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2,880 results for “Variant.”
Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international standardisation
<p>This repository contains the simulated genomes and FASTQ files used for the analyses reported in the publication: <strong>Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international standardisation</strong>.</p> <p>This dataset is based on previously published data: <a href="https://doi.org/10.1099/mgen.0.000388">https://doi.org/10.1099/mgen.0.000388</a></p> <p>Processing scripts can be found in: <a href="https://github.com/Viloleal/bTB-pipeline-comparison-data-and-tools">https://github.com/Viloleal/bTB-pipeline-comparison-data-and-tools</a></p>
Data files for manuscript "Prenatal phenotype of PNKP-related primary microcephaly associated with variants in the FHA and Phosphatase domain"
<p>#2021-08-26<br> #Summary<br> This ZIP-file contains the Excel files used for the clinical and variant analyses of the PNKP protein/gene for the manuscript "Prenatal phenotype of PNKP-related primary microcephaly associated with variants in the FHA and Phosphatase domain".</p> <p>#Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Clinical/ (contains an Excel sheet with complete clinical data of 4 affected individuals)<br> ./Variants/ (contains an Excel sheet with all variant annotation and domain information used in 6 sheets)</p> <p>#Files and checksums<br> 4B5BE914E77EB6511DF3DB94C6918E45 ./Clinical/FileS2_PNKP_Clinical.xlsx<br> 0228C6EF543D597C1C800B8D78E3097D ./Variants/FileS3_PNKP_Variants.xlsx</p>
dataset related to article "Multiple Genetic Rare Variants in Autism Spectrum Disorders: A Single-Center Targeted NGS Study"
<p>dataset contains: NGS data (.vcf; .bam; .bam.bai) of all 40 ASD patients analysed in the study at title</p>
Example variant files and corresponding annotations for GnomAD v3.1.1 on a subset of chromosome 22
<p>Example variant files and corresponding hg38 annotations for `chr22:15518158-20127355`.</p> <p>Sources:</p> <ul> <li><a href="http://dx.doi.org/10.1093/nar/gky955">Gencode v34 (hg38)</a></li> <li><a href="https://doi.org/10.1038/s41586-020-2308-7">GnomAD v3.1.1</a></li> </ul>
Pathogenic and low frequency variants in children with central precocious puberty
<p><b>Background </b>Central precocious puberty (CPP) due<span> to premature activation of GnRH secretion results in early epiphyseal fusion and to a significant compromise in the achieved final adult height. CPP is usually idiopathic and is disproportionally observed in girls compared to boys. Currently, only few </span>genetic determinants of children with CPP have been described and the role they exert on the development of the disorder. In this original study rare variants in <i>MKRN3</i>, <i>DLK1</i>, <i>KISS1</i>, <i>KISS1R</i> and <i>MAGEL2</i> genes are reported in patients with CPP.</p> <p><b>Methods </b>Fifty-four index females and 2 index males with CPP underwent whole exome sequencing (WES) by Next Generation Sequencing (NGS). The identified rare variants were initially examined by <i>in silico</i> computational algorithms and confirmed by Sanger sequencing. Additionally, a genetic network for the <i>MKRN3</i> gene mimicking a holistic regulatory depiction of the crosstalk between <i>MKRN3</i> and other genes is designed.</p> <p><b>Results </b>Three previously described pathogenic <i>MKRN3</i> variants in the coding region of the gene occurred in 12 index females with CPP. With the p.Gly312Asp pathogenic variant of the <i>MKRN3 </i>gene being the most prevalent and exclusively found among the Cypriot CPP cohort, it is projected to be the result of founder effect phenomenon. In seven additional CPP patients from the same cohort several other likely and rare pathogenic upstream variants in the <i>MKRN3</i> gene were also observed. In addition to the <i>MKRN3</i> variants, a total of 16 other rare variants in <i>DLK1</i>, <i>KISS1</i> and <i>MAGEL2 </i>were also identified in other CPP patients from the same cohort. Interestingly, the frequent variant rs10407968 (p.Gly8Ter) of the <i>KISS1R</i> gene appeared to be less frequent in the cohort of patients with CPP.</p> <p><b>Conclusion</b> The results of the present study denote the key role of the imprinted <i>MKRN3</i> gene in puberty. Additionally, pathogenic variants can also exist in the noncoding region of the MKRN3 gene such as the proximal promoter and 5'-UTR region and which can also be considered as contributing factors to CPP. Overall, the results of present study have emphasised the necessity of the allied genetic and clinical approach which is necessary for the management and treatment of CPP.</p>
