ANSWER: Annotation Software for Electronic Reporting

2022 ◽  
Author(s):  
Chelsea Raulerson ◽  
Guillaume Jimenez ◽  
Benjamin Wakeland ◽  
Erika Villa ◽  
Jeffrey Sorelle ◽  
...  
Keyword(s):  
Data Storage ◽  
Treatment Options ◽  
Web Based ◽  
Database Querying ◽  
Electronic Reporting ◽  
Quality Control Metrics ◽  
New Treatment ◽  
Using Data ◽  
Next Generation Sequencing Ngs ◽  
Range Of Values

PURPOSE To better use genetic testing, which is used by clinicians to explain the molecular mechanism of disease and to suggest clinical actionability and new treatment options, clinical next-generation sequencing (NGS) laboratories must send the results into reports in PDF and discrete data element format (HL7). Although most clinical diagnostic tests have set molecular markers tested and have a set range of values or a binary result (positive or negative), the NGS genetic test could examine hundreds or thousands of genes with no predefined list of variants. Although there are some commercial and open-source tools for clinically reporting genomics results for oncology testing, they often lack necessary features. METHODS Using several available software tools for data storage including MySQL and MongoDB, database querying with Python, and a web-based user application using JAVA and JAVA script, we have developed a tool to store and query complex genomics and demographics data, which can be manually curated and reported by the user. RESULTS We have developed a tool, Annotation SoftWare for Electronic Reporting (ANSWER), that can allow molecular pathologists to (1) filter variants to find those meeting quality control metrics in the genes that are clinically actionable by diagnosis; (2) visualize variants using data generated in the bioinformatics analysis; (3) create annotations that can be reused in future reports with association specific to the gene, variant, or diagnosis; (4) select variants and annotations that should be reported to match the details of the case; and (5) generate a report that includes demographics, reported variants, clinical actionability annotation, and references that can be exported into PDF or HL7 format, which can be electronically sent to an electronic health record. CONCLUSION ANSWER is a tool that can be installed locally and is designed to meet the clinical reporting needs of a clinical oncology NGS laboratory for reporting.

Analysis of the costs of bevacizumab plus cisplatin and gemcitabine versus cetuximab plus vinorelbine and cisplatin in patients with advanced non-small cell lung cancer (NSCLC) in France: Results from a cost modelling study

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e17560-e17560
Author(s):  
C. Chouaid ◽  
A. Vergnenègre ◽  
V. Florentin ◽  
S. Walzer
Keyword(s):  
Advanced Nsclc ◽  
Transition Probabilities ◽  
Treatment Options ◽  
Indirect Comparison ◽  
Growth Factor Receptor ◽  
Progression Free Survival ◽  
Cost Modelling ◽  
Humanized Monoclonal Antibody ◽  
New Treatment ◽  
Using Data

e17560 Background: New treatment options for advanced NSCLC can offer improved survival over standard chemotherapy (CT). Bevacizumab (BEV), a humanized monoclonal antibody (MAb) directed against VEGF when combined with CT increases overall survival (median 13.6 months in the AVAiL study) and progression-free survival (PFS) in patients with advanced NSCLC compared with CT alone. Cetuximab (CTX), an IgG1 MAb which targets the epidermal growth factor receptor, achieved a median survival of 11.3 months when combined with CT in the FLEX study; marketing authorization is anticipated during 2009. The aim of this study was to compare the costs of treating patients with BEV plus cisplatin and gemcitabine (BCG) versus CTX plus vinorelbine and cisplatin (CVC) in France. Methods: A Markov model was used to compare drug and administration costs associated with treating advanced NSCLC with either BCG or CVC. The model assumes patients move from non-progressive to progressed disease to death, according to transition probabilities derived from an indirect comparison of the efficacy of BCG and CVC in terms of PFS using data from the respective pivotal trials and appropriate indirect comparison methodology. Cost data were derived from local sources. Drug costs assumed CT was given for up to 6 cycles, that CTX was administered at an initial dose of 400 mg/m2 followed by 250 mg/m2 weekly until progression and that BEV was administered at 7.5 mg/kg every 3 weeks until progression. The model estimated average drug and administration costs per patient treated with either BCG or CVC. Results: The mean cost for BCG and CVC was €23849 and €35678 respectively, resulting in a saving of €11829 per patient for BCG. The acquisition of BEV was less costly than the acquisition of CTX (€15374 vs €23530) and, BCG acquisition and administration costs were lower than CTX's respectively, €19756 versus €24750 and €4093 versus €10928. Conclusions: Targeted therapy using BEV is less costly than CTX in France, and therefore, from a budget perspective offers the best value for money approach to improving outcomes in patients with advanced NSCLC. [Table: see text]

