens, and operative reports of 452 consecutive patients undergoing RRP by a single surgeon were reviewed to determine the presence of PNI invasion, presence of ECE, margin status, and preservation of NVB. Patients were excluded from the analysis if they underwent preoperative hormonal ablation or if their original biopsy was not reviewed by the pathologists at our institution. Both univariate and multivariate analyses were performed to determine the effect of PNI on extracapsular extension, the likelihood of performing a bilateral nerve-sparing technique, and the result of a positive surgical margin. RESULTS In the 402 evaluable cases, based on multivariate models PNI showed only a marginal association with positive surgical margin (+SM) (P = 0.10) and bilateral nerve-sparing (B-NS) (P = 0.07), but was significantly associated with organ confinement (P = 0.03). The odds ratio (OR) of PNI for +SM, although not statistically significant, was 0.36. Although showing a higher level of statistical significance, PNI for OC had an odds ratio of 0.50. Similarly, the odds ratio was 0.54 for B-NS. CONCLUSIONS Although biopsy PNI alone was associated with a higher probability of ECE, it is not predictive of bilateral nerve-sparing technique or a positive surgical margin in an individual patient.
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Affiliation(s)
- Glenn M Cannon
- Department of Urology, The University of Pittsburgh, Pittsburgh, Pennsylvania 15213-3232, USA.
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Datta MW, Dhir R, Dobbin K, Bosland MC, Melamed J, Becich MJ, Orenstein JM, Kajdacsy-Balla AA, Patel A, Macias V, Berman JJ. PROSTATE CANCER IN PATIENTS WITH SCREENING SERUM PROSTATE SPECIFIC ANTIGEN VALUES LESS THAN 4.0 NG/DL: RESULTS FROM THE COOPERATIVE PROSTATE CANCER TISSUE RESOURCE. J Urol 2005; 173:1546-51. [PMID: 15821483 DOI: 10.1097/01.ju.0000154778.06649.f5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE Prostate cancer can occur in patients with low screening serum prostate specific antigen (PSA) values (less than 4.0 ng/ml). It is currently unclear whether these tumors are different from prostate cancer in patients with high PSA levels (greater than 4.0 ng/ml). MATERIALS AND METHODS From the Cooperative Prostate Cancer Tissue Resource database through March 2004, 3,416 patients with screening PSA less than 16.0 ng/ml diagnosed with prostate cancer between 1993 and 2004 were stratified in groups based on screening serum PSA. These subsets were compared for race, age at diagnosis, clinical and pathological stage, Gleason score, positive surgical margins, posttreatment recurrent disease, and vital status. RESULTS We identified 468 (14%) patients with screening PSA less than 4.0 ng/ml, 142 (4.2%) of whom had a PSA of less than 2.0 ng/ml. This group included 40 black and 376 white patients. Men with low screening PSA treated with radical prostatectomy had smaller cancers, lower Gleason scores, lower pathological tumor (T) stage and lower PSA recurrence rates than men with high PSA levels (4 ng/ml or greater). These differences held true for men who were younger than 62 years or were white, whereas older or black men had tumor characteristics and outcomes similar to those with higher PSA levels. CONCLUSIONS Young (younger than 62 years) or white patients with screening serum PSA less than 4.0 ng/ml had smaller, lower grade tumors and lower recurrence rates than patients with PSA 4.0 ng/ml or greater. This was not true for those older than 62 years and for black men.
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Affiliation(s)
- Milton W Datta
- Departments of Pathology, New York University School of Medicine, New York, New York, USA
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Becich MJ, Gilbertson JR, Gupta D, Patel A, Grzybicki DM, Raab SS. Pathology and patient safety: the critical role of pathology informatics in error reduction and quality initiatives. Clin Lab Med 2005; 24:913-43, vi. [PMID: 15555749 DOI: 10.1016/j.cll.2004.05.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Understanding the role of pathology informatics in patient safety entails an introduction to terminology and projects that have represented efforts to date in this area. The authors provide a short alphabetized introduction to several "buzzwords" and terms related to tools and processes that are used by health care research experts and workers involved in patient safety initiatives. The authors also include short descriptions of key health care research and patient safety projects that are relevant to pathology. They aim to highlight the areas where pathology informatics in all of its flavors (production systems provided by vendors as well as research and development efforts) can play a role in promoting patient safety.
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Affiliation(s)
- Michael J Becich
- Center for Pathology Informatics, Department of Pathology, University of Pittsburgh Medical School, 5150 Centre Avenue, UPMC Cancer Pavilion, 3rd Floor, Pittsburgh, PA 15232, USA.
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Melamed J, Datta MW, Becich MJ, Orenstein JM, Dhir R, Silver S, Fidélia-Lambert M, Kadjacsy-Balla A, Macias V, Patel A, Walden PD, Bosland MC, Berman JJ. The cooperative prostate cancer tissue resource: a specimen and data resource for cancer researchers. Clin Cancer Res 2005; 10:4614-21. [PMID: 15269132 DOI: 10.1158/1078-0432.ccr-04-0240] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The Cooperative Prostate Cancer Tissue Resource (CPCTR) is a National Cancer Institute-supported tissue bank that provides large numbers of clinically annotated prostate cancer specimens to investigators. This communication describes the CPCTR to investigators interested in obtaining prostate cancer tissue samples. EXPERIMENTAL DESIGN The CPCTR, through its four participating institutions, has collected specimens and clinical data for prostate cancer cases diagnosed from 1989 onward. These specimens include paraffin blocks and frozen tissue from radical prostatectomy specimens and paraffin blocks from prostate needle biopsies. Standardized histopathological characterization and clinical data extraction are performed for all cases. Information on histopathology, demography (including ethnicity), laboratory data (prostate-specific antigen values), and clinical outcome related to prostate cancer are entered into the CPCTR database for all cases. Materials in the CPCTR are available in multiple tissue formats, including tissue microarray sections, paraffin-embedded tissue sections, serum, and frozen tissue specimens. These are available for research purposes following an application process that is described on the CPCTR web site (www.prostatetissues.org). RESULTS The CPCTR currently (as of October 2003) contains 5135 prostate cancer cases including 4723 radical prostatectomy cases. Frozen tissues, in some instances including patient serum samples, are available for 1226 cases. Biochemical recurrence data allow identification of cases with residual disease, cases with recurrence, and recurrence-free cases. CONCLUSIONS The CPCTR offers large numbers of highly characterized prostate cancer tissue specimens, including tissue microarrays, with associated clinical data for biomarker studies. Interested investigators are encouraged to apply for use of this material (www.prostatetissues.org).