Mevalonate kinase variants
<p>This dataset describes the effects of several mutations to human mevalonate kinase. The dataset is designed to be used with the Aquaria molecular graphics system (e.g., <a href="https://aquaria.app/Mouse/MVK?zenodo.3632187.V377I">https://aquaria.app/Mouse/MVK?zenodo.3632187.V377I</a> or <a href="https://aquaria.app/Mouse/MVK?zenodo.3632187.Δ91">https://aquaria.app/Mouse/MVK?zenodo.3632187.Δ91</a>).</p>
Supplementary material for: RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding
<p>Supplementary Material for the Article</p> <p>Santana-Garcia, W., Rocha-Acevedo, M., Ramirez-Navarro, L., Mbouamboua, Y., Thieffry, D., Thomas-Chollier, M., Contreras-Moreira, B., van Helden, J., Medina-Rivera, A., 2019. RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding. Comput. Struct. Biotechnol. J. 17, 1415–1428.</p> <p> </p>
RD-Connect GPAP synthetic data spiked-in variant data
<p>This data is a subset of Rare Disease Synthetic Dataset (<a href="https://ega-archive.org/datasets/EGAD00001008392">EGAD00001008392</a>) dataset. The subset only contains the chromosomal regions with the spiked-in causative variants. The associated study is the Human genomic and phenotypic synthetic data for the study of rare diseases (<a href="https://ega-archive.org/studies/EGAS00001005702">EGAS00001005702</a>) study. For more info go to <a href="https://ega-archive.org/">https://ega-archive.org/</a>.</p> <p>All this data was created with the support of the RD-Connect GPAP (<a href="https://platform.rd-connect.eu/">https://platform.rd-connect.eu/</a>), EC H2020 project EJP-RD (grant # 825575), EC H2020 project B1MG (grant # 951724) and Generalitat de Catalunya VEIS project (grant # 001-P-001647).</p>
Progeny Project DFT and TD-DFT data for MW1 and its variants with different side chain length
<p>DFT and TD-DFT data, i.e. geometries, electronic excited states for the MW1 and its variants in vacuum with different length of side chains.</p> <p>See Readme.txt for more details.</p>
COJO ARG variants from "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits"
<p>These are COJO ARG variants accompanying the manuscript "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits". For more details, view the README.md file and refer to our manuscript.</p>
A laboratory study of the photometric properties of Mars Global Soil Simulant MGS-1 and its variants
<p>Figures 2 and 5-16 of "A laboratory study of the photometric properties of Mars Global Soil Simulant MGS-1 and its variants" submitted to Planetary & Space Science.</p>
Structural variants of calreticulin mutants associated with essential thrombocythemia
<p>Video S1. CALRwt molecular simulation with Ca2+ ions binding to the structure. This movie shows the dynamics of Ca2+ ions over the 40 ns and how they rapidly bind to the CALRwt structure. Most of the ions bind to the C-terminal part of CALRwt, where the majority of the negative residues are located. The binding of Ca2+ ions creates an interaction between residues that can induce specific folding. In this example, residues E407 and E416 interact with a calcium ion and fold, as shown at the end of the movie.</p> <p>Video S2. CALRwt molecular simulation with calcium ions binding to the structure. This movie shows the dynamics of CALRwt and Ca2+ ions over 400 ns and how ions are rapidly bound to the CALRwt structure. Most of the ions bind to the C-terminal region of CALRwt, where the majority of the negative residues are located. The binding of calcium ions creates an interaction between residues that can induce specific folding (a specific example of fold is shown on Video S1). On this full movie, we are able to see the unfolding of the N-terminal region of the helix and the stabilization of the C- terminal region thanks to calcium binding.