scholarly journals Clinical data specification and coding for cross-analyses with omics data in autoimmune disease trials

2018 ◽  
Author(s):  
Lorenzon Roberta ◽  
Drakos Iannis ◽  
Claire Ribet ◽  
Sophie Harris ◽  
Cordoba Maeva ◽  
...  
Keyword(s):  
Clinical Data ◽  
Inflammatory Diseases ◽  
Clinical Investigation ◽  
Data Entry ◽  
Biological Data ◽  
Case Report Form ◽  
Omics Data ◽  
Electronic Data Capture System ◽  
Computer Scientists ◽  
Autoimmune And Inflammatory Diseases

ABSTRACTObjectivesAutoimmune and inflammatory diseases (AIDs) form a continuum of autoimmune and inflammatory diseases, yet AIDs’ nosology is based on syndromic classification. The TRANSIMMUNOM trial (NCT02466217) was designed to re-evaluate AIDs nosology through clinic-biological and multi-omics investigations of patients with one of 19 selected AIDs. To allow cross-analyses of clinic-biological data together with omics data, we needed to integrate clinical data in a harmonized database.Materials and MethodsWe assembled a clinical expert consortium (CEC) to select relevant clinic-biological features to be collected for all patients and a cohort management team comprising biologists, clinicians and computer scientists to design an electronic case report form (eCRF). The eCRF design and implementation has been done on OpenClinica, an open-source CFR-part 11 compliant electronic data capture system.ResultsThe CEC selected 865 clinical and biological parameters. The CMT selected coded the items using CDISC standards into 5835 coded values organized in 28 structured eCRFs. Examples of such coding are check boxes for clinical investigation, numerical values with units, disease scores as a result of an automated calculations, and coding of possible treatment formulas, doses and dosage regimens per disease.Discussion21 CRFs were designed using OpenClinica v3.14 capturing the 5835 coded values per patients. Technical adjustment have been implemented to allow data entry and extraction of this amount of data, rarely achieved in classical eCRFs designs.ConclusionsA multidisciplinary endeavour offers complete and harmonized CRFs for AID clinical investigations that are used in TRANSIMMUNOM and will benefit translational research team.

Development of an Open Metadata Schema for Prospective Clinical Research (openPCR) in China

2014 ◽  
Vol 53 (01) ◽  
pp. 39-46 ◽  
Author(s):  
Z. Guan ◽  
J. Sun ◽  
Z. Wang ◽  
Y. Geng ◽  
W. Xu
Keyword(s):  
Data Structure ◽  
Clinical Research ◽  
Clinical Data ◽  
Early Stage ◽  
Data Entry ◽  
Data Management System ◽  
Case Report Form ◽  
Functional Requirements ◽  
The Core ◽  
Metadata Schema

SummaryObjectives: In China, deployment of electronic data capture (EDC) and clinical data management system (CDMS) for clinical research (CR) is in its very early stage, and about 90% of clinical studies collected and submitted clinical data manually. This work aims to build an open metadata schema for Prospective Clinical Research (openPCR) in China based on openEHR archetypes, in order to help Chinese researchers easily create specific data entry templates for registration, study design and clinical data collection.Methods: Singapore Framework for Dublin Core Application Profiles (DCAP) is used to develop openPCR and four steps such as defining the core functional requirements and deducing the core metadata items, developing archetype models, defining metadata terms and creating archetype records, and finally developing implementation syntax are followed.Results: The core functional requirements are divided into three categories: requirements for research registration, requirements for trial design, and requirements for case report form (CRF). 74 metadata items are identified and their Chinese authority names are created. The minimum metadata set of openPCR includes 3 documents, 6 sections, 26 top level data groups, 32 lower data groups and 74 data elements. The top level container in openPCR is composed of public document, internal document and clinical document archetypes. A hierarchical structure of openPCR is established according to Data Structure of Electronic Health Record Architecture and Data Stand -ard of China (Chinese EHR Standard). Meta-data attributes are grouped into six parts: identification, definition, representation, relation, usage guides, and administration.Discussions and Conclusion: OpenPCR is an open metadata schema based on research registration standards, standards of the Clinical Data Interchange Standards Consortium (CDISC) and Chinese healthcare related stand -ards, and is to be publicly available throughout China. It considers future integration of EHR and CR by adopting data structure and data terms in Chinese EHR Standard. Archetypes in openPCR are modularity models and can be separated, recombined, and reused. The authors recommend that the method to develop openPCR can be referenced by other countries when designing metadata schema of clinical research. In the next steps, openPCR should be used in a number of CR projects to test its applicability and to continuously improve its coverage. Besides, metadata schema for research protocol can be developed to structurize and standardize protocol, and syntactical interoperability of openPCR with other related standards can be considered.