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Affiliation(s)
- Jonathan Melamed
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
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76
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Lyons-Weiler J, Patel S, Becich MJ, Godfrey TE. Tests for finding complex patterns of differential expression in cancers: towards individualized medicine. BMC Bioinformatics 2004; 5:110. [PMID: 15307894 PMCID: PMC514539 DOI: 10.1186/1471-2105-5-110] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2004] [Accepted: 08/12/2004] [Indexed: 11/10/2022] Open
Abstract
Background Microarray studies in cancer compare expression levels between two or more sample groups on thousands of genes. Data analysis follows a population-level approach (e.g., comparison of sample means) to identify differentially expressed genes. This leads to the discovery of 'population-level' markers, i.e., genes with the expression patterns A > B and B > A. We introduce the PPST test that identifies genes where a significantly large subset of cases exhibit expression values beyond upper and lower thresholds observed in the control samples. Results Interestingly, the test identifies A > B and B < A pattern genes that are missed by population-level approaches, such as the t-test, and many genes that exhibit both significant overexpression and significant underexpression in statistically significantly large subsets of cancer patients (ABA pattern genes). These patterns tend to show distributions that are unique to individual genes, and are aptly visualized in a 'gene expression pattern grid'. The low degree of among-gene correlations in these genes suggests unique underlying genomic pathologies and high degree of unique tumor-specific differential expression. We compare the PPST and the ABA test to the parametric and non-parametric t-test by analyzing two independently published data sets from studies of progression in astrocytoma. Conclusions The PPST test resulted findings similar to the nonparametric t-test with higher self-consistency. These tests and the gene expression pattern grid may be useful for the identification of therapeutic targets and diagnostic or prognostic markers that are present only in subsets of cancer patients, and provide a more complete portrait of differential expression in cancer.
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Affiliation(s)
- James Lyons-Weiler
- Department of Pathology, Center for Biomedical Informatics, and Interdisciplinary Biomedical Graduate Program, University of Pittsburgh, PA 15232 USA
- Clinical Genomics Facility, Center for Pathology Informatics, Benedum Center for Oncology Informatics, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232 USA
| | - Satish Patel
- Department of Pathology, Center for Biomedical Informatics, and Interdisciplinary Biomedical Graduate Program, University of Pittsburgh, PA 15232 USA
- Clinical Genomics Facility, Center for Pathology Informatics, Benedum Center for Oncology Informatics, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232 USA
| | - Michael J Becich
- Department of Pathology, Center for Biomedical Informatics, and Interdisciplinary Biomedical Graduate Program, University of Pittsburgh, PA 15232 USA
- Clinical Genomics Facility, Center for Pathology Informatics, Benedum Center for Oncology Informatics, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232 USA
| | - Tony E Godfrey
- Departments of Surgery and Human Genetics, University of Pittsburgh Medical School, Pittsburgh, PA 15232 USA
- Mount Sinai School of Medicine, One Gustave Levy Place, Box 1668, East Building, Room 1070C, New York, NY 10029 USA
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77
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Yagi Y, Ahmed I, Gross W, Becich MJ, Demetris AJ, Wells A, Wiley CA, Michalopoulos GK, Yousem SA, Barnes B, Gilbertson JR. Webcasting pathology department conferences in a geographically distributed medical center. Hum Pathol 2004; 35:790-7. [PMID: 15257541 DOI: 10.1016/j.humpath.2004.03.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As academic pathology departments have become increasingly based in large, regional medical systems spread across hundreds of square miles, new methods are needed to tie these increasingly distributed departments together as integrated units. An important part of that integration is the ability to share academic and teaching conferences across long distances. In this article we present an effective, low-cost webcasting system that has evolved at the University of Pittsburgh Medical Center Department of Pathology over the past several years based on inexpensive, widely available software. To date, the system has broadcast and archived more than 400 conferences and currently serves approximately 80 to 100 requests each week. Important factors in the success of the program include the creation of a faculty steering committee to control resources and manage growth, the availability of informatics faculty and support for technical staff, and the decision to operate the service as part of the core information technology infrastructure of the department. Webcasting will likely become an even more important academic and operational tool in the future as more of the department's conferences, seminars, and even working meetings are communicated through the webcasting infrastructure.
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Affiliation(s)
- Yukako Yagi
- University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
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78
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Abstract
A prototype, content-based image retrieval system has been built employing a client/server architecture to access supercomputing power from the physician's desktop. The system retrieves images and their associated annotations from a networked microscopic pathology image database based on content similarity to user supplied query images. Similarity is evaluated based on four image feature types: color histogram, image texture, Fourier coefficients, and wavelet coefficients, using the vector dot product as a distance metric. Current retrieval accuracy varies across pathological categories depending on the number of available training samples and the effectiveness of the feature set. The distance measure of the search algorithm was validated by agglomerative cluster analysis in light of the medical domain knowledge. Results show a correlation between pathological significance and the image document distance value generated by the computer algorithm. This correlation agrees with observed visual similarity. This validation method has an advantage over traditional statistical evaluation methods when sample size is small and where domain knowledge is important. A multi-dimensional scaling analysis shows a low dimensionality nature of the embedded space for the current test set.
