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2,880 results for “variant”
Annotated missense variants (hg38) for LoGoFunc prediction
<p>Annotated missense variants (hg38) for LoGoFunc prediction. Academic use only. For commercial use contact Yuval Itan</p>
Dataset of 803 variants from LOVD
<p>This dataset corresponds to all reviewed single amino acid nucleotide polymorphisms (SAPs) and nonsense (SNPs) from the 2017 LOVD dataset</p>
datset related to article "NEUROSYPHILIS MIMICKING BEHAVIORAL VARIANT OF FRONTOTEMPORAL DEMENTIA IN A 59-YEAR-OLD MAN"
<p>neuropsychological data (raw data) of patient involved in the study at title</p>
Training datasets of size 1K, 3K, and 9K for four utility function variants
<p>The datasets include 1K, 3K, and 9K training data points that are used for training utility-change prediction models in systems with ground truth from four different mathematical complexities:</p> <ul> <li>Linear utility function</li> <li>Saturating utility function</li> <li>Discontinuous utility function</li> <li>Combined utility function ( combining the above three variants)</li> </ul>
A custom-made AAV1 variant (AAV1-T593K) enables efficient transduction of Japanese quail neurons in vitro and in vivo
<p><span>The widespread use of rodents in neuroscience has prompted the development of optimized viral variants for transduction of brain cells, <em>in vivo</em>. However, many of the viruses developed are less efficient in other model organisms, with birds being among the most resistant to transduction by current viral tools. Resultantly, the use of genetically-encoded tools and methods in avian species is markedly lower than in rodents; likely holding the field back. We sought to bridge this gap by developing custom viruses towards the transduction of brain cells of the Japanese quail. We first develop a protocol for culturing primary neurons and glia from quail embryos, followed by characterization of cultures via immunostaining, single-cell mRNA sequencing, patch clamp electrophysiology and calcium imaging. We then leverage the cultures for the rapid screening of various viruses, only to find that all yielded poor to no infection of cells <em>in vitro</em>. However, few infected neurons were obtained by AAV1 and AAV2. Scrutiny of the sequence of the AAV receptor found in quails led us to rationally design a custom-made AAV variant (AAV1-T593K; AAV1*) that exhibits improved transduction efficiencies <em>in vitro</em> and <em>in vivo</em> (eight- and five-fold, respectively). Together, we present a unique culturing method, transcriptomic profiles of quail's brain cells and a custom-tailored AAV1 for transduction of quail neurons <em>in vitro </em>and<em> in vivo.</em></span></p>
Multiplexed On-Yeast Serological Assay for Immune Escape Screening of SARS-CoV-2 Variants
<p>Experimental data and scripts used for the development of a Yeast-based serological Assay:</p> <ol> <li>The<strong> Python scripts</strong> folder includes all scripts used in this study to analyze sera titers and plotting data.</li> <li>The<strong> Raw data</strong> folder includes: <ol> <li>The Y<strong>east Immunoassay development</strong> folder includes the flow cytometric data for serum depletion and reduction of ligand depletion effects.</li> <li>The <strong>Yeast serological data folder</strong> includes the raw data of all tested sera and related data for their analyses.</li> </ol> </li> <li>The <strong>Snapgene plasmid maps </strong>folder includes the plasmid maps for the three SARS-CoV-2 VOCs for Snapgene.</li> </ol> <p> </p> <p> </p>
SARS-CoV-2 vaccine breakthrough infections by Omicron and Delta variants in healthcare workers
<p>An observational prospective cohort study was conducted in vaccinated employees with acute SARS-CoV-2 infection between October 2021 and February 2022. Serological and molecular testing was performed to determine SARS-CoV-2 viral load, lineage, antibody levels, and neutral-ising antibody titres. A total of 571 (9.7%) employees experienced SARS-CoV-2 breakthrough infections during the enrolment period, of which 81 were included. The majority (n=79, 97.5%) was symptomatic and most (n=75, 92.6%) showed Ct-values < 30 in RT-PCR assays. Twenty-four (30%) remained PCR-positive for > 15 days. Neutralizing antibody titres were strongest for the wildtype, intermediate for Delta and lowest for Omicron variants. Omicron infections occurred at higher anti-RBD-IgG serum levels (p= 0.00001) and showed a trend for higher viral loads (p=0.14, median Ct-difference 4.3, 95% CI [-2.5-10.5]). For both variants, viral loads were signifi-cantly higher in participants with lower anti-RBD-IgG serum levels (p=0.02). </p>
Recurrent, founder and hypomorphic variants contribute to shaping the genetic landscape of Joubert syndrome
