The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data

Background:

Tissue microarrays (TMAs) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject-Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration.

Methods:

A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format.

Results:

We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES) to OWL.

Conclusion:

By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.

Proteins secreted by embryonic stem cells activate cardiomyocytes through ligand binding pathways

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.

Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs

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.

Provider management of and satisfaction with laboratory testing in the nursing home setting: results of a national internet-based survey

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.

Assessing the performance characteristics of signals used by a clinical event monitor to detect adverse drug reactions in the nursing home

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.

A multidisciplinary approach to honest broker services for tissue banks and clinical data: a pragmatic and practical model

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.

Towards a data sharing culture: recommendations for leadership from academic health centers

Rebecca Crowley and colleagues propose that academic health centers can and should lead the transition towards a culture of biomedical data sharing.

National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research

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.

Frequency of laboratory monitoring of chronic medications administered to nursing facility residents: results of a national Internet-based study

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.

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

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.

Development of an instrument for measuring clinicians' power perceptions in the workplace

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.

The importance of pathology informatics in translational research

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

Effect of Lean method implementation in the histopathology section of an anatomical pathology laboratory

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.

Synoptic tool for reporting of hematological and lymphoid neoplasms based on World Health Organization classification and College of American Pathologists checklist

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.

A novel cross-disciplinary multi-institute approach to translational cancer research: lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)

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.

Practical aspects of planning, building, and interpreting tissue microarrays: The Cooperative Prostate Cancer Tissue Resource experience

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.

Cardiac fibroblasts influence cardiomyocyte phenotype in vitro

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.

In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays

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.

An informatics model for tissue banks--lessons learned from the Cooperative Prostate Cancer Tissue Resource

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.

Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression

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.

Database construction for improving patient safety by examining pathology errors

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.

The development of common data elements for a multi-institute prostate cancer tissue bank: the Cooperative Prostate Cancer Tissue Resource (CPCTR) experience

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.

Perineural invasion in prostate cancer biopsies is not associated with higher rates of positive surgical margins

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.

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

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.

Pathology and patient safety: the critical role of pathology informatics in error reduction and quality initiatives

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.