Biomedical subjects

David S Wilkinson

Publications and source records attributed to David S Wilkinson.

10 recordsLinked to original sources

PubMed2007

Assessment monitoring of laboratory critical values: a College of American Pathologists Q-Tracks study of 180 institutions.

CONTEXT: Critical laboratory value reporting is a highly visible and essential key activity for clinical laboratories. OBJECTIVE: To measure critical laboratory value reporting in multiple institutions over time and to examine the practice patterns and demographic factors associated with sustained improvement in critical value reporting. DESIGN: A longitudinal cohort study of 180 clinical laboratories that provided quarterly critical values reporting data for 2 to 16 quarters was conducted using a uniform definition of successful caregiver notification. Mixed linear model analysis of the 2001 through 2004 dataset was performed. RESULTS: A decrease in total and inpatient rates of undocumented critical values per 1000 results was associated with (1) the American Association of Blood Banks inspection within the past 2 years (P = .01, for both total and inpatient rates); (2) unit secretary/clerical staff not authorized to accept inpatient critical value notification (P = .004 [total] and .001 [inpatient]); and (3) the mandatory practice of requiring notification of health care providers when handling inpatients known to have results repeatedly in the critical range (P = .01, for both total and inpatient rates). Continued participation in the Q-Tracks monitoring program was associated with significant and progressive improvement in total, inpatient, and outpatient critical value reporting (P = .02, .01, and .003, respectively). CONCLUSIONS: Critical value reporting improved as the duration of participation in the Q-Tracks monitoring program increased. Improved total and inpatient critical value reporting was associated with factors that may be markers for institutions with priorities of quality management and enhanced communication with responsible caregivers.

Benchmarking↗

PubMed2005

Staffing benchmarks for clinical laboratories: a College of American Pathologists Q-probes study of staffing at 151 institutions.

CONTEXT: Inadequate staffing of clinical laboratories may compromise quality and throughput, whereas excess staff unnecessarily increases the cost of testing. OBJECTIVES: To measure productivity of technical staff and management span of control in a large number of laboratories and to determine factors associated with favorable staffing ratios. DESIGN: A total of 151 clinical laboratories provided information about technical and management staffing and output (workload) for 4 laboratory sections: anatomic pathology, chemistry/hematology/immunology, microbiology, and transfusion medicine. RESULTS: For each laboratory section, there was wide variation in labor productivity (output per nonmanagement full-time equivalent) and in management span of control (nonmanagement full-time equivalent per manager). Productivity ratios for the 10th- and 90th-percentile laboratories varied more than 3-fold. Except in histology, laboratory sections with higher test volumes had higher labor productivity (P < .001 for cytology, chemistry/hematology, and transfusion medicine; P = .003 for microbiology). Even within peer groups composed of sections with similar volume, there was wide variation in labor productivity. A number of variables other than test volume were associated with labor productivity and management span of control. Staffing ratios for each laboratory section and for sections of different sizes are presented. CONCLUSIONS: Despite standardization of testing methods in the clinical laboratory industry, there is wide variation in staffing level among institutions. This variation suggests opportunities to improve staff productivity in many facilities.

Benchmarking↗

PubMed2004

Evaluation of quality-control criteria for microarray gene expression analysis.

BACKGROUND: Development of quality-control criteria to ensure reproducibility of microarray results for potential clinical application is still in its infancy. METHODS: In the present studies we developed quality-control criteria and evaluated their effect in microarray data analysis using total RNA from cell lines, frozen tumors, and a commercially available reference RNA. Quality-control criteria such as A(260)/A(280) ratios, percentage of rRNA, and median size of cDNA and cRNA synthesis products were evaluated for robustness in microarray analysis. Furthermore, precision studies using a reference material were performed on the Affymetrix HG-U133A high-density oligonucleotide microarrays. The same reference RNA sample was examined in 16 different chips run on 2 different days in the four different modules of the Affymetrix fluidics workstation. Fresh and frozen fragmented cRNAs were also compared. An ANOVA model was fit to identify the main sources of variation. RESULTS: Good-quality samples showed >30% rRNA in the electropherograms and cDNA and cRNA synthesis products with median sizes of 2.0 and 3.0 kb, respectively. Precision studies showed that the main source of variation was the day-to-day variability, minimally affecting hybridization exogenous control genes. Altogether, the results showed that the Affymetrix Genechip system is highly reproducible when RNA that meet the quality-control criteria are used (overall P >0.01). CONCLUSIONS: These results confirm the need to establish defined quality-control criteria for sample quality to distinguish between analytical and biological variability.

