Demystifying EQA statistics and reports

Reports act as an important feedback tool in External Quality Assessment (EQA). Their main role is to score laboratories for their performance in an EQA round. The most common scores that apply to quantitative data are Q- and Z-scores. To calculate these scores, EQA providers need to have an assigned value and standard deviation for the sample. Both assigned values and standard deviations can be derived chemically or statistically. When derived statistically, different anomalies against the normal distribution of the data have to be handled. Various procedures for evaluating laboratories are able to handle these anomalies. Formal tests and graphical representation techniques are discussed and suggestions are given to help choosing between the different evaluations techniques. In order to obtain reliable estimates for calculating performance scores, a satisfactory number of data is needed. There is no general agreement about the minimal number that is needed. A solution for very small numbers is proposed by changing the limits of evaluation. Apart from analyte- and sample-specific laboratory evaluation, supplementary information can be obtained by combining results for different analytes and samples. Various techniques are overviewed. It is shown that combining results leads to supplementary information, not only for quantitative, but also for qualitative and semi-quantitative analytes

Illumina sequencing of 15 deafness genes using fragmented amplicons

BACKGROUND: Resequencing of deafness related genes using GS FLX massive parallel sequencing of PCR amplicons spanning selected genes has previously been reported as a successful strategy to discover causal variants. The amplicon lengths were designed to be smaller than the sequencing read length of GS FLX technology, but are longer than Illumina sequencing technology read lengths. Fragmentation is thus required to sequence these amplicons using high throughput Illumina technology. METHODS: We performed Illumina sequencing in 4 patients on 563 multiplexed amplicons covering the exons of 15 genes involved in the hearing process. After exploring several fragmentation strategies, the amplicons were fragmented using Covaris sonication prior to library preparation. CLC genomic workbench was used to analyze the data. RESULTS: We achieve an excellent coverage with more than 99% of the amplicons bases covered. All variants that were previously validated using Sanger sequencing, were also called in this study. Variant calling revealed less false positive and false negative results compared to the previous study. For each patient, several variants were found that are reported by ClinVar as possible hearing loss variants. CONCLUSION: Migration from GS FLX amplicon sequencing to Illumina amplicon sequencing is straightforward and leads to more accurate results. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1756-0500-7-509) contains supplementary material, which is available to authorized users

Accuracy of linear measurements using three imaging modalities: two lateral cephalograms and one 3D model from CBCT data

SummaryBackground: The aim of this study was to evaluate the accuracy of linear measurements on three imaging modalities: lateral cephalograms from a cephalometric machine with a 3 m source-to-mid-sagittal-plane distance (SMD), from a machine with 1.5 m SMD and 3D models from cone-beam computed tomography (CBCT) data. Methods: Twenty-one dry human skulls were used. Lateral cephalograms were taken, using two cephalometric devices: one with a 3 m SMD and one with a 1.5 m SMD. CBCT scans were taken by 3D Accuitomo® 170, and 3D surface models were created in Maxilim® software. Thirteen linear measurements were completed twice by two observers with a 4 week interval. Direct physical measurements by a digital calliper were defined as the gold standard. Statistical analysis was performed. Results: Nasion-Point A was significantly different from the gold standard in all methods. More statistically significant differences were found on the measurements of the 3 m SMD cephalograms in comparison to the other methods. Intra- and inter-observer agreement based on 3D measurements was slightly better than others. Limitations: Dry human skulls without soft tissues were used. Therefore, the results have to be interpreted with caution, as they do not fully represent clinical conditions. Conclusions: 3D measurements resulted in a better observer agreement. The accuracy of the measurements based on CBCT and 1.5 m SMD cephalogram was better than a 3 m SMD cephalogram. These findings demonstrated the linear measurements accuracy and reliability of 3D measurements based on CBCT data when compared to 2D techniques. Future studies should focus on the implementation of 3D cephalometry in clinical practic

Pre-surgical radiographic and clinical features as predictors for temporomandibular joint discectomy prognosis

