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Practical computer validation for pharmaceutical laboratories.

Computer validation should address the scientific correctness of the application software, the business objectives of the organisation, and the concerns of regulatory agencies. It is a balance between a practical and cost effective system that must develop the confidence that the system is under control. This paper gives an overview of computer validation from the following perspectives. What is computer validation? Why can a computer system not be completely validated? Why and how should computer systems be validated? The principles outlined in this paper should be adapted to a specific system on a case by case basis depending on its scope and complexity.

Chemistry, Pharmaceutical↗

Mapping 137Cs deposition: data validation methods and data interpretation.

The "Atlas of caesium deposition on Europe after the Chernobyl accident" was prepared within the framework of the Joint Study Project 6 (JSP6) of the collaborative programme on the consequences of the Chernobyl accident between the European Commission and the Ministries responsible for Chernobyl affairs in Belarus, Russia and Ukraine. The radiological data provided by scientific institutes and competent authorities of more than 30 European countries were integrated into an information platform. Data validation and intercomparison were therefore essential before the interpretation of the deposition with the help of isoline maps prepared with a geographic information system (GIS) could be done. The data validation was a two-step procedure: after performing a primary logical consistency check, other techniques based on spatial statistics were used to outline uncertain data. The purpose of this paper is to present these validation methods and to discuss the advantages and constraints of these techniques. Rather than trying to improve the techniques of spatial data analysis, suggestions are made on how an adaptation of the sampling information could improve the final result.

Cesium Radioisotopes↗

An arrhythmia detector and heart rate estimator for overnight polysomnography studies.

We present an algorithm for automatic on-line analysis of the electrocardiography (ECG) channel acquired during overnight polysomnography (PSG) studies. The system is independent of ECG morphology, requires no manual initialization, and operates automatically throughout the night. It highlights likely occurrences of arrhythmias and intervals of bad signal quality while outputting a continual estimate of heart rate. Algorithm performance is validated against standard ECG databases and PSG data. Results demonstrate a minimal false negative rate and a low false positive rate for arrhythmia detection, and robustness over a wide range of noise contamination.

Algorithms↗

Dynamic MR urography in urinary tract obstruction: implementation and preliminary results.

BACKGROUND: Recent studies have demonstrated magnetic resonance (MR) capabilities in evaluating renal morphology and function in patients with urinary obstruction. The objective of this report is to support the introduction of dynamic MR renography on any MR equipment. METHODS: A custom-made device of vials filled with different concentrations of gadolinium was studied by combinations of T1-weighted gradient-echo sequences and coils. We compared the capabilities of two coils (phased array vs. standard body), the properties of dynamic sequences, and the effects of increasing concentrations of gadolinium on signal intensity. In a second section, we designed MR urography plug-ins of Image J (DICOM image software) for the analysis of dynamic studies. RESULTS: Optimized gradient-echo sequences acquired with a phased array body coil produced acceptable quality images with a linear relation between signal intensity and the lowest concentrations of gadolinium. In vitro measurements showed loss of linearity above 8 mmol/L. CONCLUSION: Theoretical calculation and data from the literature suggest that the gadolinium dose to the patient should not exceed one-fourth of the usual one (0.025 mmol/kg). Postprocessing using Image J software and the specifically designed plug-ins was validated. The collection of plug-ins is now available on the Internet.

Adult↗

Validity and repeatability of a new test for aniseikonia.

PURPOSE: The Aniseikonia Inspector 1.1 (AI) is a new software product to measure aniseikonia using red-green anaglyphs. The purpose of this study was to test whether the AI is a valid and reliable test. METHODS: There were two groups of sample subjects: one at risk of aniseikonia, with anisometropia greater than or equal to 1.00 D (n= 29), and a control group (n= 45). The validity was studied by comparing the measured aniseikonia with the aniseikonia simulated with size lenses. The reliability was estimated by the Bland-Altman statistical method. RESULTS: The results showed that the AI underestimated aniseikonia and that the underestimation was greater in the horizontal than in the vertical direction. The reliability was low, with biases that were clinically insignificant, but the 95% limits of agreement were around +/-2%. The behavior of the test was similar in both groups of subjects. CONCLUSIONS: The reliability of the AI is only moderate, and professionals are therefore warned to use the results of this test with caution.

