Genome‐scale sequencing creates vast amounts of genomic data, increasing the challenge of clinical sequence variant interpretation. The demand for high‐quality interpretation requires multiple ...specialties to join forces to accelerate the interpretation of sequence variant pathogenicity. With over 600 international members including clinicians, researchers, and laboratory diagnosticians, the Clinical Genome Resource (ClinGen), funded by the National Institutes of Health, is forming expert groups to systematically evaluate variants in clinically relevant genes. Here, we describe the first ClinGen variant curation expert panels (VCEPs), development of consistent and streamlined processes for establishing new VCEPs, and creation of standard operating procedures for VCEPs to define application of the ACMG/AMP guidelines for sequence variant interpretation in specific genes or diseases. Additionally, ClinGen has created user interfaces to enhance reliability of curation and a Sequence Variant Interpretation Working Group (SVI WG) to harmonize guideline specifications and ensure consistency between groups. The expansion of VCEPs represents the primary mechanism by which curation of a substantial fraction of genomic variants can be accelerated and ultimately undertaken systematically and comprehensively. We welcome groups to utilize our resources and become involved in our effort to create a publicly accessible, centralized resource for clinically relevant genes and variants.
ClinGen is organizing Variant Curation Expert Panels (VCEPs) to develop specifications to the ACMG/AMP guidelines for genes or diseases of interest, interpret variants according to these guidelines, and publish the expert interpretations through the publicly available ClinVar database. A stepwise process was iteratively developed for ClinGen VCEPs to apply to submit variant assertions to ClinVar at the Expert Panel level of review. Other groups that wish to assemble as VCEPs are encouraged, though not required, to follow these steps.
Additional variant interpretation tools are required to effectively harness genomic sequencing for clinical applications. The American College of Medical Genetics and Genomics (ACMG) and Association ...for Molecular Pathology (AMP) published guidelines for clinical sequence variant interpretation, incorporating different types of data that lend varying levels of support towards a benign or pathogenic interpretation. Variants of uncertain significance (VUS) are those with either contradictory or insufficient evidence, and their uncertainty complicates patient counseling and management. Functional assays may provide a solution to evidence gaps relegating variants to the VUS category, but the impact of functional evidence in this framework has not been assessed. We employ an algorithmic analysis of the ACMG/AMP combining rules to assess how the availability of strong functional evidence could theoretically improve the ability to make a benign or pathogenic assertion. We follow this with analysis of actual evidence combinations met by variants through expert curations as part of the Clinical Genome Resource (ClinGen). We also examine the impact of functional evidence in a Bayesian adaptation of the ACMG/AMP framework. This lays the groundwork for an evidence‐based prioritization of assay development and variant assessment by identifying genes and variants that may benefit the most from functional data.
Functional assays have the potential to resolve evidence gaps restricting variants to the category of uncertain significance, but assay development and validation is time consuming and costly. Theoretical algorithmic analysis and an examination of ClinGen Expert Panel variant curations clarify the utility of functional evidence for missense VUS reclassification in the categorical and quantitative clinical variant interpretation frameworks. This analysis lays the groundwork for identifying genes and variants that stand to benefit the most from functional data and thus an evidence‐based method for prioritizing assay development and validation.
The genetic variation underlying many heritable forms of cardiovascular disease is incompletely understood, even in patients with strong family history or early age at onset.
We used whole exome ...sequencing to detect pathogenic variants in 55 patients with suspected monogenic forms of cardiovascular disease. Diagnostic analysis of established disease genes identified pathogenic variants in 21.8% of cases and variants of uncertain significance in 34.5% of cases. Three patients harbored heterozygous nonsense or splice-site variants in the nucleoporin genes
,
, and
, which have not been implicated previously in cardiac disease. We also identified a heterozygous splice site variant in the nuclear envelope gene
in a child with severe dilated cardiomyopathy that underwent transplant, as well as in his affected father. To confirm a cardiovascular role for these candidate genes in vivo, we used morpholinos to reduce
and
gene expression in zebrafish. Morphant embryos displayed cardiac abnormalities, including pericardial edema and heart failure. Furthermore, lymphoblasts from the patient carrying a
splice-site variant displayed changes in nuclear morphology and protein localization that are consistent with disruption of the nuclear envelope.