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Affiliation(s)
- Lei Zheng
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
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79
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Berman JJ, Datta M, Kajdacsy-Balla A, Melamed J, Orenstein J, Dobbin K, Patel A, Dhir R, Becich MJ. The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. BMC Bioinformatics 2004; 5:19. [PMID: 15040818 PMCID: PMC373442 DOI: 10.1186/1471-2105-5-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 02/27/2004] [Indexed: 11/10/2022] Open
Abstract
Background Tissue Microarrays (TMAs) have emerged as a powerful tool for examining the distribution of marker molecules in hundreds of different tissues displayed on a single slide. TMAs have been used successfully to validate candidate molecules discovered in gene array experiments. Like gene expression studies, TMA experiments are data intensive, requiring substantial information to interpret, replicate or validate. Recently, an open access Tissue Microarray Data Exchange Specification has been released that allows TMA data to be organized in a self-describing XML document annotated with well-defined common data elements. While this specification provides sufficient information for the reproduction of the experiment by outside research groups, its initial description did not contain instructions or examples of actual implementations, and no implementation studies have been published. The purpose of this paper is to demonstrate how the TMA Data Exchange Specification is implemented in a prostate cancer TMA. Results The Cooperative Prostate Cancer Tissue Resource (CPCTR) is funded by the National Cancer Institute to provide researchers with samples of prostate cancer annotated with demographic and clinical data. The CPCTR now offers prostate cancer TMAs and has implemented a TMA database conforming to the new open access Tissue Microarray Data Exchange Specification. The bulk of the TMA database consists of clinical and demographic data elements for 299 patient samples. These data elements were extracted from an Excel database using a transformative Perl script. The Perl script and the TMA database are open access documents distributed with this manuscript. Conclusions TMA databases conforming to the Tissue Microarray Data Exchange Specification can be merged with other TMA files, expanded through the addition of data elements, or linked to data contained in external biological databases. This article describes an open access implementation of the TMA Data Exchange Specification and provides detailed guidance to researchers who wish to use the Specification.
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Affiliation(s)
- Jules J Berman
- Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Milton Datta
- Department of Pathology, University of Wisconsin, Milwaukee, USA
| | | | | | - Jan Orenstein
- Department of Pathology, George Washington University Medical Center, Washington, D.C., USA
| | - Kevin Dobbin
- Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Ashok Patel
- Center for Pathology Informatics and Benedum Oncology Informatics Center, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Rajiv Dhir
- Center for Pathology Informatics and Benedum Oncology Informatics Center, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Michael J Becich
- Center for Pathology Informatics and Benedum Oncology Informatics Center, University of Pittsburgh Medical Center, Pittsburgh, USA
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80
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Gilbertson JR, Gupta R, Nie Y, Patel AA, Becich MJ. Automated clinical annotation of tissue bank specimens. Stud Health Technol Inform 2004; 107:607-10. [PMID: 15360884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Modern, molecular bio-medicine is driving a growing demand for extensively annotated tissue bank specimens. With careful clinical, pathologic and outcomes annotation, samples can be better matched to the research question at hand and experimental results better understood and verified. However, the difficulty and expense of detailed specimen annotation is well beyond the capability of most banks and has made access to well documented tissue a major limitation in medical re-search. In this context, we have implemented automated annotation of banked tissue by integrating data from three clinical systems--the cancer registry, the pathology LIS and the tissue bank inventory system--through a classical data warehouse environment. The project required modification of clinical systems, development of methods to identify patients between and map data elements across systems and the creation of de-identified data in data marts for use by researchers. The result has been much more extensive and accurate initial tissue annotation with less effort in the tissue bank, as well as dynamic ongoing annotation as the cancer registry follows patients over time.
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Affiliation(s)
- John R Gilbertson
- Center for Pathology Informatics, Department of Pathology, Benedum Oncology Informatics Center, University Cancer Institute, University of Pittsburgh Medical School, 5150 Centre Avenue, Pittsburgh, PA 15232, USA.
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81
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Mitchell KJ, Becich MJ, Berman JJ, Chapman WW, Gilbertson J, Gupta D, Harrison J, Legowski E, Crowley RS. Implementation and evaluation of a negation tagger in a pipeline-based system for information extract from pathology reports. Stud Health Technol Inform 2004; 107:663-7. [PMID: 15360896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
We have developed a pipeline-based system for automated annotation of Surgical Pathology Reports with UMLS terms that builds on GATE--an open-source architecture for language engineering. The system includes a module for detecting and annotating negated concepts, which implements the NegEx algorithm--an algorithm originally described for use in discharge summaries and radiology reports. We describe the implementation of the system, and early evaluation of the Negation Tagger. Our results are encouraging. In the key Final Diagnosis section, with almost no modification of the algorithm or phrase lists, the system performs with precision of 0.84 and recall of 0.80 against a gold-standard corpus of negation annotations, created by modified Delphi technique by a panel of pathologists. Further work will focus on refining the Negation Tagger and UMLS Tagger and adding additional processing resources for annotating free-text pathology reports.
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Affiliation(s)
- Kevin J Mitchell
- Centers for Pathology and Oncology Informatics, University of Pittsburgh, UPMC Shadyside, 5230 Centre Avenue, Pittsburgh, PA 15232, USA.
