Donald P. Connelly

Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer

BackgroundTo discover prostate cancer biomarkers, we profiled gene expression in benign and malignant cells laser capture microdissected (LCM) from prostate tissues and metastatic prostatic adenocarcinomas. Here we present methods developed, optimized, and validated to obtain high quality gene expression data.ResultsRNase inhibitor was included in solutions used to stain frozen tissue sections for LCM, which improved RNA quality significantly. Quantitative PCR assays, requiring minimal amounts of LCM RNA, were developed to determine RNA quality and concentration. SuperScript II™ reverse transcriptase was replaced with SuperScript III™, and SpeedVac concentration was eliminated to optimize linear amplification. The GeneChip® IVT labeling kit was used rather than the Enzo BioArray™ HighYield™ RNA transcript labeling kit since side-by-side comparisons indicated high-end signal saturation with the latter. We obtained 72 μg of labeled complementary RNA on average after linear amplification of about 2 ng of total RNA.ConclusionUnsupervised clustering placed 5/5 normal and 2/2 benign prostatic hyperplasia cases in one group, 5/7 Gleason pattern 3 cases in another group, and the remaining 2/7 pattern 3 cases in a third group with 8/8 Gleason pattern 5 cases and 3/3 metastatic prostatic adenocarcinomas. Differential expression of alpha-methylacyl coenzyme A racemase (AMACR) and hepsin was confirmed using quantitative PCR.

An Industrial Process View of Information Delivery to Support Clinical Decision Making: Implications for Systems Design and Process Measures

Clinical decision making is driven by information in the form of patient data and clinical knowledge. Currently prevalent systems used to store and retrieve this information have high failure rates, which can be traced to well-established system constraints. The authors use an industrial process model of clinical decision making to expose the role of these constraints in increasing variability in the delivery of relevant clinical knowledge and patient data to decision-making clinicians. When combined with nonmodifiable human cognitive and memory constraints, this variability in information delivery is largely responsible for the high variability of decision outcomes. The model also highlights the supply characteristics of information, a view that supports the application of industrial inventory management concepts to clinical decision support. Finally, the clinical decision support literature is examined from a process-improvement perspective with a focus on decision process components related to information retrieval. Considerable knowledge gaps exist related to clinical decision support process measurement and improvement.

The use of the differential leukocyte count for inpatient casefinding

The differential leukocyte count is a nonspecific, imprecise, error-prone, usually labor-intensive, and expensive test to perform. Although the differential count is frequently ordered in the absence of clinical suspicion in both inpatient and outpatient settings, its effectiveness as a screening test has been studied little. From a detailed chart review of 287 cases randomly drawn from a population of 2682 adult patients for whom a differential count was performed on admission, we found that 23 per cent of the cases met criteria for admission screening, that abnormal results were found in approximately one half of these screening differential examinations, and that one third of the abnormal examinations were acknowledged in the medical record by a physician. In no instance did a screening differential count appear to have had clinical significance. It may be medically prudent to consider discontinuing the differential leukocyte count as an inpatient screening test for adults.

The impact of electronic health records on care of heart failure patients in the emergency room

OBJECTIVE To evaluate if electronic health records (EHR) have observable effects on care outcomes, we examined quality and efficiency measures for patients presenting to emergency departments (ED). MATERIALS AND METHODS We conducted a retrospective study of 5166 adults with heart failure in three metropolitan EDs. Patients were termed internal if prior information was in the EHR upon ED presentation, otherwise external. Associations of internality with hospitalization, mortality, length of stay (LOS), and numbers of tests, procedures, and medications ordered in the ED were examined after adjusting for age, gender, race, marital status, comorbidities and hospitalization as a proxy for acuity level where appropriate. RESULTS At two EDs internals had lower odds of mortality if hospitalized (OR 0.55; 95% CI 0.38 to 0.81 and 0.45; 0.21 to 0.96), fewer laboratory tests during the ED visit (-4.6%; -8.9% to -0.1% and -14.0%; -19.5% to -8.1%) as well as fewer medications (-33.6%; -38.4% to -28.4% and -21.3%; -33.2% to -7.3%). At one of these two EDs, internals had lower odds of hospitalization (0.37; 0.22 to 0.60). At the third ED, internal patients only experienced a prolonged ED LOS (32.3%; 6.3% to 64.8%) but no other differences. There was no association with hospital LOS or number of procedures ordered. DISCUSSION EHR availability was associated with salutary outcomes in two of three ED settings and prolongation of ED LOS at a third, but evidence was mixed and causality remains to be determined. CONCLUSIONS An EHR may have the potential to be a valuable adjunct in the care of heart failure patients.

The medical problem solving process.

