The diagnostic efficacy of exome data analysis using fixed neurodevelopmental gene lists: implications for prenatal setting

2021 ◽  
Author(s):  
Rivka Sukenik‐Halevy ◽  
Noa Ruhrman‐Shahar ◽  
Naama Orenstein ◽  
Claudia Gonzaga‐Jauregui ◽  
Alan R. Shuldiner ◽  
...  
Keyword(s):  
Data Analysis ◽  
Diagnostic Efficacy ◽  
Exome Data

scholarly journals New Insights on Genetic Diagnostics in Cardiomyopathy and Arrhythmia Patients Gained by Stepwise Exome Data Analysis

2020 ◽  
Vol 9 (7) ◽  
pp. 2168
Author(s):  
Konstantinos Kolokotronis ◽  
Natalie Pluta ◽  
Eva Klopocki ◽  
Erdmute Kunstmann ◽  
Daniel Messroghli ◽  
...  
Keyword(s):  
Data Analysis ◽  
Exome Sequencing ◽  
Candidate Genes ◽  
Genetic Heterogeneity ◽  
Diagnostic Yield ◽  
Genetic Diagnostics ◽  
Routine Diagnostics ◽  
Exome Data ◽  
Gene Panels ◽  
Diagnostic Benefit

Inherited cardiomyopathies are characterized by clinical and genetic heterogeneity that challenge genetic diagnostics. In this study, we examined the diagnostic benefit of exome data compared to targeted gene panel analyses, and we propose new candidate genes. We performed exome sequencing in a cohort of 61 consecutive patients with a diagnosis of cardiomyopathy or primary arrhythmia, and we analyzed the data following a stepwise approach. Overall, in 64% of patients, a variant of interest (VOI) was detected. The detection rate in the main sub-cohort consisting of patients with dilated cardiomyopathy (DCM) was much higher than previously reported (25/36; 69%). The majority of VOIs were found in disease-specific panels, while a further analysis of an extended panel and exome data led to an additional diagnostic yield of 13% and 5%, respectively. Exome data analysis also detected variants in candidate genes whose functional profile suggested a probable pathogenetic role, the strongest candidate being a truncating variant in STK38. In conclusion, although the diagnostic yield of gene panels is acceptable for routine diagnostics, the genetic heterogeneity of cardiomyopathies and the presence of still-unknown causes favor exome sequencing, which enables the detection of interesting phenotype–genotype correlations, as well as the identification of novel candidate genes.

scholarly journals Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach

PLoS ONE ◽  
2012 ◽  
Vol 7 (1) ◽  
pp. e30080 ◽  
Author(s):  
Swetansu Pattnaik ◽  
Srividya Vaidyanathan ◽  
Durgad G. Pooja ◽  
Sa Deepak ◽  
Binay Panda
Keyword(s):  
Data Analysis ◽  
Combinatorial Approach ◽  
Analysis Pipeline ◽  
Exome Data ◽  
Data Analysis Pipeline

scholarly journals Arginase and Procalcitonin: Promising Biomarkers for Early Diagnosis of Sepsis

2020 ◽  
Author(s):  
Shruti Rahul Mulgund ◽  
Subodhini Anant Abhang
Keyword(s):  
Data Analysis ◽  
Early Diagnosis ◽  
Indian Population ◽  
High Sensitivity ◽  
Roc Curves ◽  
Cost Effective ◽  
Receiver Operating Curve ◽  
Enzyme Linked Immunosorbent Assay ◽  
Ray Method ◽  
Diagnostic Efficacy

Introduction: Sepsis remains a major cause of death in critically ill patients in Indian population because of high susceptibility towards infectious diseases in the world. Procalcitonin (PCT) is a well-studied marker in foreign countries but needs to be established in Indian population. In the last few years, importance of Arginase as a marker of immunity has also increased exceptionally, because this enzyme is essentially involved in different inflammatory processes. Keeping these facts in mind PCT and Arginase were evaluated for their utility as markers to diagnose sepsis. Aim: To evaluate Arginase and PCT as biomarkers for early diagnosis of sepsis. Materials and Methods: Hundred adult patients (age >18 years) with Systemic Inflammatory Response Syndrome (SIRS) attending BJ Medical College which is affiliated with Sassoon General Hospital (Pune, Maharashtra, India) during May 2012-July 2015 were incorporated in the study. Age n sex-matched of 100 samples healthy controls were also collected. Arginase was estimated by Roman and Ray method and PCT by Enzyme-linked Immunosorbent Assay Kit (ELISA) method. Unpaired t-test was done to compare the mean biomarker levels between the cases and controls. The Area Under Curve (AUC) was calculated using Receiver Operating Curve (ROC). All the data analysis was set at 95% Confidence Interval (CI) and value p<0.05 are statistically significant. Data analysis was done using Statistical Package for Social Sciences (SPSS) version 21.0. Results: In the study, a significant increase was observed in the levels of arginase (p<0.01) and PCT (p<0.01) in cases as compared to controls. ROC curves were plotted to find out the cut-offs of arginase (4.6 IU/L) and PCT (0.04 ng/mL) to check the diagnostic efficacy of both the biomarkers. Conclusion: Serum PCT and arginase offers a high level of accuracy than other currently available tests and hence can be helpful in the management of sepsis. In addition to this apart from high sensitivity and specificity arginase estimation is cost effective as compared to PCT.

