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2,880 results for “variant”
Dataset for a study:Clinical characteristics of SARS-CoV-2 delta variant infection in Xiamen
<p>This retrospective study aims to identify the clinical and demographic features of patients infected with the SARS-CoV-2 delta variant at a single institution in Xiamen, China.</p>
Electrophysiological measurement results in patients with a missense variant in ACTG1
<p><strong>Introduction</strong>: This preliminary study identified a missense variant in ACTG1 (NM_001614.5) in a family with autosomal dominant non-syndromic hearing loss (ADNSHL). The responsiveness of the electrically stimulated cochlear nerve (CN) in two implanted participants with this missense change was also evaluated and reported.</p> <p><strong>Methods</strong>: Genetic testing was done using a custom capture panel (MiamiOtoGenes) and whole exome sequencing. The responsiveness of the electrically-stimulated CN was evaluated in two members of this family (G1 and G4) using the electrically evoked compound action potential (eCAP). eCAP results from these two participants were compared with those measured three implanted patient populations: children with cochlear nerve deficiency, children with idiopathic hearing loss and normal-sized cochlear nerves, and postlingually deafened adults.</p> <p><strong>Results</strong>: Sequencing of ACTG1 identified a missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) which is most likely the genetic cause of ADNSHL in this family. eCAP results measured in these two participants showed substantial variations.</p> <p><strong>Discussion</strong>: The results indicated the missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) co-segregated with hearing loss in this family. The responsiveness of the electrically-stimulated CN can vary among patients with the same genetic variants, which suggests the importance of evaluating the functional status of the CN for individual CI patients.</p>
TP53 synthetic genomics data for benchmarking variant callers
<p>This is a synthetic genomics dataset generated with <a href="https://github.com/ncsa/NEAT">NEAT </a> for the gene TP53 for the use case of benchmarking somatic variant callers. The reports for all bam files where created using <a href="https://github.com/genome/bam-readcount">bam-readcount</a>.</p> <p>To find out more about our pipeline please visit <a href="https://github.com/BiodataAnalysisGroup/synth4bench">the Biodata Analysis Group GitHub</a> and also our <a href="https://biodataanalysisgroup.github.io/">GitHub page</a> :)</p>
structural variants data
<p>The origin data are used to replicate our work. The topic is "<strong>Accuracy assessment of structural variation calling methods for breast cancer gene panel in the absence of gold standard</strong>". </p>
Functional dissection of human cardiac enhancers and non-coding de novo variants in congenital heart disease
<p>This is the CHD MPRA motif analysis input file. Please see the detail in : https://github.com/pulab/CHD_DNVs/tree/main/MPRA-Enhancer/CHD_MPRA_project/CHD_MPRA_library</p>
Enhancing stock price data analysis through variants of principal component analysis
<p>The dataset used in the research titled "Enhancing stock price data analysis through variants of principal component analysis". It includes the daily closing prices of top 100 stocks in S&P500 from 29th March 2020 to 28th March 2023.</p>
Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides
<p>Supplementary data related to the paper "Retention time and fragmentation predictors increase confidence in identification of common variant peptides"</p> <p>The database directory contains the FASTA files of the four protein sequence databases used in the analysis of the paper.</p> <p>The data directory contains exports with lists of all peptide-to-spectrum matches obtained from the analysis.</p> <p>More information and scripts to reproduce the post-processing steps are available at: https://github.com/ProGenNo/VariantPeptideIdentification</p>
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
<p>ncVarPred-1D3D: pretrained models of Sei (PMID: 35817977) + our 3D structure embedding models are shared. The models are trained and validated using DeepSEA (PMID: 26301843) selected 200 bp regions (we extended to 4K bp neighboring) to predict the epigenetic profile containing 21907 epigenetic events Sei processed.</p> <p>The pretrained DeepSEA (PMID: 26301843) and reproduced DanQ (PMID: 27084946) can be found in SOTA.tar.gz.</p>
Dataset related to "CFH and CFHR structural variants in atypical Hemolytic Uremic Syndrome: Prevalence, genomic characterization and impact on outcome "
<p>The upload consists of 2 excel files, including genetic and clinical data, and 6 power point files with western blot images.</p> <p>SMRT sequencing data are deposited in the EBI European Nucletide Archive; Accession number: PRJEB44176. </p>
Raw data for " Unnatural evolutionary processes of SARS-CoV-2 variants and possibility of deliberate natural selection" DOI 10.5281/zenodo.8248320
<p>Compressed raw data for " Unnatural evolutionary processes of SARS-CoV-2 variants and possibility of deliberate natural selection" </p> <p>DOI 10.5281/zenodo.8248320</p>
High prevalence of lipopolysaccharide mutants and R2-Pyocin susceptible variants in Pseudomonas aeruginosa populations sourced from cystic fibrosis lung infections