These data expand the repertoire of pathogenic variants associated with cardiovascular disease and validate the diagnostic and research use of whole exome sequencing. We identify
,
, and
as novel candidate genes for cardiovascular disease, and suggest that dysfunction of the nuclear envelope may be an under-recognized component of inherited cardiac disease in some cases.
The Clinical Genome Resource (ClinGen) is supported by the National Institutes of Health (NIH) to develop expertly curated and freely accessible resources defining the clinical relevance of genes and ...variants for use in precision medicine and research. To facilitate expert input, ClinGen has formed Clinical Domain Working Groups (CDWGs) to leverage the collective knowledge of clinicians, laboratory diagnosticians, and researchers. In the initial phase of ClinGen, CDWGs were launched in the cardiovascular, hereditary cancer, and inborn errors of metabolism clinical fields. These early CDWGs established the infrastructure necessary to implement standardized processes developed or adopted by ClinGen working groups for the interpretation of gene-disease associations and variant pathogenicity, and provided a sustainable model for the formation of future disease-focused curation groups. The establishment of CDWGs requires recruitment of international experts to broadly represent the interests of their field and ensure that assertions made are reliable and widely accepted. Building on the successes, challenges, and trade-offs made in establishing the original CDWGs, ClinGen has developed standard operating procedures for the development of CDWGs in new clinical domains, while maximizing efforts to scale up curation and facilitate involvement of external groups who wish to utilize ClinGen methods and infrastructure for expert curation.
PurposeIntegrating genomic sequencing in clinical care requires standardization of variant interpretation practices. The Clinical Genome Resource has established expert panels to adapt the American ...College of Medical Genetics and Genomics/Association for Molecular Pathology classification framework for specific genes and diseases. The Cardiomyopathy Expert Panel selected MYH7, a key contributor to inherited cardiomyopathies, as a pilot gene to develop a broadly applicable approach.MethodsExpert revisions were tested with 60 variants using a structured double review by pairs of clinical and diagnostic laboratory experts. Final consensus rules were established via iterative discussions.ResultsAdjustments represented disease-/gene-informed specifications (12) or strength adjustments of existing rules (5). Nine rules were deemed not applicable. Key specifications included quantitative frameworks for minor allele frequency thresholds, the use of segregation data, and a semiquantitative approach to counting multiple independent variant occurrences where fully controlled case-control studies are lacking. Initial inter-expert classification concordance was 93%. Internal data from participating diagnostic laboratories changed the classification of 20% of the variants (n = 12), highlighting the critical importance of data sharing.ConclusionThese adapted rules provide increased specificity for use in MYH7-associated disorders in combination with expert review and clinical judgment and serve as a stepping stone for genes and disorders with similar genetic and clinical characteristics.
Nanoparticles of zinc oxide and of ZnO doped with MgO in different concentrations (1, 2 and 4 mol%) were synthesized in a controlled and reproducible way, using the Pechini polymer precursor method. ...To determine the physicochemical and structural characteristics of the synthesized nanoparticles, Fourier transform IR (FTIR), X-ray diffraction (XRD), UV–Vis spectroscopy and transmission and scanning electron microscopy (TEM and SEM) were used. Characterization revealed the particles obtained to be nanometric in size (<50 nm) and with a deformed hexagonal morphology. Taking into account the doping percentage, the energy gap value varied between 3.3 eV for pure ZnO and 3.45 eV for ZnO with 4 mol% of Mg, which indicates that the optical properties of these nanoparticles were affected by dopant concentration. The effect of doping with Mg2+ on the capacity for removal of pollutant molecules by ZnO, for different working conditions, was evaluated by studying the removal of methyl orange (MO) in aqueous solution. Irradiation of the compounds led to a greater removal of MO from the solution such that all ZnO samples doped with MgO showed higher photoactivity than ZnO. The ZnO nanoparticles doped with 2% Mg were the most efficient in removing MO, achieving a removal percentage of ~73% after 2 h of testing and a totally transparent solution after 3 h of treatment. The kinetics of removal of MO promoted by this sample was best represented by pseudo-first-order kinetics. The results of this work showed that on combining a photosensitive semiconductor, ZnO, with a wide band gap insulator, MgO, Zn–Mg solid solutions are obtained that showed adequate capacity to remove contaminating organic molecules, specifically MO.