</p> <p>Video S3. CALRwt molecular simulation with Na+ ions. This movie shows the dynamics of CALRwt with Na+ ions. The absence of binding from calcium ions leaves the structure free of any external constraint, especially for the C-terminal region. The latter appears to be flexible but this region is in fact quite stable at the local level and has its own dynamics, unstructured slightly the C-terminal of the helix.</p> <p>Video S4. CALRm class A molecular simulation. This movie shows the dynamics of CALRm class A over 400ns. The C-terminal region of the structure is quite flexible at first and interacts with the N-terminal region after several ns. This interaction locally constrains the structure around residues 400-404, stabilizing an unstructured structure for this region.</p> <p>Video S5. CALRm class B molecular simulation. This movie shows the dynamics of CALRm class B over 400ns. The first and last helices move away from their initial position with great flexibility of the coiled regions between the helices. The first helix interacts closely with the second helix and forms a specific T-shaped fold which stabilize the whole structure.</p> <p>Video S6. CALRm class C molecular simulation. This movie shows the dynamics of CALRm class C over 400ns. Extremities are highly flexible but the helix remains stable. This high flexibility allow the C- terminal region to have some interaction with the helix at some frames</p> <p>Video S7. CALRm class D molecular simulation. This movie shows the dynamics of CALRm class D over 400ns. The C-terminal region appears to be flexible, but the helix remains stable the whole simulation.</p> <p>Video S8. CALRm class E molecular simulation. This movie shows the dynamics of CALRm class E over 400ns. This movie shows the dynamics of CALRm class E and calcium ions over 400 ns and how ions are rapidly bound to the CALRwt structure. Most of the ions bind to the C-terminal region of CALRm class E, where the majority of the negative residues are located. The N-terminal region of the helix is being unstructured and the C-terminal region is stabilized with calcium ions. This simulation of CALRm class E is very similar to the simulation of CALRwt.</p> <p>Video S9. Dimeric form of CALRm class A molecular simulation. This movie shows the dynamics of two CALRm class A monomers forming a dimer through disulphide bonds. Both chains seem to repulse each other due to electrostatic charges, but disulphide bonds maintain the dimeric form, otherwise both chains would have been separated.</p> <p>Video S10. Dimeric form of CALRm class A with broken disulphide bonds molecular simulation. This movie shows the dynamics of two CALRm class A monomers and their attempt to form a dimer with broken disulfide bonds. As each monomer repels each other, the dimeric form cannot be stable without any disulfide bonds. This is demonstrated by the separation of each chain from each other.</p> <p>Video S11. Dimeric form of CALRm class B molecular simulation. This movie shows the dynamics of two CALRm class B monomers forming a dimer through disulphide bonds. Both chains are interacting together to form a specific shape, similar to the simulation of the monomer of class B. This interaction implies that even without any disulphide bonds, the dimeric form of class B could be stable, contrary to class A.</p> <p>Video S12. Dimeric form of CALRm class B molecular simulation. It is an interesting replicate of the same system than Video S11. Helices are also well maintained.</p> <p>Video S13. Dimeric form of CALRm class C molecular simulation. This movie shows the dynamics of two CALRm class C monomers forming a dimer through disulphide bonds. Both chains seem to repulse each other due to electrostatic charges, but disulphide bonds maintain the dimeric form, otherwise both chains would have been separated.</p> <p>Video S14. Dimeric form of CALRm class E molecular simulation. This movie shows the dynamics of two CALRm class E monomers and their attempt to form a dimer without any disulphide bonds. Chains repel and are moving away from each other after several ns, indicating the inability for class E to form a dimer.</p> <p>Video S15. Dimeric form of CALRwt molecular simulation. This movie shows the dynamics of two CALRwt monomers and their attempt to form a dimer. Some interactions occur between the N- terminus of each chain, but this is not sufficient and the chains move away from each other. Subsequently, the dynamics of each chain resembles the dynamics of the CALRwt monomer simulated with sodium ions (Video S2). CALRwt is not able to be stable as dimer.</p> <p>Video S16. Dimeric form of CALRm class D molecular simulation. This movie shows the dynamics of two CALRm class D monomers and their attempt to form a dimer without any disulphide bonds. Both chains are separated very quickly which indicate that they can not be stable as dimer.</p>