<p>Chronic, highly antibiotic-resistant infections in cystic fibrosis (CF) lungs contribute to increasing morbidity and mortality. <em>Pseudomonas</em> <em>aeruginosa</em>, a common CF pathogen, exhibits resistance to multiple antibiotics, contributing to antimicrobial resistance (AMR). These bacterial populations display genetic and phenotypic diversity, but it is unclear how this diversity affects susceptibility to bacteriocins. R-pyocins, i.e. bacteriocins produced by <em>P. aeruginosa</em>, are phage-tail-like antimicrobials. R-pyocins have potential as antimicrobials, however, recent research suggests the diversity of <em>P. aeruginosa</em> variants within CF lung infections leads to varying susceptibility to R-pyocins. This variation may be linked to changes in lipopolysaccharide (LPS), acting as the R-pyocin receptor. Currently, it is unknown how frequently R-pyocin-susceptible strains are in chronic CF lung infection, particularly when considering the heterogeneity within these strains. In this study, we tested R2-pyocin susceptibility of 139 <em>P. aeruginosa</em> variants from 17 sputum samples of seven CF patients and analyzed LPS phenotypes. We found that 83% of sputum samples did not have R2-pyocin-resistant variants, while nearly all samples contained susceptible variants. There was no correlation between LPS phenotype and R2-pyocin susceptibility, though we estimate that about 76% of sputum-derived variants lack an O-specific antigen, 40% lack a common antigen, and 24% have altered LPS cores. The absence of a correlation between LPS phenotype and R-pyocin susceptibility suggests LPS packing density may play a significant role in R-pyocin susceptibility among CF variants. Our research supports the potential of R-pyocins as therapeutic agents, as many infectious CF variants are susceptible to R2-pyocins, even within diverse bacterial populations.</p>
Summary statistics for "Variants in the TERT gene increase the occurrence of solar lentigines by modifying telomerase expression exclusively in the skin"
<p>Publication: Deecke et al., Variants in the TERT gene increase the occurrence of solar lentigines by modifying telomerase expression exclusively in the skin, manuscript under revision<br> <br> Brief summary:<br> Solar lentigines (SL) are a characteristic of the aging skin. Their occurrence is likely determined by a combination of genetic variants and environmental factors such as chronic sun exposure. However, the genetic factors underlying SL formation remain largely unknown. A recently performed genome-wide association study (GWAS) of SL in two Chinese cohorts reported <em>TERT</em> and <em>OCA2</em> as novel genome-wide significant genetic loci for SL, while only the <em>TERT</em> locus could be validated in a cohort of European descent (Peng et al, 2023). The telomerase reverse transcriptase TERT is known to be involved in the process of maintenance of telomere lengths, but interestingly no causal relationship between telomere length and the SL GWAS results was observed by the investigators.</p> <p>In this study, we quantified the heritability of SL located on the back of the hands and performed a de novo GWAS in 1,137 elderly participants (aged 60 and more) of European descent from the Berlin Aging Study II. We confirmed <em>TERT</em> as the only genome-wide significant locus for SL (top SNP: rs2735940, p= 1.35E-16). In line with the previous Mendelian Randomization (MR) results by Peng et al., our updated MR using substantially larger datasets did not show a causal relationship between the occurrence of SL and telomere lengths measured in blood leukocytes. Importantly, rs2735940 modifies <em>TERT</em> expression in skin tissue (based on GTEx data), but not in any of the other GTEx tissues including blood. Furthermore, colocalization analyses suggested a shared causal effect of rs2735940 on SL occurrence and on <em>TERT</em> expression in skin but not in blood.</p> <p>Thus, we could show that variants in the <em>TERT</em> gene increase the occurrence of SL by modifying <em>TERT</em> expression exclusively in the skin, based on currently available GTEx data. This skin-specific effect was not reported previously and may provide the hitherto missing functional link for the occurrence of SLs via <em>TERT</em> expression and telomere length alterations.</p>
Defining neutralization and allostery by antibodies against COVID-19 variants
<p>The changing landscape of mutations in the SARS-CoV-2 Spike protein is linked to the emergence of variants, immune-escape and reduced efficacy of the existing repertoire of anti-viral antibodies. A major factor that contributes to the functional activity of neutralizing antibodies are the intrinsic quaternary changes that occur as a result of antibody-Spike trimer interactions. In this study, we reveal the conformational dynamics and allosteric perturbations linked to binding of human monoclonal antibodies and the viral Spike protein. We identify epitope hotspots of known and novel antibodies, and associated changes in Spike dynamics that distinguish weak, moderate and strong neutralizing antibodies. We show the impact of mutations in Wuhan-Hu-1, Delta, and Omicron variants of concern (VoCs) on differences in the antibody-induced conformational changes in Spike and illustrate how these render certain antibodies ineffective. Our comparative analyses of the antibody-footprints on Spike variants reveal how antibodies with similar binding affinities may induce destabilizing or stabilizing allosteric effects. These differences have important implications for neutralization efficacy and for developing new antibodies targeting emerging variants. Our results provide mechanistic insights into the functional modes and synergistic behavior of human antibodies against COVID-19, and provide a foundation for the design of effective antiviral strategies.</p>