<p><strong>Introduction: </strong>This database includes the raw data linked with the paper “Recurrent, founder and hypomorphic variants contribute to the genetic landscape of Joubert syndrome”. In this paper we reported eleven recurrent variants in seven distinct JS genes occurring in our large European JS cohort, including a previously unreported variant in KIAA0586 (c.1006C>T).</p> <p><strong>Methods</strong>: We evaluated the frequencies of these variants in our cohort of >500 European JS patients and compared them with controls (from three large Italian non-JS cohorts and from the gnomAD database), and with an independent cohort of about 600 JS probands from the United States.</p> <p><strong>Results: </strong>All variants were markedly enriched in the European JS cohort compared to all controls. When comparing allele frequencies in the two JS cohorts, the Ashkenazi Jewish founder variant (TMEM216 c.218G>T) was significantly enriched in American JS compared to European JS patients, while the MKS1 c.1476T>G variant was about ten times more frequent among European JS. Frequencies of all remaining variants were comparable in the two cohorts. Genotyping of several microsatellite markers across the gene loci in carriers of seven variants identified four novel founder haplotypes. Of note, MKS1 c.1476T>G was consistently detected in compound heterozygosity with deleterious variants in JS patients, while it was found in homozygosity in an unaffected parent. Functional studies on fibroblasts from this healthy carrier and her affected son showed a similarly reduced percentage of ciliated cells compared to unaffected controls, but much shorter cilia in the patient than in the unaffected homozygous parent, consistent with a hypomorphic effect.</p>
Massively parallel screens to identify splice disruptive variants in human disease genes
<p>Splicing is a critical step in mRNA maturation with roles in gene regulation and proteome diversification. Splice disruptive variants (SDVs) are implicated in diverse human diseases, and 10-33% of exonic variants may disrupt splicing. However, identifying SDVs remains challenging due to the degeneracy and redundancy of the underlying sequence code. Experimental splicing measurements from patient cells or mini-gene assays can detect SDVs but have traditionally been low-throughput. </p> <p>Massively parallel reporter assays (MPSAs) systematically measure splicing impacts at scale and could clarify variant pathogenicity and inform models of splicing regulation. In this assay, complex barcoded libraries of mutant exons are synthesized, cloned into minigene constructs, and transfected into human cells. Splicing outcomes of each mutation are quantified en masse using targeted RNA-seq of minigene-derived transcripts, and I developed custom python package to process the resulting data.</p> <p>In Chapter 2, I apply this assay to the pituitary transcription factor gene <em>POU1F1</em> (in collaboration Dr. Sally Camper’s lab). Mutations in <em>POU1F1</em> cause combined pituitary hormone deficiency (CPHD), a clinically and genetically heterogenous disorder with prevalence ~1:4000. We targeted exon 2, which has two alterative isoforms (alpha and beta) using competing splice acceptors that encode mutually antagonistic proteins. We measured the splicing effects of 1,070 SNVs across the exon and surrounding introns and identified 96 SDVs - 14 of which were synonymous substitutions. Our measurements were concordant with six nearby heterozygous missense and synonymous variants seen in unrelated hypopituitarism patients. This map identifies a putative splice silencer motif that represses the use of the normally lowly expressed beta isoform.</p> <p>In Chapter 3, I apply a MPSA to a critical developmental renal transcription factor gene, <em>WT1</em> (in collaboration with clinical nephrologist Dr. Jen Lai Yee). Mutations in <em>WT1 </em>are implicated in nephrotic syndrome and sexual differentiation phenotypes. I focus on exon 9 which is alternatively spliced at competing donor sites resulting in two isoforms (KTS+ and KTS-). KTS+ and KTS- are normally expressed in ~2:1 ratio, but perturbation of the ratio can lead to Frasier’s syndrome – a rare nephrotic syndrome. We tested 518 SNVs for splicing defects and identified 8 known Frasier’s Syndrome variants as well as 16 additional variants that similarly lowered the KTS ratio. We also detected 19 variants increasing the KTS ratio - two of which have been observed in patients with sexual differentiation phenotypes.</p> <p>Although MPSAs can measure splicing effects of hundreds of variants simultaneously, the current scale of variant discovery via exome and genome sequencing demands efficient and accurate computational approaches to identify splice disruptive variants genome-wide. To evaluate the state of the art within contemporary splice prediction algorithms, in Chapter 4 I employed the results of five high throughput splicing assays and one literature curated variant set. A unique advantage of MPSAs over typical training and validation datasets is that they avoid bias towards essential splice site variants. I found the latest deep learning tools, SpliceAI and Pangolin, were most concordant with the measured splicing effects. However, all tools showed less agreement with exonic splicing outcomes compared to intronic. Some tools’ predictions, like SpliceAI’s, were sensitive to specified annotation files. Thus, there is still room for improvement within the next generation of splice prediction algorithms which future MPSA studies may facilitate.</p>