Understanding the medical problem solving process has implications for medical education and the effectiveness of medical services. Through adaptation to the task at hand the human problem solver is able to ameliorate the effects of inherent limitations. In adapting to the medical problem solving task demands related to diagnosis and therapy, the physician uses the hypotheticodeductive process. The process draws upon the problem solvers disease centered and data centered knowledge and can be made more effective through the use of various heuristic rules and strategies that the physician develops with increasing expertise. Additional and more refined modes of laboratory support for the medical problem solver can evolve through further understanding of the problem solving process.

Evidence for an informal clinical policy resulting in high use of a very-low-yield test

The actual and self-reported practice regarding the use of cerebrospinal fluid cultures for Mycobacterium tuberculosis was examined. All neurology house staff members surveyed, 62 percent of internal medicine house staff members, and none of pediatric house staff members reported that they would order mycobacterial cultures of cerebrospinal fluid routinely. The actual practice was comparable, with 71 percent of cerebrospinal fluid specimens being subjected to culture for mycobacteria on the neurology service, 65 percent on the internal medicine service, and 6 percent on the pediatric service. In this practice, medicine and neurology house staff differ significantly from their pediatric colleagues (p less than 0.001) and from the stated practice of their respective faculties (p less than 0.01). For at least six years, most medicine and neurology house staff have commonly applied an informal clinical policy of routinely culturing cerebrospinal fluid specimens for mycobacteria, despite a low suspicion of disease, lack of faculty support for the practice, and a zero yield for the test. Informal clinical policies such as this may be an important contributor to the problem of technology overuse.

Nonparametric probability density estimation: improvements to the histogram for laboratory data

The histogram has long been used in the clinical laboratory for the depiction and manipulation of frequency data. We present recent results of refinements to the usual histogram procedures along with modern alternative methods of estimating frequency distributions, including the kernel and discrete maximum penalized likelihood estimation (DMPLE) approaches. We compared these nonparametric methods on 15 different types of simulated distributions, and on several sets (greater than 1000 subjects/set) of real data, including alanine aminotransferase, aspartate aminotransferase, and lactate dehydrogenase levels. Each frequency curve estimation technique was evaluated by measuring the integrated mean square error between each techniques prediction and the true underlying distribution, using Monte Carlo techniques on sample sets with size 49 and 119. The kernel method was the clear method of choice, both in performance (best in 22/36 cases) and in practical usage.

ESPRE: a knowledge-based system to support platelet transfusion decisions

ESPRE is a knowledge-based system which aids in the review of requests for platelet transfusions in the hospital blood bank. It is a microcomputer-based decision-support system written in Lisp and utilizes a hybrid frame and rule architecture. Most of the required patient data is automatically obtained directly from the hospitals main laboratory computers via a direct link, so that very little keyboard entry is required. Assessment of time trends computed from the data constitutes an important aspect of this system. To aid the blood bank personnel in deciding on the appropriateness of the requested transfusion, the system provides an explanatory report which includes a list of patient-specific data, a list of the conditions for which a transfusion would be appropriate for the particular patient (given the clinical condition), and the conclusions drawn by the system. In an early clinical evaluation of ESPRE, out of a random sample of 75 platelet transfusion requests, there were only three disagreements between the ESPRE and blood-bank personnel.<<ETX>>

Computer-assisted test interpretation: considerations in patient care

Computer-assisted test interpretation (CATI) is a set of developing technologies designed to support medical decision-making. This paper develops a taxonomy of computer-assisted test interpretation, giving specific consideration to the characteristics of the data that are to be interpreted, the nature of the interpretive task, the expected involvement of the health professional in the generation of the interpretation, the inference mechanism used for the interpretation, and the broader context of the interpretation. We go on to examine potential benefits and disadvantages of CATI systems in terms of accuracy, information management, interpretation time, patient management, medical communication, and expense. Finally, we examine electrocardiogram interpretation systems from the perspective of this taxonomy, and offer suggestions regarding areas of further inquiry into the effects of CATI on medical care.

Decision making and laboratory test utilization: expert-novice differences

This study investigates the medical decision making process in both expert and novice physicians in an attempt to identify specific weaknesses in this decision making process which might be targeted for medical decision support. Two groups of physicians, practicing gastroenterologists and third and fourth year medical students, were given simulated patient management problems in a paper-and-pencil format. The two problems used were both from the same medical domain, liver disease, and consisted of an initial clinical scenario followed by two opportunities to order and obtain laboratory test results. The results were analyzed using a hypothetico-deductive model of decision making as a basis for evaluation. It is assumed that weaknesses of the novices relative to the experts in one of the four primary decision making phases described by this model may indicate a possible need for decision support.