A cost analysis of treatment with bevacizumab plus cisplatin and gemcitabine (BCG) versus cetuximab plus vinorelbine and cisplatin (CVC) in patients with advanced or recurrent non-small cell lung cancer (NSCLC) in Germany

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e17553-e17553
Author(s):  
D. F. Heigener ◽  
C. Wiesner ◽  
R. Aultman
Keyword(s):  
Growth Factor ◽  
Advanced Nsclc ◽  
Transition Probabilities ◽  
Treatment Options ◽  
Indirect Comparison ◽  
Growth Factor Receptor ◽  
Progression Free Survival ◽  
Value For Money ◽  
New Treatment ◽  
Using Data

e17553 Background: Although new treatment options for advanced NSCLC can offer improved survival over standard treatment with chemotherapy (CT) they should also offer value for money. Bevacizumab (BEV), a humanized monoclonal antibody (MAb) directed against vascular endothelial growth factor when combined with CT increases overall survival (median 13.6 months in the AVAiL study) and progression-free survival (PFS) in patients with advanced NSCLC when compared with CT alone. Cetuximab (CTX), an IgG1 MAb which targets the epidermal growth factor receptor achieved a median survival time of 11.3 months when combined with CT in the FLEX study and marketing authorization is anticipated in 2009. The aim of this study was to compare the costs of treating NSCLC with BCG or CVC in Germany. Methods: A Markov model was used to compare drug and administration costs associated with treating advanced or recurrent NSCLC with either BCG or CVC. The model assumes patients move from non-progressive to progressed disease prior to death, according to transition probabilities derived from an indirect comparison of the efficacy of BCG and CVC in terms of PFS using data from the respective pivotal trials and appropriate indirect comparison methodology. Cost data were derived from local sources. Drug costs assumed CT was given for up to 6 cycles, that CTX was administered at an initial dose of 400 mg/m2 followed by 250 mg/m2 weekly until progression and that BEV was administered at 7.5 mg/kg until progression. The model estimated average drug and administration costs per patient treated with either BCG or CVC. Results: The mean total cost of BCG treatment was €4713 less per patient when compared with CVC (€28342 vs. €33055). The addition of BEV to CT was less costly than the addition of CTX to CT (€18796 vs. €29502) and the administration costs were also lower (€391 vs. €1179). Conclusions: Targeted therapy using BEV is less costly than CTX in Germany and thus, from a budget perspective, offers the best value for money strategy for improving outcomes in patients with advanced NSCLC. Furthermore, costs savings with BCG in Germany are likely to be increased when gemcitabine comes off-patent in 2009. [Table: see text]

scholarly journals Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases

2021 ◽  
Author(s):  
Thomas Linden ◽  
Frank Hanses ◽  
Daniel Domingo-Fernandez ◽  
Lauren Nicole DeLong ◽  
Alpha Tom Kodamullil ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Targets ◽  
Active Sites ◽  
Molecular Mechanisms ◽  
Treatment Options ◽  
Tyrosine Kinase 2 ◽  
Machine Learning Model ◽  
Anti Cancer ◽  
New Treatment ◽  
Using Data

Despite available vaccinations COVID-19 case numbers around the world are still growing, and effective medications against severe cases are lacking. In this work, we developed a machine learning model which predicts mortality for COVID-19 patients using data from the multi-center Lean European Open Survey on SARS-CoV-2-infected patients (LEOSS) observational study (>100 active sites in Europe, primarily in Germany), resulting into an AUC of almost 80%. We showed that molecular mechanisms related to dementia, one of the relevant predictors in our model, intersect with those associated to COVID-19. Most notably, among these molecules was tyrosine kinase 2 (TYK2), a protein that has been patented as drug target in Alzheimers Disease but also genetically associated with severe COVID-19 outcomes. We experimentally verified that anti-cancer drugs Sorafenib and Regorafenib showed a clear anti-cytopathic effect in Caco2 and VERO-E6 cells and can thus be regarded as potential treatments against COVID-19. Altogether, our work demonstrates that interpretation of machine learning based risk models can point towards drug targets and new treatment options, which are strongly needed for COVID-19.