Adult↗

Diagnostic accuracy of two software modalities for detection of caries lesions in digital radiographs from four dental systems.

OBJECTIVE: To compare the caries diagnostic accuracy of two software modalities used in the assessment of digital radiographs obtained with four different dental systems, and to evaluate whether the software used for image assessment influenced the mutual comparison of those four dental systems relating to their caries diagnostic accuracy. METHODS: Under in vitro and standardized conditions 122 teeth (with 228 unrestored approximal and 99 occlusal surfaces) were radiographed in blocks of 3 test teeth and 2 non-test teeth using two storage phosphor plate systems: Digora (Soredex, Helsinki, Finland) and DenOptix (Gendex, Dentsply, Milan, Italy) and two charge coupled device (CCD)-based sensor systems: Dixi (Planmeca, Helsinki, Finland) and Sidexis (Sirona, Bensheim, Germany). The images were displayed and examined in two software modalities: their own dedicated software and a general software. Three observers examined all images for the presence of approximal enamel and dentine and occlusal dentine caries lesions using a 5-point confidence scale. The true presence of caries was validated by ground section histology. The diagnostic accuracy of the software modalities was expressed as ROC curve areas (A(z)) and differences between modalities were tested by paired t-test. Comparison of systems was analysed by post hoc t-test. RESULTS: Results of approximal and occlusal surfaces assessed together revealed nearly identical mean A(z) with the two software modalities on images obtained with the Digora (A(z)=0.71) and DenOptix (A(z)=0.72) systems. On Dixi images the mean A(z) was 0.75 using the system's own software and 0.73 using the general software. On Sidexis images the corresponding mean A(z)s were 0.79 and 0.75. None of those differences were significant. CONCLUSION: No significant difference in caries diagnostic accuracy was found between two software modalities used for examination of digital radiographs obtained with four different digital systems, and the software modality did not influence the mutual rank of the four systems relating to their diagnostic accuracy.

Data Display↗

Psychometric instrument evaluation: the pediatric family satisfaction questionnaire.

PURPOSE: The purpose of this study was to evaluate parental satisfaction with hospital care in general pediatric units. A search for a valid parental satisfaction instrument resulted in the selection of the Pediatric Family Satisfaction Questionnaire (PFSQ) (Budreau & Chase, 1994). This paper will report on the psychometric testing of the PFSQ. METHODS: The data were retrieved from several years of patient satisfaction surveys collected at a large Midwest hospital and clinics. The SPSS statistical software was used to test the reliability and construct validity of the PFSQ. RESULTS: Alpha for the total instrument was .83, based on 327 cases and 35 items. Factor analysis indicated two main factors, nursing care and medical care, with a total of 30 items. CONCLUSION: The PFSQ is considered a promising instrument for evaluating parental satisfaction in general, inpatient pediatric units. urther development of the instrument is suggested.

Consumer Behavior↗

Prediction of dissolution profiles of acetaminophen beads using artificial neural networks.

Immediate release acetaminophen (APAP) beads with 40% drug loading were prepared using the extrusion-spheronization process. Eighteen batches of beads were prepared based on a full factorial design by varying process variables such as extruder type, extruder screw speed, spheronization speed, and spheronization time. An in vitro dissolution test was carried out using the USP 27 Apparatus II (paddle) method. Artificial Neural Network (ANN) models were developed based on the aforementioned process variables and dissolution data. The trained ANN models were used to predict the dissolution profiles of APAP from the beads, which were prepared with various processing conditions. For training the ANN models, process variables were used as inputs, and percent drug released from APAP beads was used as the output. The dissolution data from one out of 18 batches of APAP beads was selected as the validation data set. The dissolution data of other 17 batches were used to train the ANN models using the ANN software (AI Trilogy) with two different training strategies, namely, neural and genetic. The validation results showed that the ANN model trained with the genetic strategy had better predictability than the one trained with the neural strategy. The ANN model trained with the genetic strategy was then used to predict the drug release profiles of two new batches of APAP beads, which were prepared with process variables that were not used during the ANN model training process. However, the process variables used to prepare the two new batches of APAP beads were within the confines of the process variables used to prepare the 18 batches. The actual drug release profile of these two batches of APAP beads was similar to the ones predicted by the trained and validated ANN model, as indicated by the high f2 values. Furthermore, the ANN model trained with genetic strategy was also used to optimize process variables to achieve the desired dissolution profiles. These batches of APAP beads were then actually prepared using the process variables predicted by the trained and validated ANN model. The dissolution results showed that the actual dissolution profiles of the APAP beads prepared from the predicted process variables were similar to the desired dissolution profiles.