scholarly journals Complement-Related Proteins and Their Measurements: The Current Status of Clinical Investigation

Nephron ◽  
2020 ◽  
pp. 1-6
Author(s):  
Katsuki Ohtani
Keyword(s):  
Complement System ◽  
Inflammatory Diseases ◽  
Clinical Investigation ◽  
Pathological Condition ◽  
Current Status ◽  
Complement Factor ◽  
Complement Factors ◽  
Foreign Countries ◽  
Autoimmune And Inflammatory Diseases ◽  
Related Proteins

Complement has been considered to be a factor that protects the host against invading microorganisms during infection. However, in recent years, complement-related protein deficiency has been found to be involved in the onset of various diseases, such as autoimmune and inflammatory diseases. In Japan, C3, C4, and CH50 tests were generally performed only when a complement system examination was necessary and there were not enough examinations for other complement factors. Since the complement system has a very complicated activation pathway, at present, it is not well known which molecule must be measured to understand the pathological condition or pathogenesis in complement-related diseases. Furthermore, since the frequency of complement factor gene alleles also differs depending on race, data from foreign countries cannot be directly applied to Japanese populations. Under these circumstances, the Japanese Association for Complement Research (JACR) has prepared approximately 20 items for complement-related examinations, including the 5 categories of functional analysis, complement factors, complement regulators, activation products, and autoantibodies.

scholarly journals Development and design of the Hantavirus registry - HantaReg - for epidemiological studies, outbreaks and clinical studies on hantavirus disease

2021 ◽  
Author(s):  
Felix C Koehler ◽  
Linda Blomberg ◽  
Thomas Theo Brehm ◽  
Stefan Büttner ◽  
Oliver A Cornely ◽  
...  
Keyword(s):  
Data Entry ◽  
Scoring Systems ◽  
Epidemiological Studies ◽  
Incidence Rates ◽  
Case Report Form ◽  
Treatment Pathways ◽  
General Data Protection Regulation ◽  
The World ◽  
Electronic Case Report Form ◽  
Substantial Risk

Abstract Background Frequent outbreaks around the globe and endemic appearance in different parts of the world emphasize the substantial risk of hantavirus diseases. Increasing incidence rates, trends of changing distribution of hantavirus species and new insights into clinical courses of hantavirus diseases call for multinational surveillance. Furthermore, evidence-based guidelines for the management of hantavirus diseases and scoring systems, which allow stratification of patients into risk categories, are lacking. Methods Hantavirus registry (HantaReg) is a novel registry platform facilitating multinational research of hantavirus-caused diseases, such as haemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). HantaReg provides an electronic case report form and uses the General Data Protection Regulation compliant platform clinicalsurveys.net, which can be accessed from any internet browser in the world. Having a modular structure, the registry platform is designed to display or hide questions and items according to the documented case (e.g. patient with HFRS versus HCPS) to facilitate fast, but standardized, data entry. Information categories documented in HantaReg are demographics, pre-existing diseases, clinical presentation, diagnostic and therapeutic approaches, as well as outcome. Conclusions HantaReg is a novel, ready-to-use platform for clinical and epidemiological studies on hantavirus diseases and facilitates the documentation of the disease course associated with hantavirus infections. HantaReg is expected to promote international collaboration and contributes to improving patient care through the analysis of diagnostic and treatment pathways for hantavirus diseases, providing evidence for robust treatment recommendations. Moreover, HantaReg enables the development of prognosis-indicating scoring systems for patients with hantavirus disease.