Management of thoracic aortic lesions - the future is endovascular

VASA ◽  
2012 ◽  
Vol 41 (3) ◽  
pp. 163-176 ◽  
Author(s):  
Weidenhagen ◽  
Bombien ◽  
Meimarakis ◽  
Geisler ◽  
A. Koeppel
Keyword(s):  
Thoracic Aorta ◽  
Clinical Decision Making ◽  
Treatment Options ◽  
Clinical Decision ◽  
Clinical Results ◽  
Treatment Modalities ◽  
Traumatic Rupture ◽  
Descending Thoracic Aorta ◽  
New Treatment ◽  
Aneurysm Dissection

Open surgical repair of lesions of the descending thoracic aorta, such as aneurysm, dissection and traumatic rupture, has been the “state-of-the-art” treatment for many decades. However, in specialized cardiovascular centers, thoracic endovascular aortic repair and hybrid aortic procedures have been implemented as novel treatment options. The current clinical results show that these procedures can be performed with low morbidity and mortality rates. However, due to a lack of randomized trials, the level of reliability of these new treatment modalities remains a matter of discussion. Clinical decision-making is generally based on the experience of the vascular center as well as on individual factors, such as life expectancy, comorbidity, aneurysm aetiology, aortic diameter and morphology. This article will review and discuss recent publications of open surgical, hybrid thoracic aortic (in case of aortic arch involvement) and endovascular repair in complex pathologies of the descending thoracic aorta.

A Genomic Approach to Characterize the Vulnerable Patient – a Clinical Update

2019 ◽  
Vol 4 (3) ◽  
pp. 141-144
Author(s):  
Evelin Szabó ◽  
Zsolt Parajkó ◽  
Diana Opincariu ◽  
Monica Chițu ◽  
Nóra Raț ◽  
...  
Keyword(s):  
Risk Factors ◽  
Myocardial Ischemia ◽  
Treatment Options ◽  
Ischemic Heart ◽  
Pathophysiological Mechanism ◽  
Ischemia And Reperfusion Injury ◽  
Myocardial Ischemia And Reperfusion ◽  
Vulnerable Patient ◽  
Traditional Risk Factors ◽  
New Treatment

Abstract Atherosclerosis is the elemental precondition for any cardiovascular disease and the predominant cause of ischemic heart disease that often leads to myocardial infarction. Systemic risk factors play an important role in the starting and progression of atherosclerosis. The complexity of the disease is caused by its multifactorial origin. Besides the traditional risk factors, genetic predisposition is also a strong risk factor. Many studies have intensively researched cardioprotective drugs, which can relieve myocardial ischemia and reperfusion injury, thereby reducing infarct size. A better understanding of abnormal epigenetic pathways in the myocardial pathology may result in new treatment options. Individualized therapy based on genome sequencing is important for an effective future medical treatment. Studies based on multiomics help to better understand the pathophysiological mechanism of several diseases at a molecular level. Epigenomic, transcriptomic, proteomic, and metabolomic research may be essential in detecting the pathological phenotype of myocardial ischemia and ischemic heart failure.

Contested Knowledge and Information Behaviour: Treatments for Depression

2013 ◽  
Author(s):  
Tami Oliphant
Keyword(s):  
Alternative Medicine ◽  
Complementary And Alternative Medicine ◽  
Treatment Options ◽  
Award Winner ◽  
Information Behaviour ◽  
Contested Knowledge ◽  
Using Data ◽  
Depth Interviews ◽  
Complementary And Alternative

A wide variety of treatment options for depressives have been developed by both the conventional and complementary and alternative medicine (CAM) sectors. Using data collected from three online newsgroups as well as in-depth interviews, I analyze how people use information when making or justifying claims, or making decisions, about treatments for depression.Les personnes souffrant de dépression ont une grande variété d'options de traitement à leur disposition, y compris les méthodes conventionnelles et les méthodes complémentaires ou alternatives. À l'aide de données recueillies à partir de trois forums en ligne et d'entrevues en profondeur, j'ai analysé comment les gens utilisent cette information pour déclarer, justifier leurs déclarations ou encore choisir les traitements contre la dépression. ***Student to CAIS/ACSI Award Winner***

Proteomic Analysis of the Vitreous Body in Proliferative and Non-Proliferative Diabetic Retinopathy

2020 ◽  
Vol 17 ◽  
Author(s):  
Van-An Duong ◽  
Jeeyun Ahn ◽  
Na-Young Han ◽  
Jong-Moon Park ◽  
Jeong-Hun Mok ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Proliferative Diabetic Retinopathy ◽  
Microvascular Complications ◽  
Treatment Options ◽  
Vitreous Body ◽  
Control Group ◽  
Diabetic Patients ◽  
Protein Protein Interaction ◽  
Alpha Beta ◽  
New Treatment

