LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE228100 | GEO | 2023/11/15
REPOSITORIES: GEO
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Project description:LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients
| PRJNA948038 | ENA
Project description:The international, multicenter registry LOGGIC Core BioClinical Data Bank aims to enhance the understanding of tumor biology in pediatric low-grade glioma (pLGG) and provide clinical and molecular data to support treatment decisions and interventional trial participation. Hence, the question arises whether implementation of RNA sequencing (RNA-Seq) using Fresh Frozen (FrFr) tumor tissue in addition to gene panel and DNA methylation analysis improves diagnostic accuracy and provides additional clinical benefit. RNA-Seq was performed on 125 of the samples for which FrFr tumor tissue was available. We confirmed KIAA1549::BRAF-fusion (n=71), BRAF V600E-mutation (n=12) and alterations in FGFR1 (n=14) as the most frequent alterations, among other common molecular drivers (n=12). . N=16 cases (13%) presented rare gene fusions (e.g. TPM3::NTRK1, EWSR1::VGLL1, SH3PXD2A::HTRA1, PDGFB::LRP1, GOPC::ROS1). In n=27 cases (22%), RNA-Seq detected a driver alteration not otherwise identified (22/27 actionable). The rate of driver alteration detection was hereby increased from 75% to 97%. Furthermore, FGFR1 ITD (n=6) were only detected by RNA-Seq using current bioinformatics pipelines, leading to a change in analysis protocols.
| EGAS00001007072 | EGA
Project description:The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. Currently, there are several such 'science-wikis' that aim to collect specialist knowledge from the community into centralized resources. However, there is no consensus about how to achieve this goal. For example, it is not clear how to best integrate data from established, centralized databases with that provided by 'community annotation'. We created PDBWiki, a scientific wiki for the community annotation of protein structures. The wiki consists of one structured page for each entry in the the Protein Data Bank (PDB) and allows the user to attach categorized comments to the entries. Additionally, each page includes a user editable list of cross-references to external resources. As in a database, it is possible to produce tabular reports and 'structure galleries' based on user-defined queries or lists of entries. PDBWiki runs in parallel to the PDB, separating original database content from user annotations. PDBWiki demonstrates how collaboration features can be integrated with primary data from a biological database. It can be used as a system for better understanding how to capture community knowledge in the biological sciences. For users of the PDB, PDBWiki provides a bug-tracker, discussion forum and community annotation system. To date, user participation has been modest, but is increasing. The user editable cross-references section has proven popular, with the number of linked resources more than doubling from 17 originally to 39 today. Database URL: http://www.pdbwiki.org.
| S-EPMC2911844 | biostudies-literature
Project description:ObjectiveNon-criteria antiphospholipid antibodies (aPLs) increase the diagnostic value for antiphospholipid syndrome (APS) and contribute to better recognition of seronegative APS (SNAPS). However, the clinical utility and the diagnostic value of non-criteria aPLs are inconsistent. This study aimed to investigate the prevalence and clinical significance of 7 non-criteria aPLs in a large APS cohort.MethodsSeven non-criteria aPLs, including anti-phosphatidylserine/prothrombin (aPS/PT) antibodies IgG/IgA/IgM, anti-phosphatidylethanolamine antibodies (aPE) IgG/IgA/IgM, anti-Annexin V antibodies (aAnnexinV) IgG/IgA/IgM, anti-phosphatidylserine antibodies (aPS) IgM, aPS IgG, antibodies directed against a mixture of phospholipids (APhL) IgG, and APhL IgM were tested among 175 patients with APS, 122 patients with other autoimmune diseases (as disease controls), and 50 healthy controls.ResultsIn the present study, the highest prevalence of non-criteria aPLs was seen in aAnnexinV (58.86%). APhL IgG and aPS IgM showed the highest specificity (95.35%) and aPS/PT showed the highest Youden index (0.3991) for the diagnostic value of APS. The aAnnexinV also showed the highest prevalence in SNAPS (43.3%), followed by APhL IgM (21.7%), aPE (16.7%) and aPS/PT (16.7%). APhL IgG, aPS/PT, and aPS IgG showed positive association with thrombotic events in APS patients [APhL IgG: odds ratio (OR) = 2.26, 95% confidence interval (CI) 1.18-4.34, p = 0.013; aPS/PT: OR = 2.48, 95% CI: 1.32-4.69, p = 0.004; aPS IgG: OR = 1.90, 95% CI 1.01-3.60, p = 0.046; respectively). The inclusion of the non-criteria aPLs increased the accuracy of APS diagnosis from 65.7% to 87.4%.ConclusionOur data provide evidence that adding the non-criteria aPLs can improve the diagnostic accuracy in APS. APhL IgG, aPS/PT, and aPS IgG may be potential biomarkers to predict the risk of thrombosis in APS.
