A web-based educational program to support the updated ACMG/ ClinGen technical standards for constitutional copy number variant classification

Abstract Background The American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen) presented technical standards for interpretation and reporting of constitutional copy-number variants in 2019 (the standards). Although ClinGen developed a web-based CNV classification calculator based on scoring metrics, it can only track and tally points that have been assigned based on observed evidence. Here, we developed AutoCNV (a semiautomatic automated CNV interpretation system) based on the standards, which can automatically generate predictions on 18 and 16 criteria for copy number loss and gain, respectively. Results We assessed the performance of AutoCNV using 72 CNVs evaluated by external independent reviewers and 20 illustrative case examples. Using AutoCNV, it showed that 100 % (72/72) and 95 % (19/20) of CNVs were consistent with the reviewers’ and ClinGen-verified classifications, respectively. AutoCNV only required an average of less than 5 milliseconds to obtain the result for one CNV with automated scoring. We also applied AutoCNV for the interpretation of CNVs from the ClinVar database and the dbVar database. We also developed a web-based version of AutoCNV (wAutoCNV). Conclusions AutoCNV may serve to assist users in conducting in-depth CNV interpretation, to accelerate and facilitate the interpretation process of CNVs and to improve the consistency and reliability of CNV interpretation.

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Genetics for behavioral and social scientists: Web-based educational program is launched

PsycEXTRA Dataset ◽

10.1037/e519352012-011 ◽

2012 ◽

Keyword(s):

Educational Program ◽

Social Scientists ◽

Web Based

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Faculty Opinions recommendation of Systematic assessment of copy number variant detection via genome-wide SNP genotyping.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1123296.580444 ◽

2008 ◽

Author(s):

Yasushi Okazaki

Keyword(s):

Copy Number ◽

Copy Number Variant ◽

Snp Genotyping ◽

Systematic Assessment ◽

Genome Wide ◽

Variant Detection ◽

Copy Number Variant Detection

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Effects of a Web-Based Educational Program Regarding Physical Restraint Reduction in Long-Term Care Settings on Nursing Students: A Cluster Randomized Controlled Trial

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18136698 ◽

2021 ◽

Vol 18 (13) ◽

pp. 6698

Author(s):

Eun-Hi Kong ◽

Myoungsuk Kim ◽

Seonho Kim

Keyword(s):

Nursing Students ◽

Educational Program ◽

Physical Restraint ◽

Nursing Schools ◽

Control Group ◽

Term Care ◽

Web Based ◽

Restraint Reduction ◽

Cluster Randomized ◽

The Web

Physical restraint is still frequently used in many countries. However, a lack of education hinders physical restraint reduction in long-term care facilities. No study has yet to examine the effects of physical restraint reduction education on nursing students. This study aimed to evaluate the effects of a web-based educational program of physical restraint reduction on nursing students’ knowledge and perceptions. A cluster randomized controlled and single-blind design was used. This study was conducted at four nursing schools in South Korea. A total of 169 undergraduate nursing students completed this study. Using random allocation, two nursing schools (85 students) were allocated as the experimental group and the other two schools (84 students) as the control group. The experimental group received the web-based educational program, and the control group did not receive the educational program. Data were collected immediately before and after the web-based educational program. The experimental group’s knowledge and perceptions significantly improved between pre-test and post-test. The analysis of covariance showed statistically significant differences between groups in knowledge (p < 0.001) and perceptions (p < 0.001) over time, revealing positive effects of the web-based educational program. The web-based educational program regarding physical restraint reduction positively affected nursing students’ knowledge and perceptions. Future studies are required to examine the educational program’s longitudinal effects with more rigorous measurements and research methods.

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44. Reevaluation of copy number variant (CNV) classifications in the clinical laboratory setting: challenges, insights, and experiences with a laboratory-initiated process

Cancer Genetics ◽

10.1016/j.cancergen.2021.01.055 ◽

2021 ◽

Vol 252-253 ◽

pp. S15

Author(s):

Denise I Quigley ◽

Zoe K Lewis ◽

Timothy Tidwell ◽

Adam Clayton ◽

Brandon Chandler ◽

...

Keyword(s):

Copy Number ◽

Clinical Laboratory ◽

Copy Number Variant ◽

Laboratory Setting

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Genomic heterogeneity and copy number variant burden are associated with poor recurrence‐free survival and 11q loss in human papillomavirus‐positive squamous cell carcinoma of the oropharynx

Cancer ◽

10.1002/cncr.33504 ◽

2021 ◽

Author(s):

Travis P. Schrank ◽

Nicholas Lenze ◽

Lee P. Landess ◽

Alan Hoyle ◽

Joel Parker ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Human Papillomavirus ◽

Cell Carcinoma ◽

Squamous Cell ◽

Copy Number ◽

Copy Number Variant ◽

Recurrence Free Survival ◽

Free Survival

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Exome sequencing in patients with antiepileptic drug exposure and complex phenotypes

Archives of Disease in Childhood ◽

10.1136/archdischild-2018-316547 ◽

2019 ◽

Vol 105 (4) ◽

pp. 384-389 ◽

Cited By ~ 1

Author(s):

Adam Jackson ◽

Heather Ward ◽

Rebecca Louise Bromley ◽

Charulata Deshpande ◽

Pradeep Vasudevan ◽

...

Keyword(s):

Exome Sequencing ◽

Copy Number ◽

Developmental Disorders ◽

Drug Exposure ◽

Genetic Disorders ◽

Copy Number Variants ◽

Copy Number Variant ◽

In Utero ◽

Developmental Problems ◽

Number Of Children

IntroductionFetal anticonvulsant syndrome (FACS) describes the pattern of physical and developmental problems seen in those children exposed to certain antiepileptic drugs (AEDs) in utero. The diagnosis of FACS is a clinical one and so excluding alternative diagnoses such as genetic disorders is essential.MethodsWe reviewed the pathogenicity of reported variants identified on exome sequencing in the Deciphering Developmental Disorders (DDD) Study in 42 children exposed to AEDs in utero, but where a diagnosis other than FACS was suspected. In addition, we analysed chromosome microarray data from 10 patients with FACS seen in a Regional Genetics Service.ResultsSeven children (17%) from the DDD Study had a copy number variant or pathogenic variant in a developmental disorder gene which was considered to explain or partially explain their phenotype. Across the AED exposure types, variants were found in 2/15 (13%) valproate exposed cases and 3/14 (21%) carbamazepine exposed cases. No pathogenic copy number variants were identified in our local sample (n=10).ConclusionsThis study is the first of its kind to analyse the exomes of children with developmental disorders who were exposed to AEDs in utero. Though we acknowledge that the results are subject to bias, a significant number of children were identified with alternate diagnoses which had an impact on counselling and management. We suggest that consideration is given to performing whole exome sequencing as part of the diagnostic work-up for children exposed to AEDs in utero.

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