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82
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Li S, Becich MJ, Gilbertson J. Microarray data mining using gene ontology. Stud Health Technol Inform 2004; 107:778-82. [PMID: 15360918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
DNA microarray technology allows scientists to study the expression of thousands of genes--potentially entire genomes--simultaneously. However the large number of genes, variety of statistical methods employed and the complexity of biologic systems complicate analysis of microarray results. We have developed a web based environment that simplifies the presentation of microarray results by combining microarray results processed for statistical significance with probe set annotation by Genbank, NCBI RefSeqs, GeneCards and the Gene Ontology. This allows rapid examination and classification of microarray experiments--annotated by NCIBI tools --by Statistical Significance and Gene Oncology Classes. By providing a simple, easily understood interface to large microarray data sets, this tool has been particularly useful for small research groups focused on a small number of related genes and for researchers who want to ask simple questions without the overhead of complex data management and analysis.
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Affiliation(s)
- S Li
- Center for Pathology Informatics, Department of Pathology, Benedum Oncology Informatics Center, University of Pittsburgh, Cancer Institute, University Pittsburgh, Medical School, 15232, USA.
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83
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Bunker CH, Patrick AL, Konety BR, Dhir R, Brufsky AM, Vivas CA, Becich MJ, Trump DL, Kuller LH. High prevalence of screening-detected prostate cancer among Afro-Caribbeans: the Tobago Prostate Cancer Survey. Cancer Epidemiol Biomarkers Prev 2002; 11:726-9. [PMID: 12163325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
Risk for prostate cancer is high among African Americans. We hypothesized that risk for prostate cancer is also high in other populations of African descent. Our objective was to determine the screening-detected prevalence of prostate cancer in the predominantly Afro-Caribbean population on the island of Tobago. Male residents, ages 40-79 years, were invited to participate in a population-based screening for prostate cancer using serum prostate-specific antigen (PSA) and digital rectal exam (DRE). Men with elevated PSA (>or=4 ng/ml) or abnormal DRE were offered an ultrasound-guided sextant biopsy of the prostate gland. Men (2484), ages 40-79 years, underwent prostate cancer screening between September 1997 and June 2001. Mean age was 55.9, SD was 10.6 years, and median was 54 years. Mean serum PSA was 14.8 ng/ml, SD was 376 [excluding 4 values >or= 2 SD above the mean (1,112, 1,317, 1,818, and 18,330 ng/ml) mean PSA was 5.5 ng/ml and SD was 29.6], and median PSA was 1.2 ng/ml. Elevated PSA and/or abnormal DRE were observed in 31% (759 of 2484) overall, and in age groups 40-49 (87 of 843, 10%), 50-59 (201 of 729, 28%), 60-69 (262 of 584, 45%), and 70-79 (209 of 328, 64%). Of 681 men biopsied, 259 (38%, or 10% of the 2484 screened) were diagnosed with prostate cancer. Age-specific rates of screening detected prostate cancer were: 1%, ages 40-79 years; 7%, ages 50-59 years; 18%, ages 60-69 years; and 28%, ages 70-79 years. These screening results indicate a very high screening-detected prevalence of prostate cancer in this population of West African descent. These data support the hypothesis that populations of African descent share genetic and/or lifestyle factors that contribute to their elevated risk for prostate cancer.
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Affiliation(s)
- Clareann H Bunker
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA. bunkerc+@pitt.edu
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84
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Lin F, Yu YP, Woods J, Cieply K, Gooding B, Finkelstein P, Dhir R, Krill D, Becich MJ, Michalopoulos G, Finkelstein S, Luo JH. Myopodin, a synaptopodin homologue, is frequently deleted in invasive prostate cancers. The American Journal of Pathology 2001; 159:1603-12. [PMID: 11696420 PMCID: PMC3277320 DOI: 10.1016/s0002-9440(10)63006-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Prostate cancer is one of the leading causes of cancer-related deaths for men in the United States. Like other malignancies, prostate cancer is underscored by a variety of aberrant genetic alterations during its development. Although loss of heterozygosity or allelic loss is frequently identified among prostate cancers, few genes have been identified thus far as critical to the development of invasive prostate cancers. In this report, we used the recently developed technology, the "differential subtraction chain," to perform a genome-wide search for sequences that are deleted in an aggressive prostate cancer. Among the deleted sequences, we found that one sequence was deleted in >50% of prostate cancers we tested. We mapped this sequence to chromosome 4q25 by screening the Genebridge 4 hamster radiation panel with primers specific to this probe, and subsequently identify a 54-kb minimal common deletion region that contains the sequence encoding myopodin. Sequence analysis indicates that myopodin shares significant homology with synaptopodin, a protein closely associated with podocyte and neuron differentiation. Further study shows that frequent complete or partial deletions of the myopodin gene occurred among invasive prostate cancer cases (25 of 31 cases, or 80%). Statistical analysis indicates that deletion of myopodin is highly correlated with the invasiveness of prostate cancers, and thus may hold promise as an important prognostic marker for prostate cancers.
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Affiliation(s)
- F Lin
- Department of Pathology, School of Medicine, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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85
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Abstract
UV exposure and serum levels of vitamin D have been linked in several studies with prostate cancer risk. At the cellular level, the principal action of vitamin D is mediated though vitamin D receptors (VDR). Since prostate cancer is a disease strongly associated with age, we examined the presence of VDR in normal prostate from donors of various ages to determine if the VDR expression pattern changed with age. We also compared the VDR expression in the peripheral and central zones of the prostate to determine if the expression pattern varied by location. Immunohistochemical studies were performed on paraffin-embedded tissue from cases selected by the following age decades; 10-19, 20-29, 30-39, 40-49, 50-59, and 60-69. Both the central and peripheral zones were examined for VDR expression. The intensity of VDR expression in prostate was compared with expression in different types of human tissues. Mean VDR expression was lowest in the 10-19 years of age group. The intensity of the nuclear VDR was higher though the fifth decade, and then declined in cases of ages 60-70. When multiple sections of the same donor prostate were compared, VDR expression was greater in the peripheral zone compared to the central zone.