Analysis of Variance↗

PubMed2004

Evaluation of a linear amplification method for small samples used on high-density oligonucleotide microarray analysis.

High-density oligonucleotide microarray analysis has proven to be an excellent approach for gene expression profiling in human cancers. This technique assesses the expression of thousands of genes simultaneously, from at least 5 microg of total RNA per sample per experiment. This total RNA requirement poses a challenge when studying small, unique clinical samples, like biopsies. Recently, a new standardized protocol for small samples was released by Affymetrix, which includes a linear amplification step. To evaluate the impact of such amplification in the gene expression profiling of human ovarian cancer, we compared results obtained from 5 microg and 100 ng of total RNA from the same tumor sample, using the standard Affymetrix protocol and the new linear RNA amplification protocol, respectively. We identified a small bias in gene expression data caused by linear amplification, potentially due to shorter elongation products leading to misclassification of probe sets directed to the middle-5' region of the transcripts. Interestingly, the magnitude of the bias varied when different normalization and expression summary algorithms were used. However, this bias does not affect tumor gene expression profiling. Consequently, linear amplification may be of utility in cases of extremely low RNA recovery from critical and unique samples, such as small biopsies.

Cluster Analysis↗

PubMed2003

Hepatic artery thrombosis after liver transplantation and genetic factors: prothrombin G20210A polymorphism.

Hepatic artery thrombosis (HAT) after liver transplantation is associated with a high incidence of graft failure. The incidence ranges between 2% and 25%, with an overall incidence of approximately 7%. Different risk factors have been associated, but the participation of genetic factors in the cause of HAT is less well studied. A single-base change (G to A) at position 20210 in the 3' untranslated region of the prothrombin gene is associated with increased plasma levels of prothrombin and might therefore increase the risk for thrombosis. We reviewed our HAT experience in 11 years at Medical College of Virginia hospitals of 491 patients undergoing 533 liver transplantations. There were 14 liver grafts with documented HAT (2.62%) in 13 patients. Prothrombin G20210A polymorphism was found in the DNA obtained from 2 of 14 liver allograft tissues (14.2%) but not in the DNA from leukocytes obtained from the peripheral blood of recipients with HAT.

Amino Acid Substitution↗

PubMed2003

Genome-wide detection of LOH in prostate cancer using human SNP microarray technology.

Loss of heterozygosity (LOH) of chromosomal regions is crucial in tumor progression. In this study we assessed the potential of the Affymetrix GeneChip HuSNP mapping assay for detecting genome-wide LOH in prostate tumors. We analyzed two human prostate cell lines, P69SV40Tag (P69) and its tumorigenic subline, M12, and 11 prostate cancer cases. The M12 cells showed LOH in chromosomes 3p12.1-p22.1, 11q22.1-q24.2, 19p13.12, and 19q13.42. All of the prostate cases with informative single-nucleotide polymorphism (SNP) markers showed LOH in 1p31.2, 10q11.21, 12p13.1, 16q23.1-q23.2, 17p13.3, 17q21.31, and 21q21.2. Additionally, a high percentage of cases showed LOH at 6p25.1-p25.3 (75%), 8p22-p23.2, and 10q22.1 (70%). Several tumor suppressor genes (TSGs) have been mapped in these loci. These results demonstrate that the HuSNP mapping assay can serve as an alternative to comparative genomic hybridization for assessing genome-wide LOH and can identify chromosomal regions harboring candidate TSGs implicated in prostate cancer.

Adult↗

PubMed2003

Sentinel node biopsy for breast cancer: using local results for estimation of risk to the patient.