scholarly journals Selective Targeting of Epigenetic Readers and Histone Deacetylases in Autoimmune and Inflammatory Diseases: Recent Advances and Future Perspectives

2021 ◽  
Vol 11 (5) ◽  
pp. 336
Author(s):  
Mohammed Ghiboub ◽  
Ahmed M. I. Elfiky ◽  
Menno P. J. de Winther ◽  
Nicola R. Harker ◽  
David F. Tough ◽  
...  
Keyword(s):  
Histone Deacetylases ◽  
Inflammatory Diseases ◽  
Selective Inhibition ◽  
In Vivo Studies ◽  
Beneficial Effects ◽  
Domain Specific ◽  
Recent Advances ◽  
Autoimmune And Inflammatory Diseases

Histone deacetylases (HDACs) and bromodomain-containing proteins (BCPs) play a key role in chromatin remodeling. Based on their ability to regulate inducible gene expression in the context of inflammation and cancer, HDACs and BCPs have been the focus of drug discovery efforts, and numerous small-molecule inhibitors have been developed. However, dose-limiting toxicities of the first generation of inhibitors, which typically target multiple HDACs or BCPs, have limited translation to the clinic. Over the last decade, an increasing effort has been dedicated to designing class-, isoform-, or domain-specific HDAC or BCP inhibitors, as well as developing strategies for cell-specific targeted drug delivery. Selective inhibition of the epigenetic modulators is helping to elucidate the functions of individual epigenetic proteins and has the potential to yield better and safer therapeutic strategies. In accordance with this idea, several in vitro and in vivo studies have reported the ability of more selective HDAC/BCP inhibitors to recapitulate the beneficial effects of pan-inhibitors with less unwanted adverse events. In this review, we summarize the most recent advances with these strategies, discussing advantages and limitations of these approaches as well as some therapeutic perspectives, focusing on autoimmune and inflammatory diseases.

scholarly journals Roles of XBP1s in Transcriptional Regulation of Target Genes

Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 791
Author(s):  
Sung-Min Park ◽  
Tae-Il Kang ◽  
Jae-Seon So
Keyword(s):  
Transcriptional Regulation ◽  
Er Stress ◽  
Target Genes ◽  
Inflammatory Diseases ◽  
Vital Role ◽  
Genes Encoding ◽  
Autoimmune And Inflammatory Diseases ◽  
Active Transcription ◽  
Transcriptional Regulatory Mechanisms ◽  
The Unfolded Protein Response

The spliced form of X-box binding protein 1 (XBP1s) is an active transcription factor that plays a vital role in the unfolded protein response (UPR). Under endoplasmic reticulum (ER) stress, unspliced Xbp1 mRNA is cleaved by the activated stress sensor IRE1α and converted to the mature form encoding spliced XBP1 (XBP1s). Translated XBP1s migrates to the nucleus and regulates the transcriptional programs of UPR target genes encoding ER molecular chaperones, folding enzymes, and ER-associated protein degradation (ERAD) components to decrease ER stress. Moreover, studies have shown that XBP1s regulates the transcription of diverse genes that are involved in lipid and glucose metabolism and immune responses. Therefore, XBP1s has been considered an important therapeutic target in studying various diseases, including cancer, diabetes, and autoimmune and inflammatory diseases. XBP1s is involved in several unique mechanisms to regulate the transcription of different target genes by interacting with other proteins to modulate their activity. Although recent studies discovered numerous target genes of XBP1s via genome-wide analyses, how XBP1s regulates their transcription remains unclear. This review discusses the roles of XBP1s in target genes transcriptional regulation. More in-depth knowledge of XBP1s target genes and transcriptional regulatory mechanisms in the future will help develop new therapeutic targets for each disease.

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