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Affiliation(s)
- D Krill
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15261, USA.
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86
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Abstract
Prostate-specific antigen (PSA) is the most widely used marker for the diagnosis of prostate cancer and is an independent predictor of prostatic capsular invasion. A number of studies have identified E-cadherin, a cell adhesion protein, as a potential invasion suppressor which is decreased in prostate adenocarcinoma. Our goal in the present study was to evaluate E-cadherin expression in primary cultures and determine the relationship between E-cadherin expression and PSA secretion in both primary cultures and the prostate tumor cell line, LNCaP. Immunohistochemical studies and Western blot analysis confirmed greater expression of E-cadherin in normal epithelial cells than tumor-derived prostate cells. This is the first report that the incubation of normal prostate epithelial cells with E-cadherin antibody increases the amount of PSA detected in the media of normal cells as well as in LNCaP. Since E-cadherin may function as an invasion suppressor, an understanding of the decreased expression of this adhesion factor and the impact on PSA secretion may aid in understanding epithelial tumorigenesis.
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Affiliation(s)
- D Krill
- University of Pittsburg School of Medicine, C920 Presbyterian University Hospital, PA 15261, USA.
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87
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Affiliation(s)
- Y P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, Pennsylvania 15261, USA
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88
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Becich MJ. The role of the pathologist as tissue refiner and data miner: the impact of functional genomics on the modern pathology laboratory and the critical roles of pathology informatics and bioinformatics. Mol Diagn 2000; 5:287-99. [PMID: 11172493 DOI: 10.1007/bf03262090] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
This article provides an overview of how functional genomics is likely to impact on the pathology laboratory and highlights how informatics and tissue banking will greatly facilitate the molecular age of medicine. Important aspects of functional genomics in the post-genome era, including the roles of laser capture microdissection, DNA- and complementary DNA-based microarrays, proteomic methods, collaborative human tissue banking, tissue microarrays, and pathobioinformatics in the modern pathology laboratory are discussed. The role of mass spectroscopy in the analysis of RNA, DNA, and protein and its impact on the clinical laboratory, particularly in cost-effectiveness and time savings, are evaluated. This article explores how laboratory information systems (LISs) and the devices that feed them information may need to be modified to adapt to greater volumes of data for the new testing modalities that require understanding sophisticated fluorescence detection methods and image processing. Emerging genomic testing methods and their impact on pathology laboratory testing, especially in the area of molecular classification of neoplasms, are examined. The role of the tissue bank in the modern pathology laboratory as an archive of control normal tissues, as well as subsamples of the spectrum of progressive neoplastic states, is discussed in light of its critical importance to the molecular classification of cancer. Establishing a database that combines structured reports in pathology LISs and construction of tissue banking information systems will provide a rich resource for pathology departments. The article discusses a hypothetical resource, such as the Shared Tumor Expression Profiler, that would provide access to well-characterized tissue-based research resources for clinicians and researchers. Last, the article emphasizes how LISs can prepare for these changes, and how training pathologists in pathology informatics and bioinformatics (pathobioinformatics) is critical to ensure pathology's overall leadership role in the post-genome era.
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Affiliation(s)
- M J Becich
- Center for Pathology Informatics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Health System, Pittsburgh, PA 15232, USA.
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89
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Becich MJ. Information management: moving from test results to clinical information. Clin Leadersh Manag Rev 2000; 14:296-300. [PMID: 11210218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- M J Becich
- Center for Pathology Informatics, University of Pittsburgh School of Medicine, PA, USA
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90
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Wang J, Krill D, Torbenson M, Wang Q, Bisceglia M, Stoner J, Thomas A, DeFlavia P, Dhir R, Becich MJ. Expression of cadherins and catenins in paired tumor and non-neoplastic primary prostate cultures and corresponding prostatectomy specimens. Urol Res 2000; 28:308-15. [PMID: 11127708 DOI: 10.1007/s002400000131] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cadherins are a family of transmembrane proteins that play a crucial role in cell differentiation, cell migration, and intercellular adhesion. Cadherins are associated with catenins through their highly conserved cytoplasmic domain. Down-regulation of E-cadherin protein has been shown in various human cancers. This study examined the expression of cadherins and associated catenins at the mRNA level. Paired tumor and nonneoplastic primary prostate cultures were obtained from surgical specimens. Quantitative multiplex fluorescence reverse transcriptase-polymerase chain reaction (QMF RT-PCR) and quantitative analysis were performed and correlated with immunostain results. Six of seven cases of neoplastic cultures showed moderately-to-markedly decreased levels of E-cadherin and P-cadherin mRNA. Similar losses of alpha-catenin and beta-catenin mRNA were also observed. The results of QMF RT-PCR showed good correlation with the results of immunohistochemical studies based on corresponding formalin-fixed sections. In conclusion, this paper presents a coordinated down-regulation in the expression of E-cadherin and associated catenins at the mRNA and protein level in most of the cases studied. This down-regulation may play an important role in the pathogenesis of prostate cancer.