Acetaminophen↗

Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data.

BACKGROUND: We use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant categories, and enables the identification of genes and pathways most significantly associated to each phenotypic group, while allowing for the participation of a given gene in more than one cluster. Genes assigned to each cluster are used for the detection of pathways predominantly activated in that cluster by finding statistically significant associated GO terms. We tested the approach with a published dataset of microarray experiments in yeast. Upon validation with the yeast dataset, we applied the technique to a prostate cancer dataset. RESULTS: Two major pathways are shown to be activated in organ-confined, non-metastatic prostate cancer: those regulated by the androgen receptor and by receptor tyrosine kinases. A number of gene markers (HER3, IQGAP2 and POR1) highlighted by the software and related to the later pathway have been validated experimentally a posteriori on independent samples. CONCLUSION: Using a new microarray analysis tool followed by a posteriori experimental validation of the results, we have confirmed several putative markers of malignancy associated with peptide growth factor signalling in prostate cancer and revealed others, most notably ERRB3 (HER3). Our study suggest that, in primary prostate cancer, HER3, together or not with HER4, rather than in receptor complexes involving HER2, could play an important role in the biology of these tumors. These results provide new evidence for the role of receptor tyrosine kinases in the establishment and progression of prostate cancer.

Biomarkers, Tumor↗

The CCPN data model for NMR spectroscopy: development of a software pipeline.

To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR community (CCPN) created a "Data Model" that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high-throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research.

Computer Graphics↗

Postmarketing surveillance based on electronic patient records: the IPCI project.

Researchers claim that data in electronic patient records can be used for a variety of purposes including individual patient care, management, and resource planning for scientific research. Our objective in the project Integrated Primary Care Information (IPCI) was to assess whether the electronic patient records of Dutch general practitioners contain sufficient data to perform studies in the area of postmarketing surveillance studies. We determined the data requirements for postmarketing surveillance studies, implemented additional software in the electronic patient records of the general practitioner, developed an organization to monitor the use of data, and performed validation studies to test the quality of the data. Analysis of the data requirements showed that additional software had to be installed to collect data that is not recorded in routine practice. To avoid having to obtain informed consent from each enrolled patient, we developed IPCI as a semianonymous system: both patients and participating general practitioners are anonymous for the researchers. Under specific circumstances, the researcher can contact indirectly (through a trusted third party) the physician that made the data available. Only the treating general practitioner is able to decode the identity of his patients. A Board of Supervisors predominantly consisting of participating general practitioners monitors the use of data. Validation studies show the data can be used for postmarketing surveillance. With additional software to collect data not normally recorded in routine practice, data from electronic patient record of general practitioners can be used for postmarketing surveillance.

Family Practice↗

Multislice mapping and quantification of brain perfusion MR imaging data: a comparative study of homemade and commercial software.

PURPOSE: We developed a homemade computer program for analysis of perfusion weighted MR imaging (PW-MRI) data in order to produce colored multislice rCBV, rCBF, and MTT maps. We then compared those maps with others produced by a commercially available program, obtained from the same PW-MRI data, to determine the feasibility of using our program in clinical practice. MATERIALS AND METHODS: Studies of 20 patients were performed on a high field MR scanner. Imaging protocol consisted of perfusion study (EPI, TR/TE: 1430/46 msec, 10 mm gap, matrix: 128x128, FOV: 240 cm, NEX: 1). Twenty ml of Gd-DTPA was administered at a rate of 4-5 ml/sec beginning at the 5th acquisition of 50 dynamic series. MATLAB software was used for writing codes of both mathematical equations and the graphical user interface. All images were in DICOM standard. For validation of the results, all maps were compared with another commercially available program, which is widely being used in daily practice, and was installed on the MR scanner. Ability to define the lesion contours and extension, and artifacts at the bone-soft tissue interface were the criteria used for statistical evaluation. RESULTS: Field definition was equally good in 38% of the patient scans for both software programs; our homemade software was better in 23% of the cases and the commercial software was better in 31%. In 6% of the results, either software program was not sufficient. For the elimination of artifacts, our homemade software was 100% successful in every case. CONCLUSION: Our homemade program is a user friendly one that gives comparable results with those of a commonly used commercial one. However, this program should be tested with different categories of diseases and a larger patient population and then compared with different commercial software programs to be validated more clearly.

