Quality Control Protocols Research Articles

Computational Biology Methods for Characterization of Pluripotent Cells.

Pluripotent cells are a powerful tool for regenerative medicine and drug discovery. Several techniques have been developed to induce pluripotency, or to extract pluripotent cells from different tissues and biological fluids. However, the characterization of pluripotency requires tedious, expensive, time-consuming, and not always reliable wet-lab experiments; thus, an easy, standard quality-control protocol of pluripotency assessment remains to be established. Here to help comes the use of high-throughput techniques, and in particular, the employment of gene expression microarrays, which has become a complementary technique for cellular characterization. Research has shown that the transcriptomics comparison with an Embryonic Stem Cell (ESC) of reference is a good approach to assess the pluripotency. Under the premise that the best protocol is a computer software source code, here I propose and explain line by line a software protocol coded in R-Bioconductor for pluripotency assessment based on the comparison of transcriptomics data of pluripotent cells with an ESC of reference. I provide advice for experimental design, warning about possible pitfalls, and guides for results interpretation.

Changing the paradigm of laboratory quality control through implementation of real-time test results monitoring: For patients by patients

ObjectivesTo develop and implement a quality control protocol using real-time patient data with immediate failure analysis and prevention of releasing results that exceed the allowable total error. Design and methodsPatient data are analyzed in real time using algorithms that incorporate moving medians and moving means for selected chemistry analytes. Simulation software was developed to determine optimal algorithms, establish error limits, and number of patient results for calculation of a single cumulative datum point. Algorithms for moving median (MovMed) and mean (MovMen) were chosen and validated for each analyte. Error limits (TEa) were established using biological and analytical variation with a goal of greater than 90% error detection rate during simulation runs. Middleware software was developed to prohibit the release of patient results upon error detection. ResultsA block size of 50 was determined to be the optimal number of patient results used in cumulative calculations. The application of MovMed and MovMen algorithms achieved 0% false rejection for 24 out of 28 tests (85.7%) during the simulation phase. Four tests had a false rejection rate ranging from 0.2 to 1.0%. Error detection rates of 100% were achieved for 16 out of 28 tests (57.1%). Twelve tests had error detection rates ranging from 94.5 to 99.8%. Traditional QC material utilization was reduced by approximately 75–85% and repeat analysis was reduced by approximately 50%. ConclusionsWe successfully developed and implemented a real-time quality control protocol using patient results with true error detection and without release of erroneous results.

Investigation of the spatial genome organization of mouse sperm and fibroblasts by the Hi-C method

The spatial organization of eukaryotic genome plays an important role in the control of gene expression. The new Hi-C method allows investigation of chromosome contact in the three-dimensional architecture of the whole genome; however, it has not yet been applied to study the spatial configuration of the germ cells genome. Here we describe a protocol for production and quality control of Hi-C DNA libraries from mouse sperm cells and fibroblasts. Our results demonstrate that the Hi-C method can be used for studying the spatial organization of the densely packed sperm genome.

Urinary Free Bisphenol a and Bisphenol a Glucuronide Concentrations in a Sample of Neonates in Baltimore, Maryland

Background: Bisphenol A (BPA) exposure is widespread in the general population. Public health concerns stem from its estrogenic properties. Poor glucuronidation capacity at birth may impede its conjugation to BPA glucuronide, a biologically inert form. Aim: To determine the impact of poor glucuronidation capacity on BPA toxicokinetics in healthy full-term neonates. Methods: Mothers and healthy full-term neonates were recruited at the Johns Hopkins Hospital in Baltimore, Maryland from December 2012 to July 2013. Urine samples were collected and a questionnaire administered at ages 3-6 and 7-28 days. A quality control protocol was implemented to reduce contamination of samples with BPA from field and laboratory sources. Free BPA and BPA glucuronide concentrations were quantified by high performance liquid chromatography, tandem mass spectrometry with dansyl chloride derivatization (LOQ=0.1 ug/L). BPA glucuronide concentrations were adjusted for the difference in the molecular weights of free BPA and BPA glucuronide. Results: BPA glucuronide was quantified in 71% of 78 urine samples from 44 neonates. No free BPA concentrations exceeded the LOQ in any sample. BPA glucuronide concentrations were higher at age 3-6 days (geometric mean: 0.25 ug BPA/L) than at age 7-28 days (geometric mean: 0.11 ug BPA/L). In a linear regression analysis that accounted for within-person correlation of BPA glucuronide concentrations (?=0.46), age group (ß=-0.5 [95% CI: -0.94, -0.06]) and breastfeeding (ß=-0.72 [95% CI: -1.4, -0.06]) were significantly associated with a decrease in urinary BPA glucuronide. Conclusions: Quantification of BPA glucuronide in these samples demonstrates exposure to and efficient glucuronidation of BPA during the neonatal period among healthy full-term neonates aged 3-6 and 7-28 days. These data include the first urinary BPA measurements in healthy full-term neonates in the first week of life. Formula intake may be a risk factor for BPA exposure.