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Affiliation(s)
- J Wang
- Department of Pathology, University of Pittsburgh Medical Center, PA, USA
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91
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Konety BR, Nguyen TS, Dhir R, Day RS, Becich MJ, Stadler WM, Getzenberg RH. Detection of bladder cancer using a novel nuclear matrix protein, BLCA-4. Clin Cancer Res 2000; 6:2618-25. [PMID: 10914702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
We have identified previously six nuclear matrix proteins (NMPs) that are bladder cancer specific. In this study, we analyzed the expression of one of these proteins, BLCA-4, in bladder tumors and normal bladder tissue. We also examined the appearance of BLCA-4 in the urine as a biomarker for bladder cancer. BLCA-4 was isolated from nuclear matrix preparations of bladder tumors, and its peptide sequence was determined. The antibodies generated against the resulting BLCA-4 peptides were then used to detect its presence in immunoblots and in urine samples by immunoassay. We analyzed tissue samples of bladder tumor and normal donor bladders and urine obtained from 51 normal individuals and 54 patients with pathologically confirmed bladder cancer. The BLCA-4 peptide sequences do not resemble any known human protein sequences. On immunoblot analysis, BLCA-4 expression was detectable in tumor and normal tissues from patients with bladder cancer but not in any of the normal bladder tissue obtained from organ donors. Using a prospectively determined cutoff level of 13 A (absorbance) units/microg protein, all 51 normal individuals tested were negative for BLCA-4 expression, whereas 53 of 55 samples from patients with bladder cancer were positive. These results suggest that BLCA-4 is present throughout the bladder in both the tumor and morphologically normal areas in bladder cancer patients. BLCA-4 is a very sensitive (96.4%) and specific (100%) marker for bladder cancer. BLCA-4 is a bladder cancer-specific marker that can be detected using a urine-based assay and can be used in the diagnosis of bladder cancer.
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Affiliation(s)
- B R Konety
- University of Pittsburgh Cancer Institute, Department of Urology, Pennsylvania 15213-2582, USA
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Landman A, Yagi Y, Gilbertson J, Dawson R, Marchevsky A, Becich MJ. Prototype Web-based continuing medical education using FlashPix images. Proc AMIA Symp 2000:462-6. [PMID: 11079926 PMCID: PMC2244070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Continuing Medical Education (CME) is a requirement among practicing physicians to promote continuous enhancement of clinical knowledge to reflect new developments in medical care. Previous research has harnessed the Web to disseminate complete pathology CME case studies including history, images, diagnoses, and discussions to the medical community. Users submit real-time diagnoses and receive instantaneous feedback, eliminating the need for hard copies of case material and case evaluation forms. This project extends the Web-based CME paradigm with the incorporation of multi-resolution FlashPix images and an intuitive, interactive user interface. The FlashPix file format combines a high-resolution version of an image with a hierarchy of several lower resolution copies, providing real-time magnification via a single image file. The Web interface was designed specifically to simulate microscopic analysis, using the latest Javascript, Java and Common Gateway Interface tools. As the project progresses to the evaluation stage, it is hoped that this active learning format will provide a practical and efficacious environment for continuing medical education with additional application potential in classroom demonstrations, proficiency testing, and telepathology. Using Microsoft Internet Explorer 4.0 and above, the working prototype Web-based CME environment is accessible at http://telepathology.upmc.edu/WebInterface/NewInterface/welcome.html.
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Affiliation(s)
- A Landman
- H. John Heinz III School of Public Policy and Management, Carnegie-Mellon University, USA
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93
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Luo JH, Puc JA, Slosberg ED, Yao Y, Bruce JN, Wright TC, Becich MJ, Parsons R. Differential subtraction chain, a method for identifying differences in genomic DNA and mRNA. Nucleic Acids Res 1999; 27:e24. [PMID: 10481036 PMCID: PMC148634 DOI: 10.1093/nar/27.19.e24] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Identifying the genetic differences between two organisms or cell types has been a major goal in modern biomedical research. Recently, we developed a novel methodology that can rapidly identify the differences between two populations of DNA. This method, termed 'differential subtraction chain' (DSC), is based on a novel 'negative amplification' strategy that converts (amplifiable) tester sequences to counterpart (unamplifiable) driver sequences. The result is a double exponential elimination of amplifiable sequences in the testers, while preserving the sequences in the testers that have no counterpart in the drivers. We applied this methodology to the genome of a glioblastoma cell line. A homozygous deletion was rapidly identified. We extended this technique to identifying the unique sequences in mRNA. Two CDC25 transgene fragments were quickly identified in a cdc25B transgenic mouse. We also applied this methodology to systems with profound differences in mRNA expression. In a 'prostate epithelia subtracting blood cells' DSC reaction, a sample of unique gene fragments which are absent in the prostate but present in the blood were identified. Lastly, we detected rare (1 virus/100 cells) Herpes simplex virus type 2 (HSV-2) sequences in a tissue culture, indicating good sensitivity of this methodology. Overall, DSC represents a fast, efficient and sensitive method for identifying differences in genomic DNA and mRNA and can be easily applied in a variety of biological systems.