Blood Flow Velocity↗

Required steps for the validation of a Laboratory Information Management System.

The task of managing laboratory data is not a new one. Over the past two decades, the use of Laboratory Information Management Systems (LIMS) has revolutionized how laboratories manage their data. A LIMS is more than software; it has become the workhorse of the laboratory, encompassing laboratory work-flow combined with user input, data collection, instrument integration, data analysis, user notification, and delivery of information and reporting. Types of organizations that utilize LIMS vary greatly from research laboratories to manufacturing laboratories to environmental testing laboratories. Commercially-available LIMS have been around since the 1980s. In addition, many laboratories have designed, implemented, and maintained in-house LIMS. The heart of any LIMS is the software. Like other laboratory systems, the LIMS software is subject to quality control and quality assurance checks. In regulatory environments this associated QA/QC is referred to as "system validation." The primary purpose of system validation is to ensure that the software is performing in a manner for which it was designed. For example, the system acceptance criteria should be established and tested against quantifiable tasks to determine if the desired outcome has been achieved. LIMS features, such as autoreporting, reproducibility, throughput, and accuracy must be quantifiable and verifiable. System validation ensures that the entire system has been properly tested, incorporates required controls, and maintains and will continue to maintain data integrity. Laboratories must establish protocols and standards for the validation process and associated documentation. Although vendors of commercial LIMS perform initial internal system validations, the system must be revalidated whenever the end user, vendor or third party adds modifications or customizations to the LIMS. Currently, detailed guidance regarding system validation of LIMS is not available to the user. The issue is addressed in Good Automated Laboratory Practices (GALP) and National Environmental Laboratory Accreditation Conference (NELAC) documents which indicate specific requirements or recommendations for operational checks and periodic testing; however, it is up to the laboratory to determine suitable methods to accomplish these tasks. Proper validation of a LIMS will allow a laboratory to comply with regulations and also provide comprehensive documentation on the system that is necessary to troubleshoot future problems.

Clinical Laboratory Information Systems↗

Validation of a computer analysis to determine 3-D rotations and translations of the rib cage in upright posture from three 2-D digital images.

Since thoracic cage posture affects lumbar spine coupling and loads on the spinal tissues and extremities, a scientific analysis of upright posture is needed. Common posture analyzers measure human posture as displacements from a plumb line, while the PosturePrint claims to measure head, rib cage, and pelvic postures as rotations and translations. In this study, it was decided to evaluate the validity of the PosturePrint Internet computer system's analysis of thoracic cage postures. In a university biomechanics laboratory, photographs of a mannequin thoracic cage were obtained in different postures on a stand in front of a digital camera. For each mannequin posture, three photographs were obtained (left lateral, right lateral, and AP). The mannequin thoracic cage was placed in 68 different single and combined postures (requiring 204 photographs) in five degrees of freedom: lateral translation (Tx), lateral flexion (Rz), axial rotation (Ry), flexion-extension (Rx), and anterior-posterior translation (Tz). The PosturePrint system requires 13 reflective markers to be placed on the subject (mannequin) during photography and 16 additional "click-on" markers via computer mouse before a set of three photographs is analyzed by the PosturePrint computer system over the Internet. Errors were the differences between the positioned mannequin and the calculated positions from the computer system. Average absolute value errors were obtained by comparing the exact inputted posture to the PosturePrint computed values. Mean and standard deviation of computational errors for sagittal displacements of the thoracic cage were Rx=0.3+/-0.1 degrees , Tz=1.6+/-0.7 mm, and for frontal view displacements were Ry=1.2+/-1.0 degrees , Rz=0.6+/-0.4 degrees , and Tx=1.5+/-0.6 mm. The PosturePrint system is sufficiently accurate in measuring thoracic cage postures in five degrees of freedom on a mannequin indicating the need for a further study on human subjects.