Methods of increasing the performance of radionuclide generators used in nuclear medicine: daughter nuclide build-up optimisation, elution-purification-concentration integration, and effective control of radionuclidic purity.

Methods of increasing the performance of radionuclide generators used in nuclear medicine radiotherapy and SPECT/PET imaging were developed and detailed for 99Mo/99mTc and 68Ge/68Ga radionuclide generators as the cases. Optimisation methods of the daughter nuclide build-up versus stand-by time and/or specific activity using mean progress functions were developed for increasing the performance of radionuclide generators. As a result of this optimisation, the separation of the daughter nuclide from its parent one should be performed at a defined optimal time to avoid the deterioration in specific activity of the daughter nuclide and wasting stand-by time of the generator, while the daughter nuclide yield is maintained to a reasonably high extent. A new characteristic parameter of the formation-decay kinetics of parent/daughter nuclide system was found and effectively used in the practice of the generator production and utilisation. A method of “early elution schedule” was also developed for increasing the daughter nuclide production yield and specific radioactivity, thus saving the cost of the generator and improving the quality of the daughter radionuclide solution. These newly developed optimisation methods in combination with an integrated elution-purification-concentration system of radionuclide generators recently developed is the most suitable way to operate the generator effectively on the basis of economic use and improvement of purposely suitable quality and specific activity of the produced daughter radionuclides. All these features benefit the economic use of the generator, the improved quality of labelling/scan, and the lowered cost of nuclear medicine procedure. Besides, a new method of quality control protocol set-up for post-delivery test of radionuclidic purity has been developed based on the relationship between gamma ray spectrometric detection limit, required limit of impure radionuclide activity and its measurement certainty with respect to optimising decay/measurement time and product sample activity used for QC quality control. The optimisation ensures a certainty of measurement of the specific impure radionuclide and avoids wasting the useful amount of valuable purified/concentrated daughter nuclide product. This process is important for the spectrometric measurement of very low activity of impure radionuclide contamination in the radioisotope products of much higher activity used in medical imaging and targeted radiotherapy.

Genome-wide association study in obsessive-compulsive disorder: results from the OCGAS.

Obsessive-compulsive disorder (OCD) is a psychiatric condition characterized by intrusive thoughts and urges and repetitive, intentional behaviors that cause significant distress and impair functioning. The OCD Collaborative Genetics Association Study (OCGAS) is comprised of comprehensively assessed OCD patients, with an early age of OCD onset. After application of a stringent quality control protocol, a total of 1 065 families (containing 1 406 patients with OCD), combined with population-based samples (resulting in a total sample of 5 061 individuals), were studied. An integrative analyses pipeline was utilized, involving association testing at SNP- and gene-levels (via a hybrid approach that allowed for combined analyses of the family- and population-based data). The smallest P-value was observed for a marker on chromosome 9 (near PTPRD, P=4.13×10−7). Pre-synaptic PTPRD promotes the differentiation of glutamatergic synapses and interacts with SLITRK3. Together, both proteins selectively regulate the development of inhibitory GABAergic synapses. Although no SNPs were identified as associated with OCD at genome-wide significance level, follow-up analyses of GWAS signals from a previously published OCD study identified significant enrichment (P=0.0176). Secondary analyses of high confidence interaction partners of DLGAP1 and GRIK2 (both showing evidence for association in our follow-up and the original GWAS study) revealed a trend of association (P=0.075) for a set of genes such as NEUROD6, SV2A, GRIA4, SLC1A2, and PTPRD. Analyses at the gene-level revealed association of IQCK and C16orf88 (both P<1×10−6, experiment-wide significant), as well as OFCC1 (P=6.29×10−5). The suggestive findings in this study await replication in larger samples.