scholarly journals Exploring the global landscape of genetic variation in coagulation factor XI deficiency

Blood ◽  
2017 ◽  
Vol 130 (4) ◽  
pp. e1-e6 ◽  
Author(s):  
Rosanna Asselta ◽  
Elvezia Maria Paraboschi ◽  
Valeria Rimoldi ◽  
Marzia Menegatti ◽  
Flora Peyvandi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Data Analysis ◽  
Coagulation Factor ◽  
Type Ii ◽  
Factor Xi ◽  
Exome Data ◽  
Factor Xi Deficiency ◽  
Type Iii ◽  
Key Points

Key Points Exome-data analysis revealed that FXI deficiency is from 2 to 20 times more frequent than expected in most populations. Exome-data analysis evidenced novel recurrent and ethnic-specific mutations other than the well-known type II and type III defects.

Microchemical imaging in biomedical research

1992 ◽  
Vol 50 (2) ◽  
pp. 1118-1119
Author(s):  
P. Ingram
Keyword(s):  
Data Analysis ◽  
Electron Probe ◽  
The Other ◽  
X Ray ◽  
Cell Element ◽  
Physiological Information ◽  
Functional States ◽  
Elemental Maps ◽  
Electron Energy Loss ◽  
Secondary Ion

It is well established that unique physiological information can be obtained by rapidly freezing cells in various functional states and analyzing the cell element content and distribution by electron probe x-ray microanalysis. (The other techniques of microanalysis that are amenable to imaging, such as electron energy loss spectroscopy, secondary ion mass spectroscopy, particle induced x-ray emission etc., are not addressed in this tutorial.) However, the usual processes of data acquisition are labor intensive and lengthy, requiring that x-ray counts be collected from individually selected regions of each cell in question and that data analysis be performed subsequent to data collection. A judicious combination of quantitative elemental maps and static raster probes adds not only an additional overall perception of what is occurring during a particular biological manipulation or event, but substantially increases data productivity. Recent advances in microcomputer instrumentation and software have made readily feasible the acquisition and processing of digital quantitative x-ray maps of one to several cells.

Perceptions of a Collaborative Professional Learning Program: Seeing the “Bigger Picture”

2020 ◽  
Vol 5 (1) ◽  
pp. 290-303
Author(s):  
P. Charlie Buckley ◽  
Kimberly A. Murza ◽  
Tami Cassel
Keyword(s):  
Data Analysis ◽  
Professional Learning ◽  
Social Communication ◽  
Special Educators ◽  
Service Providers ◽  
Integrative Approach ◽  
Theory Approach ◽  
Learning Program ◽  
Speech Language Pathologists ◽  
Related Service

Purpose The purpose of this study was to explore the perceptions of special education practitioners (i.e., speech-language pathologists, special educators, para-educators, and other related service providers) on their role as communication partners after participation in the Social Communication and Engagement Triad (Buckley et al., 2015 ) yearlong professional learning program. Method A qualitative approach using interviews and purposeful sampling was used. A total of 22 participants who completed participation in either Year 1 or Year 2 of the program were interviewed. Participants were speech-language pathologists, special educators, para-educators, and other related service providers. Using a grounded theory approach (Glaser & Strauss, 1967 ) to data analysis, open, axial, and selective coding procedures were followed. Results Three themes emerged from the data analysis and included engagement as the goal, role as a communication partner, and importance of collaboration. Conclusions Findings supported the notion that educators see the value of an integrative approach to service delivery, supporting students' social communication and engagement across the school day but also recognizing the challenges they face in making this a reality.

Communicative Performance of Adolescents with Severe Speech Impairment

1989 ◽  
Vol 54 (3) ◽  
pp. 403-421 ◽  
Author(s):  
Beth M. Dalton ◽  
Jan L. Bedrosian
Keyword(s):  
Data Analysis ◽  
Peer Interactions ◽  
Consistent Pattern ◽  
Clinical Implications ◽  
Speech Impairment ◽  
Communication Mode ◽  
Mode Function ◽  
Communicative Performance ◽  
Therapy Room ◽  
Communication Board

The communicative performance of 4 preoperational-level adolescents, using limited speech, gestures, and communication board techniques, was examined in a two-part investigation. In Part 1, each subject participated in an academic interaction with a teacher in a therapy room. Data were transcribed and coded for communication mode, function, and role. Two subjects were found to predominantly use the speech mode, while the remaining 2 predominantly used board and one other mode. The majority of productions consisted of responses to requests, and the initiator role was infrequently occupied. These findings were similar to those reported in previous investigations conducted in classroom settings. In Part 2, another examination of the communicative performance of these subjects was conducted in spontaneous interactions involving speaking and nonspeaking peers in a therapy room. Using the same data analysis procedures, gesture and speech modes predominated for 3 of the subjects in the nonspeaking peer interactions. The remaining subject exhibited minimal interaction. No consistent pattern of mode usage was exhibited across the speaking peer interactions. In the nonspeaking peer interactions, requests predominated. In contrast, a variety of communication functions was exhibited in the speaking peer interactions. Both the initiator and the maintainer roles were occupied in the majority of interactions. Pertinent variables and clinical implications are discussed.

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