Biomechanical Phenomena↗

Safely reducing manual urine microscopy analyses by combining urine flow cytometer and strip results.

We aimed to reduce the number of manual urine microscopy examinations safely by cross-interpretation of the Sysmex UF-100 (TOA Medical Electronics, Kobe, Japan) and urine strip results such that microscopy would be performed if there was discordance between the UF-100 and urine strip results. We also evaluated the usefulness of the optional UF-100 expert software. We performed 2 studies: study 1 to establish review rules for eventual microscopic examination; study 2, a validation study. Our review rates were 40% and 48% and those of UF-100 software were 16% and 32% for the 2 studies. Our false-positive and false-negative results, among the samples not flagged for microscopic review, were acceptably low. We did not find a good correlation between the microscopic classification of RBC morphologic features and the classification given by the UF-100. Since incorporation of the automated urine strip reader and the UF-100 in routine use, our manual microscopy has been reduced to less than 40%.

Adolescent↗

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗

Fibroblast-like synoviocytes derived from patients with rheumatoid arthritis show the imprint of synovial tissue heterogeneity: evidence of a link between an increased myofibroblast-like phenotype and high-inflammation synovitis.

OBJECTIVE: Given the heterogeneity of gene expression patterns and cellular distribution between rheumatoid arthritis (RA) synovial tissues, we sought to determine whether this variability was also reflected at the level of the fibroblast-like synoviocyte (FLS) cultured from RA synovial tissues. METHODS: Gene expression profiles in FLS cultured from synovial tissues obtained from 19 RA patients were analyzed using complementary DNA microarrays and hierarchical cluster analysis. To validate the subclassification, we performed prediction analysis and principal components analysis. Genes that differed significantly in their expression between FLS cultures were selected using Statistical Analysis of Microarrays software. Real-time quantitative polymerase chain reaction was performed to validate the microarray data. Immunocytochemistry was applied to study the expression of the genes of interest in FLS and synovial tissues. RESULTS: Hierarchical clustering identified 2 main groups of FLS characterized by distinctive gene expression profiles. FLS from high-inflammation synovial tissues revealed increased expression of a transforming growth factor beta/activin A-inducible gene profile that is characteristic of myofibroblasts, a cell type considered to be involved in wound healing, whereas increased production of growth factor (insulin-like growth factor 2/insulin-like growth factor binding protein 5) appeared to constitute a characteristic feature of FLS derived from low-inflammation synovial tissues. The molecular feature that defines the myofibroblast-like phenotype was reflected as an increased proportion of myofibroblast-like cells in the heterogeneous FLS population. Myofibroblast-like cells were also found upon immunohistochemical analysis of synovial tissue. CONCLUSION: Our findings support the notion that heterogeneity between synovial tissues is reflected in FLS as a stable trait, and provide evidence of a possible link between the behavior of FLS and the inflammation status of RA synovium.

Arthritis, Rheumatoid↗

Increased power of microarray analysis by use of an algorithm based on a multivariate procedure.

MOTIVATION: The power of microarray analyses to detect differential gene expression strongly depends on the statistical and bioinformatical approaches used for data analysis. Moreover, the simultaneous testing of tens of thousands of genes for differential expression raises the 'multiple testing problem', increasing the probability of obtaining false positive test results. To achieve more reliable results, it is, therefore, necessary to apply adjustment procedures to restrict the family-wise type I error rate (FWE) or the false discovery rate. However, for the biologist the statistical power of such procedures often remains abstract, unless validated by an alternative experimental approach. RESULTS: In the present study, we discuss a multiplicity adjustment procedure applied to classical univariate as well as to recently proposed multivariate gene-expression scores. All procedures strictly control the FWE. We demonstrate that the use of multivariate scores leads to a more efficient identification of differentially expressed genes than the widely used MAS5 approach provided by the Affymetrix software tools (Affymetrix Microarray Suite 5 or GeneChip Operating Software). The practical importance of this finding is successfully validated using real time quantitative PCR and data from spike-in experiments. AVAILABILITY: The R-code of the statistical routines can be obtained from the corresponding author. CONTACT: Schuster@imise.uni-leipzig.de

Algorithms↗