Bomb dating, age validation and quality control of age determinations of monodontids and other marine mammals

Methods for confirming the accuracy of age determination methods are reasonably well established in fishes, but the millions of routine age determinations which take place every year require their own quality control protocols. In contrast, methods for ensuring accuracy in age determination of monodontids and other marine mammals are still being developed. Here we review the basis and application of bomb radiocarbon to marine mammal age validation, highlighting its value for providing unambiguous estimates of age for belugas and other long-lived animals which form growth bands. Bomb radiocarbon is particularly useful for marine mammals, given that the age of an individual animal can be determined to within ±1-3 years, as long as it was alive during the 1960s. However, ongoing age determinations require careful monitoring to ensure that age interpretations remain consistent across ages and through time. Quality control protocols using reference collections of ageing material, in conjunction with age bias plots and measures of precision, are capable of detecting virtually all of the systematic ageing errors that often occur once age determinations of an animal become routine.

URJC GB dataset: Community-based seed bank of Mediterranean high-mountain and semi-arid plant species at Universidad Rey Juan Carlos (Spain).

The Germplasm Bank of Universidad Rey Juan Carlos was created in 2008 and currently holds 235 accessions and 96 species. This bank focuses on the conservation of wild-plant communities and aims to conserve ex situ a representative sample of the plant biodiversity present in a habitat, emphasizing priority ecosystems identified by the Habitats Directive. It is also used to store plant material for research and teaching purposes. The collection consists of three subcollections, two representative of typical habitats in the center of the Iberian Peninsula: high-mountain pastures (psicroxerophylous pastures) and semi-arid habitats (gypsophylic steppes), and a third representative of the genus Lupinus. The high-mountain subcollection currently holds 153 accessions (63 species), the semi-arid subcollection has 76 accessions (29 species,) and the Lupinus subcollection has 6 accessions (4 species). All accessions are stored in a freezer at -18 °C in Kilner jars with silica gel. The Germplasm Bank of Universidad Rey Juan Carlos follows a quality control protocol which describes the workflow performed with seeds from seed collection to storage. All collectors are members of research groups with great experience in species identification. Herbarium specimens associated with seed accessions are preserved and 63% of the records have been georreferenced with GPS and radio points. The dataset provides unique information concerning the location of populations of plant species that form part of the psicroxerophylous pastures and gypsophylic steppes of Central Spain as well as populations of genus Lupinus in the Iberian Peninsula. It also provides relevant information concerning mean seed weight and seed germination values under specific incubation conditions. This dataset has already been used by researchers of the Area of Biodiversity and Conservation of URJC as a source of information for the design and implementation of experimental designs in these plant communities. Since they are all active subcollections in continuous growth, data is updated regularly every six months and the latest version can be accessed through the GBIF data portal at http://www.gbif.es:8080/ipt/resource.do?r=germoplasma-urjc. This paper describes the URJC Germplasm Bank and its associated dataset with the aim of disseminating the dataset and explaining how it was derived.

3-D extracellular matrix from sectioned human tissues.

Cell adhesion, migration, and signaling in physiologically normal and pathological processes depend highly on the extracellular matrix that the cell interacts with. A variety of in vitro models of two-dimensional and three-dimensional extracellular matrices have been developed to study multiple aspects of cellular behavior. However, there is a profound need for in vitro models of extracellular matrices to closely mimic both biochemical and physical aspects of a three-dimensional in vivo cellular environment. This unit outlines the preparation of human-tissue-derived, cell-free, three-dimensional extracellular matrices for studying cellular behavior and cell-extracellular matrix interactions ex vivo. These protocols can be used to prepare cell-free matrices from a variety of normal and cancerous tissues. This unit also provides protocols for quality control of acellular matrix preparations, and for immunostaining of cells for specific cellular proteins as well as of extracellular matrices for their components.