Background: Diabetic Retinopathy (DR), one of the major microvascular complications commonly occurring in diabetic patients, can be classified into Proliferative Diabetic Retinopathy (PDR) and Non-Proliferative Diabetic Retinopathy (NPDR). Currently available therapies are only targeted for later stages of the disease in which some pathologic changes may be irreversible. Thus, there is a need to develop new treatment options for earlier stages of DR through revealing pathological mechanisms of PDR and NPDR. Objective: The purpose of this study was to characterize proteomes of diabetic through quantitative analysis of PDR and NPDR. Methods: Vitreous body was collected from three groups: control (non-diabetes mellitus), NPDR, and PDR. Vitreous proteins were digested to peptide mixtures and analyzed using LC-MS/MS. MaxQuant was used to search against the database and statistical analyses were performed using Perseus. Gene ontology analysis, related-disease identification, and protein-protein interaction were performed using the differential expressed proteins. Results: Twenty proteins were identified as critical in PDR and NPDR. The NPDR group showed different expressions of kininogen-1, serotransferrin, ribonuclease pancreatic, osteopontin, keratin type II cytoskeletal 2 epidermal, and transthyretin. Also, prothrombin, signal transducer and activator of transcription 4, hemoglobin subunit alpha, beta, and delta were particularly up-regulated proteins for PDR group. The up-regulated proteins related to complement and coagulation cascades. Statherin was down-regulated in PDR and NPDR compared with the control group. Transthyretin was the unique protein that increased its abundance in NPDR compared with the PDR and control group. Conclusion: This study confirmed the different expressions of some proteins in PDR and NPDR. Additionally, we revealed uniquely expressed proteins of PDR and NPDR, which would be differential biomarkers: prothrombin, alpha-2-HS-glycoprotein, hemoglobin subunit alpha, beta, and transthyretin.

Immunotherapy and potential predictive biomarkers in the treatment of neuroendocrine neoplasia

2020 ◽  
Author(s):  
Guanghui Xu ◽  
Yuhao Wang ◽  
Hushan Zhang ◽  
Xueke She ◽  
Jianjun Yang
Keyword(s):  
Current Knowledge ◽  
Checkpoint Inhibitors ◽  
Treatment Options ◽  
Predictive Biomarkers ◽  
The Body ◽  
Low Grade ◽  
Ablative Therapies ◽  
Cancer Types ◽  
New Treatment ◽  
Well Differentiated

Neuroendocrine neoplasias (NENs) are a heterogeneous group of rare tumors scattered throughout the body. Surgery, locoregional or ablative therapies as well as maintenance treatments are applied in well-differentiated, low-grade NENs, whereas cytotoxic chemotherapy is usually applied in high-grade neuroendocrine carcinomas. However, treatment options for patients with advanced or metastatic NENs are limited. Immunotherapy has provided new treatment approaches for many cancer types, including neuroendocrine tumors, but predictive biomarkers of immune checkpoint inhibitors (ICIs) in the treatment of NENs have not been fully reported. By reviewing the literature and international congress abstracts, we summarize the current knowledge of ICIs, potential predicative biomarkers in the treatment of NENs, implications and efficacy of ICIs as well as biomarkers for NENs of gastroenteropancreatic system, lung NENs and Merkel cell carcinoma in clinical practice.

scholarly journals Inhibition of Proinflammatory Cytokines in Cutibacterium acnes-Induced Inflammation in HaCaT Cells by Using Buddleja davidii Aqueous Extract

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Anh Thu Nguyen ◽  
Ki-young Kim
Keyword(s):  
Proinflammatory Cytokines ◽  
Proinflammatory Cytokine ◽  
Treatment Options ◽  
Mapk Signaling ◽  
Cytokine Expression ◽  
Proinflammatory Cytokine Expression ◽  
Cutibacterium Acnes ◽  
Anti Inflammatory ◽  
New Treatment ◽  
Hacat Keratinocyte

Acne is an inflammatory skin disorder; although some anti-inflammatory medicines for treating acne are available in a market, they have considerable side effects; therefore, new treatment options are needed. In the present study, among the 16 aqueous extracts of plants collected from Jeju Island in Korea which are used to test anti-inflammatory activity, B. davidii showed the strong decline of the proinflammatory cytokine expression against the inflammatory process caused by C. acnes in Human HaCaT keratinocyte cells. B. davidii downregulated the expression of 57% of COX-2, 41% of iNOS, and proinflammatory cytokines 29% of TNF-α, 32% of IL-1β, 21% of IL-6, and 35% of IL-8. Furthermore, B. davidii inhibited NF-κB and MAPK signaling cascades in keratinocytes that activated by toll-like receptor 2 (TLR-2) in response to C. acnes. Given those results, B. davidii is a potential agent to reduce the proinflammatory cytokine expression against C. acnes-induced inflammation and might provide an alternative to the current medications.

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