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Affiliation(s)
- J H Luo
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA. luojh+@pitt.edu
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94
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Krill D, Stoner J, Konety BR, Becich MJ, Getzenberg RH. Differential effects of vitamin D on normal human prostate epithelial and stromal cells in primary culture. Urology 1999; 54:171-7. [PMID: 10414747 DOI: 10.1016/s0090-4295(99)00103-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVES Because epidemiologic evidence has demonstrated that vitamin D may play a role in the etiology of prostate cancer, we tested the inhibitory effect of the biologically active form of vitamin D (1,25-D) on the cell proliferation of human prostate epithelial and stromal cells in a chemically defined situation in the presence and absence of dihydrotestosterone (DHT). We also tested the effect of 1,25-D in castrated rats in the presence and absence of flutamide, an androgen receptor blocker. METHODS Prostate stromal and epithelial cells were isolated from freshly collected human prostatectomy specimens, and cell proliferation was measured with the MTT assay. Immunohistochemistry was performed to detect the presence of 1,25-D receptors, androgen receptors, smooth muscle actin, and E-cadherin. For in vivo analysis of 1,25-D, male Sprague-Dawley rats were castrated, then treated with either 1,25-D, 1,25-D with flutamide, or vehicle control. RESULTS Incubation of primary cultures of prostate epithelial cells with 1,25-D at a concentration of 10(-8) M reduced cell proliferation by 40% of controls. The inhibition of growth by 1,25-D was maintained in the presence of DHT. Conversely, the effect of a similar dose of 1,25-D on stromal cell exposure was increased proliferation. In vivo, 1,25-D increased the prostatic weight of castrated rats that had serum testosterone levels below the detectable limit. The addition of flutamide did not alter this effect. CONCLUSIONS These results confirm that vitamin D may be an effective antiproliferative agent of epithelial cells in prostate cancer therapy and support in vivo studies performed in the normal rat prostate.
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Affiliation(s)
- D Krill
- Department of Pathology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Pennsylvania 15213-2582, USA
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95
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Lou W, Krill D, Dhir R, Becich MJ, Dong JT, Frierson HF, Isaacs WB, Isaacs JT, Gao AC. Methylation of the CD44 metastasis suppressor gene in human prostate cancer. Cancer Res 1999; 59:2329-31. [PMID: 10344738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Previous studies demonstrated that CD44 is a metastasis suppressor gene for prostate cancer and that the expression of CD44 both at mRNA and protein levels is down-regulated during prostate cancer progression, with down-regulation being correlated with higher tumor grade, aneuploidy, and distant metastasis. In this study, we evaluated DNA hypermethylation as a potential mechanism accompanying this decreased CD44 expression in human prostate cancer. Nucleotide sequence analysis revealed a CpG island in the CD44 transcriptional regulatory region. We found that cytosine methylation of CD44 promoter occurs in CD44-negative prostate cancer cell line (i.e., LNCaP) but not in prostate cancer cell lines (i.e., TSU, PC3, and DU145) expressing this gene. In addition, we examined methylation status of CD44 in 84 matched normal and cancer prostate specimens. Hypermethylation of the 5' CpG island of CD44 gene was observed in 31 of 40 primary prostate cancer specimens, 3 of 4 distant organ site metastases obtained at autopsy from men who died of prostate cancer, and 4 of the 40 matched normal tissues. These results demonstrated that methylation of the 5' CpG island of CD44 gene is closely associated with transcriptional inactivation, resulting in a decreased expression of CD44 in human prostate cancer.
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Affiliation(s)
- W Lou
- Department of Pathology and Cancer Institute, University of Pittsburgh Medical Center, Pennsylvania 15213, USA
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96
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Nezu FM, Dhir R, Logan TF, Lavelle J, Becich MJ, Chancellor MB. Malignant priapism as the initial clinical manifestation of metastatic renal cell carcinoma with invasion of both corpora cavernosum and spongiosum. Int J Impot Res 1998; 10:101. [PMID: 9647945 DOI: 10.1038/sj.ijir.3900342] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- F M Nezu
- Division of Urologic Surgery, University of Pittsburgh School of Medicine, USA
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97
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Torbenson M, Dhir R, Nangia A, Becich MJ, Kapadia SB. Prostatic carcinoma with signet ring cells: a clinicopathologic and immunohistochemical analysis of 12 cases, with review of the literature. Mod Pathol 1998; 11:552-9. [PMID: 9647593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Prostatic adenocarcinoma with a signet ring cell (SRC) component is a rare, incompletely characterized variant that must be distinguished from similar tumors of bladder or gastric origin. In this study, we used mucin and immunoperoxidase stains on formalin-fixed, paraffin-embedded sections from 12 prostatic adenocarcinomas with SRC components, with antibodies to prostate-specific antigen (PSA), cytokeratins, MIB-1, bcl-2, c-MET, CD44v6, and CD44v7; we performed a comparison study on six bladder and seven gastric carcinomas with SRCs. The prostatic SRC component was always associated with the usual high-grade adenocarcinoma. Both components were positive for PSA, AE1/AE3, and CAM 5.2 (12 cases of 12) and also expressed c-MET (5 cases of 9), CD44v6 (9 of 10), and CDv7 (9 of 10). Only rare cells stained for bcl-2 (3 cases of 9). The mean MIB-1 proliferation index was 8%. Intracellular mucin was identified (periodic acid-Schiff with diastase predigestion (PAS-D) in 9 cases of 10, mucicarmine in 5 of 10, alcian blue in 6 of 10). Bladder and gastric tumors were positive for PSA (3 cases of 6 and 2 of 7, respectively), using a polyclonal antibody, and for bcl-2 (5 cases of 6, 2 of 7), c-MET (6 of 6, 6 of 7), CD44v6 (5 of 6, 6 of 7), and CD44v7 (4 of 6, 4 of 7), with mean MIB-1 proliferation indices of 15 and 35%, respectively. All were negative for cytokeratin 34 beta E12. We conclude that prostatic adenocarcinomas with SRC components are typically accompanied by high-grade adenocarcinoma; are variably positive for mucin, with PAS-D being the most sensitive stain; show expression of PSA, cytokeratins, MIB-1, bcl-2, c-MET, and CD44 similar to that shown by high-grade adenocarcinoma components; have a low MIB-1 proliferation index; and are not always distinguishable from SRC components of bladder and stomach carcinomas with any of the above stains, including PSA.