Method of measuring NEQ as a quality control metric for digital mammography

Current quality control protocols for digital mammography rely on subjective assessments of image quality or simple measures that are not comparable between vendor platforms. The noise-equivalent quanta (NEQ) can be expressed in units of image quanta (fluence) for the spatial frequency range of interest, enabling comparisons between systems and x-ray spectra. The purpose of this work is to explore use of a simple phantom to measure the components of the noise-equivalent quanta of digital mammography systems for use in routine quality control. A simple phantom is imaged on six mammography systems from different vendors. The phantom contains uniform regions for measurement of noise power spectrum (NPS), slanted edges for measurement of modulation transfer function (MTF), and objects of various thicknesses for measurement of contrast. Images were acquired at a range of dose levels on each system to examine how measurements scale with dose, and multiple images were taken at a single dose point to examine measurement reproducibility. The phantom and measurement methods show good reproducibility, with average coefficient of variation values of less than or equal to 15% on all systems evaluated. Measured MTF and NPS values are comparable to other published results when the increase in scattered radiation generated by placing the phantom on the breast support is accounted for. Measurement of the parameters required to calculate NEQ from a single image of a simple phantom is practical, and shows promise as a method of evaluating image quality for routine quality control of digital mammography systems.

Quality assurance and quality control of pressure relief systems

Pressure relief systems are important for the safe operation of refineries and chemical plants. They are generally considered to be the last line of defense against abnormal operation which could lead to serious accidents, resulting in loss of life and property. To ensure that the system provides proper protection for the range of potential process deviations, it is important to properly size the pressure relief systems considering all the possible applicable overpressure scenarios. Quality Assurance (QA) and Quality Control (QC) are important work processes which help to ensure that relief systems are properly designed and documented. This article discusses best practices regarding QA and QC protocols for pressure relief systems. Definitions are given for the terminology used for the QA/QC process of pressure relief system studies. A sample workflow of a typical pressure relief system analysis is also provided. Different steps of the pressure relief analysis process are briefly discussed, and sample work instructions are given for each step. An example set of documentation required for a pressure relief system study, as well as a recommended sequence of documents therein, are described. Work instructions are given for the QA/QC process in the different sections of the studies—system information, overpressure contingency analysis, relief rate calculation and relief device sizing, deficiency identification, and final documentation. Lastly, some common mistakes which have been observed during the QA/QC of numerous studies of pressure relief systems from commercial refineries and chemical plants are reviewed. © 2014 American Institute of Chemical Engineers Process Saf Prog 33: 136–142, 2014

A quality control protocol for gas condensate fluid samples

Abstract Several quality control (QC) methods have been introduced for gas condensate fluid samples in the literature. However, a comprehensive protocol to check the quality and validity of reservoir fluid samples and their analysis results is absent. This paper introduces a robust protocol which involves diagnostic methods consisting of using appropriate plots to identify outlying data and general trends in different properties, checking stabilization of flowing parameters during conditioning and sampling period, applying suitable criteria for selection of the best gas and oil samples in laboratory, QC of recombination of fluids and composition analysis, evaluating experimental data by material balance, and using appropriate fluid property correlations. This protocol is further applied to the fluid samples taken from a gas condensate field located in the Middle East. This stepwise protocol evaluates the existing data from well conditioning, fluid sampling, recombination and PVT experiments. This careful and thorough examination identifies the representative fluid samples and, moreover, clarifies the flaws of unrepresentative samples. It also helps avoid occurrence of errors in the future fluid sampling and experimental analysis. Such a comprehensive quality control protocol could be utilized extensively in the industry as a part of a fluid characterization project.