| S-EPMC9643638 | biostudies-literature
Project description:OBJECTIVES:Double reading in diagnostic radiology can find discrepancies in the original report, but a systematic program of double reading is resource consuming. There are conflicting opinions on the value of double reading. The purpose of the current study was to perform a systematic review on the value of double reading. METHODS:A systematic review was performed to find studies calculating the rate of misses and overcalls with the aim of establishing the added value of double reading by human observers. RESULTS:The literature search resulted in 1610 hits. After abstract and full-text reading, 46 articles were selected for analysis. The rate of discrepancy varied from 0.4 to 22% depending on study setting. Double reading by a sub-specialist, in general, led to high rates of changed reports. CONCLUSIONS:The systematic review found rather low discrepancy rates. The benefit of double reading must be balanced by the considerable number of working hours a systematic double-reading scheme requires. A more profitable scheme might be to use systematic double reading for selected, high-risk examination types. A second conclusion is that there seems to be a value of sub-specialisation for increased report quality. A consequent implementation of this would have far-reaching organisational effects. KEY POINTS:• In double reading, two or more radiologists read the same images. • A systematic literature review was performed. • The discrepancy rates varied from 0.4 to 22% in various studies. • Double reading by sub-specialists found high discrepancy rates.
| S-EPMC5990995 | biostudies-literature
Project description:Global value chains are formed through value-added trade, and some regions promote economic integration by concluding regional trade agreements to promote these chains. However, it has not been established to quantitatively assess the scope and extent of economic integration involving various sectors in multiple countries. In this study, we used the World Input-Output Database to create a cross-border sector-wise network of trade in value-added (international value-added network) covering the period of 2000-2014 and evaluated them using network science methods. By applying Infomap to the international value-added network, we confirmed two regional communities: Europe and the Pacific Rim. We applied Helmholtz-Hodge decomposition to the value-added flows within the region into potential and circular flows, and clarified the annual evolution of the potential and circular relationships between countries and sectors. The circular flow component of the decomposition was used to define an economic integration index. Findings confirmed that the degree of economic integration in Europe declined sharply after the economic crisis in 2009 to a level lower than that in the Pacific Rim. The European economic integration index recovered in 2011 but again fell below that of the Pacific Rim in 2013. Moreover, sectoral economic integration indices suggest what Europe depends on Russia in natural resources makes the European economic integration index unstable. On the other hand, the indices of the Pacific Rim suggest the steady economic integration index of the Pacific Rim captures the stable global value chains from natural resources to construction and manufactures of motor vehicles and high-tech products.