Rice genetic variants with dbSNP and pseudoDB
<p>Rice genetic variants with dbSNP and pseudoDB</p>
Chickpea genetic variants with dbSNP and pseudoDB
<p>Chickpea genetic variants with dbSNP and pseudoDB</p>
Defining Categorical Reasoning of Numerical Feature Models with Feature-Wise and Variant-Wise Quality Attributes
<p><strong>To watch it in Youtube:</strong></p> <p><a href="https://youtu.be/Uq2qtb4_K2U">https://youtu.be/Uq2qtb4_K2U</a></p> <p><strong>This is a pre-print, please access and cite the published version:</strong></p> <p><a href="https://doi.org/10.1145/3503229.3547057">https://doi.org/10.1145/3503229.3547057</a></p> <p>Automatic analysis of variability is an important stage of <em>Software Product Line</em> (SPL) engineering. Incorporating quality information into this stage poses a significant challenge. However, quality-aware automated analysis tools are rare, mainly because in existing solutions variability and quality information are not unified under the same model.</p> <p>In this paper, we make use of the <em>Quality Variability Model</em> (QVM), based on <em>Category Theory</em> (CT), to redefine reasoning operations. We start defining and composing the six most common operations in SPL, but now as quality-based queries, which tend to be unavailable in other approaches. Consequently, QVM supports interactions between variant-wise and feature-wise quality attributes. As a proof of concept, we present, implement and execute the operations as lambda reasoning for CQL IDE -- the state-of-the-art CT tool.</p>
Adsorption of the WT, delta and omicron variants onto hydrophobic and hydrophilic surfaces
<p>Adsorption of the WT, delta and omicron variants onto hydrophobic and hydrophilic surfaces. This contains 3 replicas of each.</p>
dataset relate to article: "Functional Characterization of Two Variants at the Intron 6-Exon 7 Boundary of the KCNQ2 Potassium Channel Gene Causing Distinct Epileptic Phenotypes"
<p><strong>Sequencing Analysis performed at Fondazione Besta and carried out as part of the study mentioned at title</strong></p>
Patient-specific induced pluripotent stem cell properties implicate Ca2+-homeostasis in clinical arrhythmia associated with combined heterozygous RYR2 and SCN10A variants
<p class="MsoNormal"><span>We illustrate the use of induced pluripotent stem cells (iPSCs) as platforms for investigating cardiomyocyte phenotypes in a human family pedigree exemplified by novel heterozygous RYR2-A1855D and SCN10A-Q1362H variants occurring alone and in combination. The proband, a four-month-old boy, presented with </span><span>polymorphic</span><span> ventricular tachycardia (</span><span>P</span><span>VT). Genetic tests revealed double novel heterozygous RYR2-A1855D and SCN10A-Q1362H variants inherited from his father (F) and mother (M) respectively. His father showed ventricular premature beats (VPB); his mother was asymptomatic. Molecular biological characterisations demonstrated greater <em>TNNT2</em> mRNA expression in the iPSCs-induced cardiomyocytes (iPS-CMs) than in the iPSCs</span><span>.</span><span> </span><span>c</span><span>TNTs became progressively organised, but cytoplasmic RYR2 and SCN10A aggregations occurred in the iPS-CMs. Proband-specific iPS-CMs showed decreased <em>RYR2</em> and <em>SCN10A</em> mRNA expression. The RYR2-A1855D variant resulted in premature spontaneous sarcoplasmic reticular (SR) Ca<sup>2+</sup> transients (PCTs), Ca<sup>2+</sup> oscillations (COs), and increased action potential durations (APDs). SCN10A-Q1362H did not confer any specific phenotype. However, the </span><span>combined </span><span>heterozygous RYR2-A1855D and SCN10A-Q1362H variants in the proband iPS-CMs resulted in accentuated Ca<sup>2+</sup> homeostasis disorders, AP prolongation and susceptibility to early afterdepolarisations (EADs) at high stimulus frequencies. These findings attribute the clinical phenotype in the proband to effects of the heterozygous <em>RYR2</em> variant exacerbated by heterozygous <em>SCN10A</em> modification. </span></p>