Objectives This study aimed to identify potential clinical and radiological predictors associated with the outcome of discectomies. Methods In this retrospective observational study, the material comprised preoperative CBCT images and medical records of 62 patients with disc derangement disorders, who had undergone discectomy because of disc displacement with reduction (DDwR), disc displacement without reduction (DDwoR), systemic arthritis (SA), or joint hypermobility. Clinical and radiographic variables were analysed in relation to success rate determined by subjective, objective and combined outcomes. Results The success odds ratio was 11 times higher in patients with painful DDwR versus that of SA (p = 0.03), and even 25.9 times higher when considering solely objective outcome (p = 0.03). In the absence of subchondral pseudocyst, there were 5.2 times higher odds to have a successful subjective outcome (p = 0.04). Extensive bone apposition on the temporal joint component indicated a 9.3 times higher likelihood of a failed objective outcome (p = 0.04). Conclusions There is a significant higher risk for combined outcome failure for the diagnosis SA involving the TMJ compared with DDwR. Predictors of importance based on CBCT findings related to the objective outcome failure were extensive bone apposition on the temporal joint component and condylar subchondral pseudocysts for the subjective outcome failure.publishedVersio

The role of Solobacterium moorei in oral malodour.

peer reviewedThis study aims to analyze the correlation between Solobacterium moorei (S. moorei), both on the tongue and in saliva, and several oral malodour- and clinical parameters. Data from 193 patients visiting a halitosis clinic were used for analysis. A questionnaire assessed their general health, allergies, medication, smoking habits and oral hygiene. Following halitosis parameters were recorded: organoleptic score (OLS) (0-5), total concentration of volatile sulfur compounds (VSC) (Halimeter), individual concentrations of VSC (Oral Chroma), tongue coating (MTCI, WTCI and mWTCI), salivary parameters (flow rate and pH), oral hygiene, tonsil health and periodontal health. In all subjects, microbiological samples were collected from the tongue coating and from the saliva, and a quantitative polymerase chain reaction was performed to detect S. moorei. A significant correlation could be established between S. moorei, from both tongue and saliva, and several breath parameters (OLS, H2S, CH3SH, (CH3)2S and total VSCs), tongue coating indices and periodontal indices (gingivitis, periodontitis and oral hygiene). This study suggests a strong association between the presence of S. moorei and oral malodour (s54747)

Distributed learning: Developing a predictive model based on data from multiple hospitals without data leaving the hospital – A real life proof of concept

AbstractPurposeOne of the major hurdles in enabling personalized medicine is obtaining sufficient patient data to feed into predictive models. Combining data originating from multiple hospitals is difficult because of ethical, legal, political, and administrative barriers associated with data sharing. In order to avoid these issues, a distributed learning approach can be used. Distributed learning is defined as learning from data without the data leaving the hospital.Patients and methodsClinical data from 287 lung cancer patients, treated with curative intent with chemoradiation (CRT) or radiotherapy (RT) alone were collected from and stored in 5 different medical institutes (123 patients at MAASTRO (Netherlands, Dutch), 24 at Jessa (Belgium, Dutch), 34 at Liege (Belgium, Dutch and French), 48 at Aachen (Germany, German) and 58 at Eindhoven (Netherlands, Dutch)).A Bayesian network model is adapted for distributed learning (watch the animation: http://youtu.be/nQpqMIuHyOk). The model predicts dyspnea, which is a common side effect after radiotherapy treatment of lung cancer.ResultsWe show that it is possible to use the distributed learning approach to train a Bayesian network model on patient data originating from multiple hospitals without these data leaving the individual hospital. The AUC of the model is 0.61 (95%CI, 0.51–0.70) on a 5-fold cross-validation and ranges from 0.59 to 0.71 on external validation sets.ConclusionDistributed learning can allow the learning of predictive models on data originating from multiple hospitals while avoiding many of the data sharing barriers. Furthermore, the distributed learning approach can be used to extract and employ knowledge from routine patient data from multiple hospitals while being compliant to the various national and European privacy laws

Comparison of methods for in-house screening of HLA*B57:01 to prevent abacavir hypersensitivity in HIV-1 care

Abacavir is a nucleoside reverse transcriptase inhibitor used as part of combination antiretroviral therapy in HIV-1-infected patients. Because this drug can cause a hypersensitivity reaction that is correlated with the presence of the HLA-B*57:01 allotype, screening for the presence of HLA-B*57:01 is recommended before abacavir initiation. Different genetic assays have been developed for HLA-B*57:01 screening, each with specific sensitivity, turnaround time and assay costs. Here, a new real-time PCR (qPCR) based analysis is described and compared to sequence specific primer PCR with capillary electrophoresis (SSP PCR CE) on 149 patient-derived samples, using sequence specific oligonucleotide hybridization combined with high resolution SSP PCR as gold standard. In addition to these PCR based methods, a complementary approach was developed using flow cytometry with an HLA-B17 specific monoclonal antibody as a pre-screening assay to diminish the number of samples for genetic testing. All three assays had a maximum sensitivity of >99. However, differences in specificity were recorded, i.e. 84.3%, 97.2% and >99% for flow cytometry, qPCR and SSP PCR CE respectively. Our data indicate that the most specific and sensitive of the compared methods is the SSP PCR CE. Flow cytometry pre-screening can substantially decrease the number of genetic tests for HLA-B*57:01 typing in a clinical setting

Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform

Background: Hereditary hearing loss (HL) can originate from mutations in one of many genes involved in the complex process of hearing. Identification of the genetic defects in patients is currently labor intensive and expensive. While screening with Sanger sequencing for GJB2 mutations is common, this is not the case for the other known deafness genes (> 60). Next generation sequencing technology (NGS) has the potential to be much more cost efficient. Published methods mainly use hybridization based target enrichment procedures that are time saving and efficient, but lead to loss in sensitivity. In this study we used a semi-automated PCR amplification and NGS in order to combine high sensitivity, speed and cost efficiency. Results: In this proof of concept study, we screened 15 autosomal recessive deafness genes in 5 patients with congenital genetic deafness. 646 specific primer pairs for all exons and most of the UTR of the 15 selected genes were designed using primerXL. Using patient specific identifiers, all amplicons were pooled and analyzed using the Roche 454 NGS technology. Three of these patients are members of families in which a region of interest has previously been characterized by linkage studies. In these, we were able to identify two new mutations in CDH23 and OTOF. For another patient, the etiology of deafness was unclear, and no causal mutation was found. In a fifth patient, included as a positive control, we could confirm a known mutation in TMC1. Conclusions: We have developed an assay that holds great promise as a tool for screening patients with familial autosomal recessive nonsyndromal hearing loss (ARNSHL). For the first time, an efficient, reliable and cost effective genetic test, based on PCR enrichment, for newborns with undiagnosed deafness is available

Usefulness of a new malodour-compound detection portable device in oral malodour diagnosis.

peer reviewedA new device (BB Checker) able to detect malodour compounds has recently been made available. This retrospective analysis aimed at evaluating the usefulness of this device as adjunct tool for the diagnosis of oral malodour. Data from 100 consecutive volunteers with bad breath complaints attending their first consultation at a halitosis clinic were analysed. In addition to the standard protocol (organoleptic ratings from mouth and nose air, and from tongue coating when present; OralChroma and Halimeter measurements from mouth air; and intra-oral examinations), oral, exhaled and nasal air samples were examined with the BB Checker. We could not establish a correlation between the BB Checker values and the organoleptic scores, or the sulfur-compound levels determined by the OralChroma or the Halimeter (R 0.05). The overall sensitivity and specificity of the new device did not exceed the 50%. The correlations between the organoleptic scores and the OralChroma and the Halimeter measurements were good and in line with previous reports (R between 0.56 and 0.73). Our results do not favour the use of the BB Checker as adjunct tool in the diagnosis of oral malodour

Analytical performance of eight enzymatic assays for ethanol in serum evaluated by data from the Belgian external quality assessment scheme

Abstract Objectives Fast and reliable ethanol assays analysis are used in a clinical context for patients suspected of ethanol intoxication. Mostly, automated systems using an enzymatic reaction based on ethanol dehydrogenase are used. The manuscript focusses on the evaluation of the performance of these assays. Methods Data included 30 serum samples used in the Belgian EQA scheme from 2019 to 2021 and concentrations ranged from 0.13 to 3.70 g/L. A regression line between target concentrations and reported values was calculated to evaluate outliers, bias, variability and measurement uncertainty. Results A total of 1,611 results were taken into account. Bias was the highest for Alinity c over the whole concentration range and the lowest for Vitros for low concentrations and Cobas 8000 using the c702 module for high concentrations. The Architect and Cobas c501/c502 systems showed the lowest variability over the whole concentration range. Highest variability was observed for Cobas 8000 using the 702 module, Thermo Scientific and Alinity c. Cobas 8000 using the c702 module showed the highest measurement uncertainty for lower concentrations. For higher concentrations, Alinity c, Thermo Scientific and Vitros were the methods with the highest measurement uncertainty. Conclusions The bias of the enzymatic techniques is nearly negligible for all methods except Alinity c. Variability differs strongly between measurement procedures. This study shows that the Alinity c has a worse measurement uncertainty than other systems for concentrations above 0.5 g/L. Overall, we found the differences in measurement uncertainty to be mainly influenced by the differences in variability