| S-EPMC8378758 | biostudies-literature
Project description:The costs, benefits and risks associated with diagnostic imaging investigations for epilepsy surgery necessitate the identification of an optimal pathway in the pre-surgical workup. In order to assess the added value of additional investigations a full cost-effectiveness evaluation should be conducted, taking into account all of the life-time costs and benefits associated with undertaking additional investigations. This paper considers and applies the appropriate framework against which a full evaluation should be assessed. We conducted a systematic review to evaluate the progression of the literature through this framework, finding that only isolated elements of added value have been appropriately evaluated. The results from applying the full added value framework are also presented, identifying an optimal strategy for pre-surgical evaluation for temporal lobe epilepsy surgery. Our results suggest that additional FDG-PET and invasive EEG investigations after an initially discordant MRI and video-EEG appears cost-effective, and that the value of subsequent invasive-EEGs is closely linked to the maintenance of longer-term benefits after surgery. It is integral to the evaluation of imaging technologies in the work-up for epilepsy surgery that the impact of the use of these technologies on clinical decision-making, and on further treatment decisions, is considered fully when informing cost-effectiveness.
| S-EPMC4000270 | biostudies-literature
Project description:Severe Chronic Neutropenia International Registry
| PRJNA771428 | ENA
Project description:ObjectiveOur aim is to define the capabilities of radiomics in predicting pseudoprogression from pre-treatment MR images in patients diagnosed with high-grade gliomas using T1 non-contrast-enhanced and contrast-enhanced images.Material & methodsIn this retrospective IRB-approved study, image segmentation of high-grade gliomas was semi-automatically performed using 3D Slicer. Non-contrast-enhanced T1-weighted images and contrast-enhanced T1-weighted images were used prior to surgical therapy or radio-chemotherapy. Imaging data was split into a training sample and an independent test sample at random. We extracted 107 radiomic features by use of PyRadiomics. Feature selection and model construction were performed using Generalized Boosted Regression Models (GBM).ResultsOur cohort included 124 patients (female: n = 53), diagnosed with progressive (n = 61) and pseudoprogressive disease (n = 63) of primary high-grade gliomas. Based on non-contrast-enhanced T1-weighted images of the independent test sample, the mean area under the curve (AUC), mean sensitivity, mean specificity and mean accuracy of our model were 0.651 [0.576, 0.761], 0.616 [0.417, 0.833], 0.578 [0.417, 0.750] and 0.597 [0.500, 0.708] to predict the development of pseudoprogression. In comparison, the independent test data of contrast-enhanced T1-weighted images yielded significantly higher values of AUC = 0.819 [0.760, 0.872], sensitivity = 0.817 [0.750, 0.833], specificity = 0.723 [0.583, 0.833] and accuracy = 0.770 [0.687, 0.833].ConclusionOur findings show that it is possible to predict pseudoprogression of high-grade gliomas with a Radiomics model using contrast-enhanced T1-weighted images with comparatively good discriminatory power. The use of a contrast agent results in a clear added value.
| S-EPMC9364026 | biostudies-literature
Project description:Background: Diffuse gliomas, which are at WHO grade II-IV, are progressive primary brain tumors with great variability in prognosis. Our aim was to investigate whether pre-operative cognitive functioning is of added value in survival prediction in these patients. Methods: In a retrospective cohort study of patients undergoing awake craniotomy between 2010 and 2019 we performed pre-operative neuropsychological assessments in five cognitive domains. Their added prognostic value on top of known prognostic factors was assessed in two patient groups [low- (LGG) and high-grade gliomas (HGG]). We compared Cox proportional hazards regression models with and without the cognitive domain by means of loglikelihood ratios tests (LRT), discriminative performance measures (by AUC), and risk classification [by Integrated Discrimination Index (IDI)]. Results: We included 109 LGG and 145 HGG patients with a median survival time of 1,490 and 511 days, respectively. The domain memory had a significant added prognostic value in HGG as indicated by an LRT (p-value = 0.018). The cumulative AUC for HGG with memory included was.78 (SD = 0.017) and without cognition 0.77 (SD = 0.018), IDI was 0.043 (0.000-0.102). In LGG none of the cognitive domains added prognostic value. Conclusions: Our findings indicated that memory deficits, which were revealed with the neuropsychological examination, were of additional prognostic value in HGG to other well-known predictors of survival.
| S-EPMC8639204 | biostudies-literature