Pre-Treatment Dose Verification of Imrt Using Gafchromic Ebt3 Film and 2DArray

Purpose: The present work deals with pre-treatment dosimetric verification of 10 prostate intensity-modulated radiotherapy (IMRT) plans obtained by Gafchromic EBT3 film and 2D-Array seven29 to establish quality control protocol for the delivery of prostate IMRT in our clinic. Methods: 10 prostate patients were irradiated according to IMRT techniques with 6 MV photon beams produced by a Varian DHX linear accelerator. Dose plans were computed using Eclipse 8.9 (version8.9, Varian, Palo Alto, CA, United States) treatment planning system (TPS). Pre-treatment dosimetric verification was carried out on field-perfield and total IMRT plan basis measuring 2D dose distributions in RW3 solid water phantom (PTW-Freiburg, Germany). For 10 patient plans, the dose distribution was re-calculated with the phantom CT scan and delivered to the phantom with the original and 0 degrees gantry, collimator and table angles. Thus IMRT quality control (QC) plans were generated. Dose distribution measurements were measured with Gafchromic EBT3 film and 2D-Array seven29 (PTW-Freiburg, Germany) two dimensional ionization chamber system. Verification measurements of total IMRT plans and each individual beams were compared with expected dose maps, and differences were evaluated by Verisoft program (PTW-Freiburg, Germany). To provide comparisons of multidimensional dose distributions, dose comparison tools such as gamma dose distribution, distance- to- agreement (DTA) and dose difference (DD) have been developed. The gamma dose distribution tool was used in our study. Three different gamma criteria of dose difference (DD) and distance to agreement (DTA) (3%/3 mm, 4%/4 mm and 5%/5 mm DD / DTA) are selected. These criteria are evaluated while suppressing the dose of 5% from dose distribution. Criterion validity accepted as section with gamma value less than or equal to 1 (γ ≤ 1) to be 90%. Results: In the comparison of dose distributions obtained from TPS and the results of PTW 2D-Array seven29 and Gafchromic EBT3 film dosimetry systems, it was showed that the compatibility of both methods were above 90% with respect to 3% DD and 3mm DTA criteria. PTW 2D-Array seven29 results compared to the results of the film was closer to the TPS data and this difference was statistically meaningful (p 0.05). Conclusions: The measurements performed with PTW 2D-Array seven29 were closer to the TPS data than film measurements and it takes less time during clinical use, so it could be preferred for routine use. The present results suggest the gamma criteria of 3%/3 mm as the most suitable criteria for prostate IMRT quality assurance.

Development of quality control protocol in Linac-based stereotactic radiation therapy

Development of quality control protocol in Linac-based stereotactic radiation therapy

Definition and impact of a quality index for radar-based reference measurements in the H-SAF precipitation product validation

Abstract. The EUMETSAT Satellite Application Facility on Support to Operational Hydrology and Water Management (H-SAF) provides rainfall estimations based on infrared and microwave satellite sensors on board polar and geostationary satellites. The validation of these satellite estimations is performed by the H-SAF Precipitation Product Validation Group (PPVG). A common validation methodology has been defined inside the PPVG in order to make validation results from several institutes comparable and understandable. The validation of the PR-OBS-3 (blended infrared–microwave (IR–MW) instantaneous rainfall estimation) product using radar-based rainfall estimations as ground reference is described herein. A network of C-band and Ka-band radars throughout Europe ensures a wide area coverage with different orographic configurations and climatological regimes, but the definition of a quality control protocol for obtaining consistent ground precipitation fields across several countries is required. Among the hydro-meteorological community, the evaluation of the data quality is a quite consolidated practice, even though a unique definition of a common evaluation methodology between different countries and institutions has not been set up yet. Inside H-SAF, the first definition of the quality index of the radar rainfall observations has been introduced at the Italian Civil Protection Department (DPC). In the evaluation of the DPC quality index, several parameters are considered, some measured by the radar itself (static clutter map, range distance, radial velocity, texture of differential reflectivity, texture of co-polar correlation coefficient and texture of differential phase shift) and some obtained by external sources (digital elevation model, freezing layer height). In some cases, corrections were applied for clutter and beam blocking. The DPC quality index was calculated and applied to some relevant meteorological events reported by a radar test site in Italy. The precipitation field derived by radar data was compared with the PR-OBS-3 precipitation product, with varying thresholds of quality index: the impact of the introduction of the quality index defined on the statistical results of the satellite product validation as well as their sensitivity to the threshold choice were thus evaluated. Results show that PR-RMSE (a relative RMSE here introduced) is reduced from values between 2.5 and 3 to values around 1 when the quality threshold is increased from 0 (no threshold) to 0.8. Fractional standard error also decreases, from values around 2 to values around 1.5 in the same span of the quality threshold.

