Biomedical subjects

John R Gilbertson

Publications and source records attributed to John R Gilbertson.

9 recordsLinked to original sources

PubMed2006

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.

Databases as Topic↗

PubMed2006

Primary histologic diagnosis using automated whole slide imaging: a validation study.

BACKGROUND: Only prototypes 5 years ago, high-speed, automated whole slide imaging (WSI) systems (also called digital slide systems, virtual microscopes or wide field imagers) are becoming increasingly capable and robust. Modern devices can capture a slide in 5 minutes at spatial sampling periods of less than 0.5 micron/pixel. The capacity to rapidly digitize large numbers of slides should eventually have a profound, positive impact on pathology. It is important, however, that pathologists validate these systems during development, not only to identify their limitations but to guide their evolution. METHODS: Three pathologists fully signed out 25 cases representing 31 parts. The laboratory information system was used to simulate real-world sign-out conditions including entering a full diagnostic field and comment (when appropriate) and ordering special stains and recuts. For each case, discrepancies between diagnoses were documented by committee and a "consensus" report was formed and then compared with the microscope-based, sign-out report from the clinical archive. RESULTS: In 17 of 25 cases there were no discrepancies between the individual study pathologist reports. In 8 of the remaining cases, there were 12 discrepancies, including 3 in which image quality could be at least partially implicated. When the WSI consensus diagnoses were compared with the original sign-out diagnoses, no significant discrepancies were found. Full text of the pathologist reports, the WSI consensus diagnoses, and the original sign-out diagnoses are available as an attachment to this publication. CONCLUSION: The results indicated that the image information contained in current whole slide images is sufficient for pathologists to make reliable diagnostic decisions and compose complex diagnostic reports. This is a very positive result; however, this does not mean that WSI is as good as a microscope. Virtually every slide had focal areas in which image quality (focus and dynamic range) was less than perfect. In some cases, there was evidence of over-compression and regions made "soft" by less than perfect focus. We expect systems will continue to get better, image quality and speed will continue to improve, but that further validation studies will be needed to guide development of this promising technology.

Journal Article↗

PubMed2006

Use of whole slide imaging in surgical pathology quality assurance: design and pilot validation studies.

By imaging large numbers of slides automatically at high resolution, modem automated whole slide imaging (WSI) systems have the potential to become useful tools in pathology practice. This article describes a pilot validation study for use of automated high-speed WSI systems for surgical pathology quality assurance (QA). This was a retrospective comparative study in which 24 full genitourinary cases (including 47 surgical parts and 391 slides) were independently reviewed with traditional microscopy and whole slide digital images. Approximately half the cases had neoplasia in the diagnostic line. At the end of the study, diagnostic discrepancies were evaluated by a pathology consensus committee. The study pathologists felt that the traditional and WSI methods were comparable for case review. They reported no difference in perceived case complexity or diagnostic confidence between the methods. There were 4 clinically insignificant discrepancies with the signed-out cases: 2 from glass slide and 2 with WSI review. Of the 2 discrepancies reported by the WSI method, the committee agreed with the reviewer once and the original report once. At the end of the study, the participants agreed that automated WSI is a viable potential modality for surgical pathology QA, especially in multifacility health systems that would like to establish interfacility QA. The participants felt that major issues limiting the implementation of WSI-based QA did not involve image acquisition or quality but rather image management issues such as the pathologist's interface, the hospital's network, and integration with the laboratory information system.

Humans↗

PubMed2006

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.

Gene Expression Profiling↗

PubMed2005

Digital imaging in pathology: the case for standardization.

The process of digital imaging in microscopy is a series of operations, each contributing to the quality of the final image that is displayed on the computer monitor. The operations include sample preparation and staining by histology, optical image formation by the microscope, digital image sampling by the camera sensor, postprocessing and compression, transmission across the network and display on the monitor. There is an extensive literature about digital imaging and each step of the process is fairly well understood. However, the complete process is very hard to standardize or even to understand fully. The important concepts for pathology imaging standards are: (1) systems should be able to share image files, (2) the standards should allow the transmission of information on baseline colours and recommended display parameters, (3) the images should be useful to the pathologist, not necessarily better or worse than direct examination of a slide under the microscope, (4) a mechanism to evaluate image quality objectively should be present, (5) a mechanism to adjust and correct the minor errors of tissue processing should be developed, (6) a public organization should support pathologists in the development of standards.

Image Interpretation, Computer-Assisted↗

PubMed2005

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.

Databases, Factual↗

PubMed2004

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.

Diagnostic Errors↗

PubMed2004

Webcasting pathology department conferences in a geographically distributed medical center.

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.

Academic Medical Centers↗

PubMed2004

Automated clinical annotation of tissue bank specimens.

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.

Clinical Laboratory Information Systems↗