The SiO2 particles system is one of the most common ways to protect colloidal metal systems, such as gold nanoparticles, from aggregation and activity loss due to their high chemical stability and ...low reactivity. In this study, silica green gold nanoparticles (AuNPs synthesized with mullein extract) were fabricated using two different sol–gel methods. The nanoparticles were characterized by Scanning Electron Microscopy (SEM), X-ray diffraction (XRD), Fourier Transformed Infrared (FTIR), and the antibacterial activity against pathogens (Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, and Salmonella enterica). Synthesis-1 nanoparticles had a kidney-shaped form and uniform distribution, while synthesis-2 nanoparticles had a spherical and non-uniform form. Characterization showed that temperature is an important factor in the distribution of AuNPs in silica; a decrease allowed the formation of Janus-type, and an increase showed a higher concentration of gold in energy-dispersive spectroscopy (EDS) analysis. Overall, similar bands of the two synthesis silica nanoparticles were observed in FTIR, while XRD spectra showed differences in the preferential growth in AuNPs depending on the synthesis. Higher antibacterial activity was observed against S. aureus, which was followed by L. monocytogenes. No differences were observed in the antibacterial activity between the two different sol–gel methods.
Transparent conducting electrodes (TCE) are extensively applied in a great range of optoelectronic and photovoltaic equipment (e.g., solar cells, touch panels, and flexible devices). Carbon-based ...nanomaterials are considered as suitable replacements to substitute traditional materials to manufacture TCE due to their remarkable characteristics, for example, high optical transmittance and outstanding electrical properties. In comparison with traditional indium tin oxide electrodes, carbon-based electrodes show good mechanical properties, chemical stability, and low cost. Nevertheless, major issues related to the development of good quality manufacture methods to produce carbon-based nanomaterials have to be overcome to meet massive market requirements. Hence, the development of alternative TCE materials as well as appropriate large production techniques that meet the requirements of a proper sheet resistance along with a high optical transparency is a priority. Therefore, in this work, we summarize and discuss novel production and synthesis methods, chemical treatments, and hybrid materials developed to satisfy the worldwide request for carbon-based nanomaterials.
Introduction
The transcription factor Nuclear factor of activated T cells 5 (NFAT5), pivotal in immune regulation and function, can be induced by osmotic stress and tonicity-independent signals.
...Objective
We aimed to investigate and characterize two unrelated patients with Epstein-Barr virus susceptibility and no known genetic etiology.
Methods
After informed consent, we reviewed the electronic charts, extracted genomic DNA, performed whole-exome sequencing, filtered, and prioritized their variants, and confirmed through Sanger sequencing, family segregation analysis, and some functional assays, including lymphoproliferation, cytotoxicity, and characterization of natural killer cells.
Results
We describe two cases of pediatric Mexican patients with rare heterozygous missense variants in
NFAT5
and EBV susceptibility, a school-age girl with chronic-active infection of the liver and bowel, and a teenage boy who died of hemophagocytic lymphohistiocytosis.
Discussion
NFAT5 is an important regulator of the immune response. NFAT5 haploinsufficiency has been described as an immunodeficiency syndrome affecting both innate and adaptive immunity. EBV susceptibility might be another manifestation in the spectrum of this disease.
To determine the role of early acquisition of blood oxygen level-dependent (BOLD) signals and diffusion tensor imaging (DTI) for analysis of the connectivity of the ascending arousal network (AAN) in ...predicting neurological outcomes after acute traumatic brain injury (TBI), cardiopulmonary arrest (CPA), or stroke. A prospective analysis of 50 comatose patients was performed during their ICU stay. Image processing was conducted to assess structural and functional connectivity of the AAN. Outcomes were evaluated after 3 and 6 months. Nineteen patients (38%) had stroke, 18 (36%) CPA, and 13 (26%) TBI. Twenty-three patients were comatose (44%), 11 were in a minimally conscious state (20%), and 16 had unresponsive wakefulness syndrome (32%). Univariate analysis demonstrated that measurements of diffusivity, functional connectivity, and numbers of fibers in the gray matter, white matter, whole brain, midbrain reticular formation, and pontis oralis nucleus may serve as predictive biomarkers of outcome depending on the diagnosis. Multivariate analysis demonstrated a correlation of the predicted value and the real outcome for each separate diagnosis and for all the etiologies together. Findings suggest that the above imaging biomarkers may have a predictive role for the outcome of comatose patients after acute TBI, CPA, or stroke.
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