BACKGROUND: Sentinel node biopsy (SNB) is being increasingly used but its place outside randomized trials has not yet been established. METHODS: The first 114 sentinel node (SN) biopsies performed for breast cancer at the Princess Alexandra Hospital from March 1999 to June 2001 are presented. In 111 cases axillary dissection was also performed, allowing the accuracy of the technique to be assessed. A standard combination of preoperative lymphoscintigraphy, intraoperative gamma probe and injection of blue dye was used in most cases. Results are discussed in relation to the risk and potential consequences of understaging. RESULTS: Where both probe and dye were used, the SN was identified in 90% of patients. A significant number of patients were treated in two stages and the technique was no less effective in patients who had SNB performed at a second operation after the primary tumour had already been removed. The interval from radioisotope injection to operation was very wide (between 2 and 22 h) and did not affect the outcome. Nodal metastases were present in 42 patients in whom an SN was found, and in 40 of these the SN was positive, giving a false negative rate of 4.8% (2/42), with the overall percentage of patients understaged being 2%. For this particular group as a whole, the increased risk of death due to systemic therapy being withheld as a consequence of understaging (if SNB alone had been employed) is estimated at less than 1/500. The risk for individuals will vary depending on other features of the particular primary tumour. CONCLUSION: For patients who elect to have the axilla staged using SNB alone, the risk and consequences of understaging need to be discussed. These risks can be estimated by allowing for the specific surgeon's false negative rate for the technique, and considering the likelihood of nodal metastases for a given tumour. There appears to be no disadvantage with performing SNB at a second operation after the primary tumour has already been removed. Clearly, for a large number of patients, SNB alone will be safe, but ideally participation in randomized trials should continue to be encouraged.

Adult↗

PubMed2002

Analytical validation of a real-time reverse transcription-polymerase chain reaction quantitation of different transcripts of the Wilms' tumor suppressor gene (WT1).

Transcript variants of the same gene may play distinct functions in the tissue where they are expressed. Absolute quantitation of different transcript variants in malignant and normal tissues can address the specific role of each particular isoform in cancer development and progression. We have recently demonstrated differential expression of the wild-type Wilms' tumor transcript (wtWT1) and a novel truncated WT1 transcript (trWT1) which lacks the first five exons of wtWT1, among human prostate cancer, leukemia, and breast cancer cell lines. Here we report the analytical validation of a real-time RT-PCR assay for the absolute quantitation of these two different WT1 transcripts with specific primers and probes that ensure specificity for each WT1 variant. By cloning each WT1 transcript in a T3 promoter-containing plasmid, we obtained two WT1 transcript-specific in vitro-generated RNA calibrators for absolute quantitation. Serial dilution of each RNA calibrator demonstrated a 5 log linear dynamic range (5 x 10(1) to 5 x 10(6) copies/reaction, R(2)=0.9963 for wtWT1 and R(2)=0.9993 for trWT1). Dilution of the calibrators in total RNA from 1 x 10(3) non-WT1-expressing cells showed a decreased sensitivity without affecting the linear dynamic range. Precision studies for values within the linear dynamic range showed a coefficient of variation of less than 4% for both transcripts. The described method provides a sensitive and reliable technique for quantitating different WT1 mRNA transcripts.

Calibration↗

PubMedDate not supplied

Using benchmarking to manage your laboratory.

How does your cost per test compare with the competition? Does your productivity measure up? Benchmarking data provide the answers, but you may not realize just how far the information can go. In times of budget cuts, comparing your laboratory operations with the best performers can be crucial. The Virginia Commonwealth University Health System (VCUHS) Pathology Department in Richmond, Virginia, demonstrated that benchmarking is more than a paper exercise. It literally saved the laboratory. The keys were clarification, consistency, and communication.

Benchmarking↗

PubMedDate not supplied

Consumer direct access to clinical laboratory testing: what are the critical issues?

Americans are demanding, independent people. In most aspects of our lives, we are used to walking into a store or other place of business with the expectation that the personnel working for the business will make every effort to satisfy our requests quickly and without the need for a third party to intervene or approve the transaction. Hence, the popularity of convenience stores, do-it-yourself stores and kits, and e-commerce. The delivery of health-care services, however, generally does not conform to this model. Before most diagnostic tests or treatments are ordered, patients usually consult a physician. In many cases, prior to tests or treatments being performed, additional consultations are required with insurance plans. But the winds of change, they are a-blowing. More and more, people demand an active role in managing their health care. One emerging trend is direct patient access to clinical laboratory testing (1).

Clinical Laboratory Techniques↗