An audit of a hospital-based Doppler ultrasound quality control protocol using a commercial string Doppler phantom

Results from a four-year audit of a Doppler quality assurance (QA) program using a commercially available Doppler string phantom are presented. The suitability of the phantom was firstly determined and modifications were made to improve the reliability and quality of the measurements. QA of Doppler ultrasound equipment is very important as data obtained from these systems is used in patient management. It was found that if the braided-silk filament of the Doppler phantom was exchanged with an O-ring rubber filament and the velocity range below 50 cm/s was avoided for Doppler quality control (QC) measurements, then the maximum velocity accuracy (MVA) error and intrinsic spectral broadening (ISB) results obtained using this device had a repeatability of 18 ± 3.3% and 19 ± 3.5%, respectively. A consistent overestimation of the MVA of between 12% and 56% was found for each of the tested ultrasound systems. Of more concern was the variation of the overestimation within each respective transducer category: MVA errors of the linear, curvilinear and phased array probes were in the range 12.3–20.8%, 32.3–53.8% and 27–40.7%, respectively. There is a dearth of QA data for Doppler ultrasound; it would be beneficial if a multicentre longitudinal study was carried out using the same Doppler ultrasound test object to evaluate sensitivity to deterioration in performance measurements.

A climatology-based quality control procedure for profiling float oxygen data

[1] Over 450 Argo profiling floats equipped with oxygen sensors have been deployed, but no quality control (QC) protocols have been adopted by the oceanographic community for use by Argo data centers. As a consequence, the growing float oxygen data set as a whole is not readily utilized for many types of biogeochemical studies. Here we present a simple procedure that can be used to correct first-order errors (offset and drift) in profiling float oxygen data by comparing float data to a monthly climatology (World Ocean Atlas 2009). Float specific correction terms for the entire array were calculated. This QC procedure was evaluated by (1) comparing the climatology-derived correction coefficients to those derived from discrete samples for 14 floats and (2) comparing correction coefficients for seven floats that had been calibrated twice prior to deployment (once in the factory and once in-house), with the second calibration ostensibly more accurate than the first. The corrections presented here constrain most float oxygen measurements to better than 3% at the surface.

PET/CT in malignant lymphoma: basic information, clinical application, and proposal

Coregistered fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) provides functional and morphologic data useful for the management of lymphoma. PET/CT is a promising tool in initial staging/re-staging, monitoring post-treatment recurrence/exacerbation, and evaluating prognosis at mid-treatment use [interim PET/CT (iPET/CT)]. Many multicenter studies are currently underway to investigate the effectiveness and safety of stratified treatment protocols using iPET/CT. Thus, the establishment of a system focusing on standardization of image quality through established protocols for scanning or quality control (QC) of the acquired data and organization of a core laboratory facility to promote standardization would be beneficial. Uniformity of image quality across multiple institutions can be guaranteed through optimization of imaging conditions and appropriate QC of PET/CT scanners to ensure standardization. Further research is required to ensure the standardization of PET/CT protocols used in the management of malignant lymphoma.

Three-stage quality control strategies for DNA re-sequencing data

Advances in next-generation sequencing (NGS) technologies have greatly improved our ability to detect genomic variants for biomedical research. In particular, NGS technologies have been recently applied with great success to the discovery of mutations associated with the growth of various tumours and in rare Mendelian diseases. The advance in NGS technologies has also created significant challenges in bioinformatics. One of the major challenges is quality control of the sequencing data. In this review, we discuss the proper quality control procedures and parameters for Illumina technology-based human DNA re-sequencing at three different stages of sequencing: raw data, alignment and variant calling. Monitoring quality control metrics at each of the three stages of NGS data provides unique and independent evaluations of data quality from differing perspectives. Properly conducting quality control protocols at all three stages and correctly interpreting the quality control results are crucial to ensure a successful and meaningful study.

An automatic MRI quality control procedure: Multisite reports for slice thickness and geometric accuracy

In this work, we report multi-scanner quality control monitoring using a standard and automated protocol. This magnetic resonance imaging quality control protocol, based on the American College of Radiology procedures, includes weekly scans of a dedicated phantom followed by specific measurements. The processing step commonly involves manually-performed operations which can be tedious and time-consuming hence motivating their automation. QC data were collected in four sites; data from one of them served for the validation of the automatic analysis tool. Designed as a package of MATLAB® functions, this tool was successfully validated using Student's t-test and the correlation between automatic measurements and the manual ones. Besides, the multisite QC study enabled to compare the performances of these four MR facilities. In order to avoid misinterpretation or errors in multicenter clinical studies, such approach can be recommended as a preliminary step for including a site in the studies.