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Affiliation(s)
- M Torbenson
- Department of Pathology, University of Pittsburgh Medical Center, Pennsylvania, USA
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98
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Konety BR, Nangia AK, Nguyen TS, Veitmeier BN, Dhir R, Acierno JS, Becich MJ, Hrebinko RL, Getzenberg RH. Identification of nuclear matrix protein alterations associated with renal cell carcinoma. J Urol 1998; 159:1359-63. [PMID: 9507884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Neoplastic transformation, including renal cell carcinoma (RCC), is always accompanied by changes in nuclear morphology. Nuclear grading of RCC is based on characteristic alterations in nuclear shape, size, area and other morphologic parameters. The nuclear matrix, which forms the skeleton of the nucleus, determines nuclear morphology. Alterations in nuclear matrix protein (NMP) composition specific to tissue and cancer type have been described in a variety of human cancers. We conducted a study to analyze the nuclear matrix protein composition of renal cell carcinoma and compare it to that of normal renal tissue and renal cell carcinoma cells grown in culture. MATERIALS AND METHODS We analyzed the nuclear matrix protein composition of RCC tumor tissue and that of normal kidney tissue obtained from seventeen patients undergoing radical nephrectomy for RCC. We also analyzed the NMP composition of two renal cancer cell lines (A-498 and 769-P). RESULTS We were able to identify five different and unique NMPs which were present only in the human RCC tumor samples and were absent in all normal kidney tissue. One NMP was found specifically in the normal kidney tissue. All five RCC specific NMPs were also identified in the nuclear matrix of the two cell lines analyzed. CONCLUSIONS Five nuclear matrix proteins specific and unique to RCC were identified. These NMPs are different from those previously identified in other tissues and neoplasms. The RCC specific NMPs identified in this study can potentially be used as diagnostic markers for renal cell carcinoma and for therapeutic tumor targeting.
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Affiliation(s)
- B R Konety
- Department of Pathology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pennsylvania 15213, USA
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99
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Michaels MG, Alcendor DJ, St George K, Rinaldo CR, Ehrlich GD, Becich MJ, Hayward GS. Distinguishing baboon cytomegalovirus from human cytomegalovirus: importance for xenotransplantation. J Infect Dis 1997; 176:1476-83. [PMID: 9395357 DOI: 10.1086/514144] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The severe shortage of human organs for transplantation is the driving force behind xenotransplant research. Nonhuman primates, particularly baboons, are potential sources of organs and tissues. Human cytomegalovirus (HCMV) is the most common donor-associated infection after allotransplantation. Baboon cytomegalovirus (BCMV) is endemic in baboon populations and therefore is a potential cause of donor-associated disease after xenotransplantation. Accordingly, the ability for BCMV to grow in human cells was determined and a sensitive method to distinguish BCMV from HCMV was developed. Human fibroblasts were permissive for BCMV, isolates exhibited cytopathology characteristic of HCMV, and herpesvirus-like virions were observed by electron microscopy. BCMV and HCMV could be distinguished by restriction fragment length polymorphism patterns and by polymerase chain reaction with primers targeting the BCMV major immediate-early gene promoter. These methods can be used to evaluate BCMV pathogenicity in laboratory and clinical xenotransplant trials.
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Affiliation(s)
- M G Michaels
- University of Pittsburgh, School of Medicine, Department of Pediatrics, Children's Hospital of Pittsburgh, Pennsylvania 15213, USA
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100
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Gau JT, Salter RD, Krill D, Grove ML, Becich MJ. The biosynthesis and secretion of prostate-specific antigen in LNCaP cells. Cancer Res 1997; 57:3830-4. [PMID: 9288795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Prostate-specific antigen (PSA) has been demonstrated to release the active form of insulin-like growth factor I in vitro (P. Cohen et al., J. Clin. Endocrinol. & Metab., 75: 1046-1053, 1992; P. Cohen et al., J. Clin. Endocrinol. & Metab., 79: 1410-1415, 1994; P. Cohen et al., Horm. Metab. Res., 26: 81-84, 1994) and has significant mitogenic activity on osteoblast cells, fibroblasts, and other cultured cells (C. S. Killian et al., Biochem. Biophys. Res. Commun., 192: 940-947, 1993). Recently, PSA has been found not only in prostate tissues but also in breast, colon, ovarian, and other tissues (E. P. Diamandis and H. Yu, J. Clin. Endocrinol. & Metab., 80: 1515-1517, 1995; E. P. Diamandis and H. Yu, Clin. Chem., 41: 204-210, 1995; A. Clements and A. Mukhtar, J. Clin. Endocrinol. & Metab., 78: 1536-1539, 1994). Therefore, PSA has been proposed as a candidate growth factor, cytokine, or growth factor regulator. In this setting, knowing how to manipulate or block the secretion of PSA by the prostate cancer cells could be a useful approach to controlling the progression of human prostate cancers. Using metabolic labeling experiments, we have studied the biosynthesis and secretion of PSA in LNCaP cells. We have also examined the effects of DTT, tunicamycin, 1-deoxymannojirimycin, pilocarpine, and testosterone on PSA biosynthesis and secretion. The results indicate that the secretion of PSA in LNCaP cells is constitutive instead of regulated and that the disruption of intramolecular disulfide bonds affects the transport of PSA from the endoplasmic reticulum to the Golgi apparatus. The biosynthesis of PSA is potentiated by testosterone and inhibited by brefeldin A and DTT. These results will help us understand PSA biosynthesis and secretion in human prostate cancers.
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Affiliation(s)
- J T Gau
- Department of Pathology, University of Pittsburgh School of Medicine, Pennsylvania 15213-2582, USA
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