Dataset: Disease-associated KCNMA1 variants decrease circadian clock robustness in channelopathy mouse models
<p><em>KCNMA1</em> encodes the voltage- and calcium-activated K<sup>+</sup> (BK) channel, which regulates suprachiasmatic nucleus (SCN) neuronal firing and circadian behavioral rhythms. Gain-of-function (GOF) and loss-of-function (LOF) alterations in BK channel activity disrupt circadian behavior, but the effect of human disease-associated <em>KCNMA1</em> channelopathy variants has not been studied on clock function. Here, we assess circadian behavior in two GOF and one LOF mouse lines. Heterozygous <em>Kcnma1</em><sup>N999S/WT</sup> and homozygous <em>Kcnma1</em><sup>D434G/D434G</sup> mice are validated as GOF models of paroxysmal dyskinesia (PNKD3), but whether circadian rhythm is affected in this hypokinetic locomotor disorder is unknown. Conversely, homozygous LOF <em>Kcnma1</em><sup>H444Q/H444Q </sup>mice do not demonstrate PNKD3. We assessed circadian behavior by locomotor wheel running activity. All three mouse models were rhythmic, but <em>Kcnma1</em><sup>N999S/WT</sup> and <em>Kcnma1</em><sup>D434G/D434G</sup> showed reduced circadian amplitude and decreased wheel activity, corroborating prior studies focused on acute motor coordination. In addition, <em>Kcnma1</em><sup>D434G/D434G</sup> mice had a small decrease in period. However, the phase-shifting sensitivity for both GOF mouse lines was abnormal. Both <em>Kcnma1</em><sup>N999S/WT</sup> and <em>Kcnma1</em><sup>D434G/D434G</sup> mice displayed increased responses to light pulses and took fewer days to re-entrain to a new light:dark cycle. In contrast, the LOF <em>Kcnma1</em><sup>H444Q/H444Q </sup>mice showed no difference in any of the circadian parameters tested. The enhanced sensitivity to phase-shifting stimuli in <em>Kcnma1</em><sup>N999S/WT</sup> and <em>Kcnma1</em><sup>D434G/D434G</sup> mice was similar to other <em>Kcnma1</em> GOF mice. Together with previous studies, these results suggest that increasing BK channel activity decreases circadian clock robustness, without rhythm ablation.</p>
The Genomic Reference Resource for African Cattle: genome sequences and high-density array variants.
<p><em>The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. We report here the genome sequences of 573 samples (198 new genomes) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.4 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetic and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource. We hope this resource will be utilised by the global scientific community and breeders for sustainable global livestock improvement.</em></p>
Supporting data for "Software pipelines for RNA-Seq, ChIP-Seq and Germline Variant calling analyses in Common Workflow Language (CWL)"
<p>Datasets produced during the validation of CWL-based pipelines, designed for the analysis of data from RNA-Seq, ChIP-Seq and germline variant calling experiments. Specifically, the workflows were tested using publicly available High-throughput (HTS) data from published studies on Chronic Lymphocytic Leukemia (CLL) (accession numbers: E-MTAB-6962, GSE115772) and Genome in a Bottle (GIAB) project samples (accession numbers: SRR6794144, SRR22476789, SRR22476790, SRR22476791).</p> <p>The supporting data include:</p> <ul> <li>Differential transcript and gene expression results produced during the analysis with the CWL-based RNA-Seq pipeline</li> <li>Bigwig and narrowPeak files, differential binding results, table of consensus peaks and read counts of EZH2 and H3K27me3, produced during the analysis with the CWL-based ChIP-Seq pipeline</li> <li>VCF files containing the detected and filtered variants, along with the respective hap.py () results regarding comparisons against the GIAB golden standard truth sets for both CWL-based germline variant calling pipelines</li> </ul>
Supplemental Material Outcomes of SDHB pathogenic variant carriers a systematic review and meta-analysis
<p>Supplemental Material Outcomes of SDHB pathogenic variant carriers a systematic review and meta-analysis</p>
A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants
<p>Underrepresentation of non-European populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72K subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East-Asian-specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell-type-specific effects. We suggest this data set will add to the potential value of Asian precision medicine.</p>
Keccak variant - transformation rules
<p>Contains the additional transformation rules used to transform the keccak variant to whileplus.</p><p>Stored in ASCII format, because they are too lengthy to display in LaTeX.</p>
High-Dose Isoniazid Among Adult Patients With Different Genetic Variants of INH-Resistant Tuberculosis (TB)
ClinicalTrials.gov study NCT01936831. IPD Sharing: Not stated. Countries: 2. Publications: 3.
ScienceDex guides
Understand access before you commit
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.