spindle cell variant diffuse large B-cell lymphoma (NGS annotation file; high confidence calls) hematolrep-2136295
<p>Diffuse large B-cell lymphoma with spindle cell morphology is a rare variant. We present the case of a 74-year-old male who initially presented with a right supraclavicular (lymph) node enlargement. Histological analysis showed a proliferation of spindle-shaped cells with narrow cytoplasms. An immunohistochemical panel was used to exclude other tumors, such as melanoma, carcinoma, and sarcoma. The lymphoma was characterized by a cell-of-origin subtype of germinal center B-cell-like (GCB) based on Hans’ classifier (CD10-negative, BCL6-positive, and MUM1-negative); EBER negativity, and the absence of BCL2, BCL6, and MYC rearrangements. Mutational profiling using a custom panel of 168 genes associated with aggressive B-cell lymphomas confirmed mutations in ACTB, ARID1B, DUSP2, DTX1, HLA-B, PTEN, and TNFRSF14. Based on the LymphGen 1.0 classification tool, this case had an ST2 subtype prediction. The immune microenvironment was characterized by moderate infiltration of M2-like tumor-associated macrophages (TMAs) with positivity of CD163, CSF1R, CD85A (LILRB3), and PD-L1; moderate PD-1 positive T cells, and low FOXP3 regulatory T lymphocytes (Tregs). Immunohistochemical expression of PTX3 and TNFRSF14 was absent. Interestingly, the lymphoma cells were positive for HLA-DP-DR, IL-10, and RGS1, which are markers associated with poor prognosis in DLBCL. The patient was treated with R-CHOP therapy, and achieved a metabolically complete response.</p> <p>Carreras J, Kikuti YY, Miyaoka M, Hiraiwa S, Tomita S, Ikoma H, Kondo Y, Ito A, Nagase S, Miura H, Roncador G, Colomo L, Hamoudi R, Campo E, Nakamura N. Mutational Profile and Pathological Features of a Case of Interleukin-10 and RGS1-Positive Spindle Cell Variant Diffuse Large B-Cell Lymphoma. <em>Hematology Reports</em>. 2023; 15(1):188-200. https://doi.org/10.3390/hematolrep15010020</p>
spindle cell variant diffuse large B-cell lymphoma (hematolrep-2136295)
<p>Diffuse large B-cell lymphoma with spindle cell morphology is a rare variant. We present the case of a 74-year-old male who initially presented with a right supraclavicular (lymph) node enlargement. Histological analysis showed a proliferation of spindle-shaped cells with narrow cytoplasms. An immunohistochemical panel was used to exclude other tumors, such as melanoma, carcinoma, and sarcoma. The lymphoma was characterized by a cell-of-origin subtype of germinal center B-cell-like (GCB) based on Hans’ classifier (CD10-negative, BCL6-positive, and MUM1-negative); EBER negativity, and the absence of BCL2, BCL6, and MYC rearrangements. Mutational profiling using a custom panel of 168 genes associated with aggressive B-cell lymphomas confirmed mutations in ACTB, ARID1B, DUSP2, DTX1, HLA-B, PTEN, and TNFRSF14. Based on the LymphGen 1.0 classification tool, this case had an ST2 subtype prediction. The immune microenvironment was characterized by moderate infiltration of M2-like tumor-associated macrophages (TMAs) with positivity of CD163, CSF1R, CD85A (LILRB3), and PD-L1; moderate PD-1 positive T cells, and low FOXP3 regulatory T lymphocytes (Tregs). Immunohistochemical expression of PTX3 and TNFRSF14 was absent. Interestingly, the lymphoma cells were positive for HLA-DP-DR, IL-10, and RGS1, which are markers associated with poor prognosis in DLBCL. The patient was treated with R-CHOP therapy, and achieved a metabolically complete response.</p> <p>Carreras J, Kikuti YY, Miyaoka M, Hiraiwa S, Tomita S, Ikoma H, Kondo Y, Ito A, Nagase S, Miura H, Roncador G, Colomo L, Hamoudi R, Campo E, Nakamura N. Mutational Profile and Pathological Features of a Case of Interleukin-10 and RGS1-Positive Spindle Cell Variant Diffuse Large B-Cell Lymphoma. <em>Hematology Reports</em>. 2023; 15(1):188-200. https://doi.org/10.3390/hematolrep15010020</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.