Comparison between the results from JGA analysis somatic short variant discovery workflow and those from the compatible Terra workflow
<p>Files starting from <code>HCC1143.somatic</code> are the results from <a href="https://github.com/ddbj/jga-analysis/tree/main/somatic-short-variant">JGA analysis somatic short variant discovery workflow</a>. Files starting from <code>submissions_</code> are the results from the compatible Terra workflow.</p> <p>VCFs are identical between two workflows except for the header lines. MAFs are also identical except for the header lines.</p>
Supplementary Data for: "The principles of SARS-CoV-2 inter-variant competition are exemplified in the pre-Omicron era of the Colombian epidemic"
<p>Supplementary data files, including BEAST XMLs and logs from the study "The principles of SARS-CoV-2 inter-variant competition are exemplified in the pre-Omicron era of the Colombian epidemic".</p>
Comparison between the results from JGA analysis mitochondrial short variant discovery workflow and those from the compatible Terra workflow
<p>Files starting from <code>NA12878.chrM</code> are the results from <a href="https://github.com/ddbj/jga-analysis/tree/mitocondrial-variant">JGA analysis mitochondrial short variant discovery workflow</a>. Files starting from <code>submissions_</code> are the results from the compatible Terra workflow.</p> <p>VCFs are identical between two workflows except for the header lines.</p>
COVID-19 PBMC sample information and the VCF file of variants around OAS1 gene.
<p>We investigated our recently published PBMC scRNA-seq data (Stephenson et al. 2021 Nat Med) obtained from 112 donors, including 84 COVID-19 positive individuals, and profiled using the CITE-seq approach, as an independent in vivo validation of OAS1 eQTL colocalisation with GWAS locus for COVID-19 susceptibility. The dataset includes both sample information and genotype information of variants around OAS1 gene (chr12:111906777-113906777) as in VCF format. The whole variant data of the COVID-19 PBMC samples is available upon request.</p>
Data set: genetic variants related to SARS-CoV-2 viremia
<p>Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and the presence of viremia.</p>
Structural variants of 20 wild isolates of Caenorhabditis elegans
<p>20 VCFs of 20 <em>Caenorhabditis elegans</em> wild isolates against VC2010 reference assembly.</p> <p>Reads come Pacific Biosciences sequencing.</p> <p>Alignment was done using ngmlr.</p> <p>Variant calling was done using Sniffles.</p> <p> </p>
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
<p>ncVarPred-1D3D:</p> <p>The data used for testing the inconsistency among genome sequence, epigenetic profile, and later, to show its relation to 3D chromatin structure can be found in sanity_check_data.tar.gz.</p> <p>Some trained model for noncoding mutation effect prediction (mapping genome sequence to epigenetic profile) can be found in CNN_MLP, CNN_GCN, CNN_RNN_MLP, CNN_RNN_GCN.tar.gz.</p> <p>The trained model for pathogenic variants prediction can be found in fewshot_pathogenic_model.tar.gz. </p> <p>The training data can be found in training_data.tar.gz.</p> <p>Some noncoding variant effects prediction results, e.g. eQTL and pathogenic variants, can be replicated using the data shared in ncVar_data.tar.gz.</p>
Amplicon sequence variants (ASV) of gut pathogens in hooded cranes and domestic geese
<p>Driven by habitat loss from anthropogenic activities, wintering migratory birds forage together with poultry in paddy fields, and thus impose risks of cross transmitting pathogens. To date, there is little evidence for such risks of pathogen transmission between wild birds and poultry. Using the high-throughput sequencing, we report on detected potential pathogens of both wild hooded cranes <em>Grus monacha</em> and sympatric domestic geese <em>Anser</em> <em>anser</em> <em>domesticus</em> during the wintering period and infer the possibility of cross-species pathogen transmission. The results revealed that the number of shared amplicon sequence variants (ASVs) of potential pathogens between the gut microbiota of the two species was low during the early wintering stage (17.2%; 5 ASVs shared) but increased to 56.3% (18 ASVs shared) during the late wintering stage. That is, potential pathogens in the gut microbial communities of the two species became more similar through co-foraging in paddy fields, supporting cross-transmission of pathogens between hooded cranes and domestic geese during the wintering period. Importantly, transmission appeared to be largely from wild hooded cranes to domestic geese, although some potential pathogens may have become specialized to the domestic goose in late wintering stage. Humans are also facing the risks of contracting these potential pathogens from migratory birds through their frequent contact with domestic poultry. It is, therefore, necessary to closely monitor this pathway of pathogen transmission from wild birds to domestic animals and even to humans.</p>
Vascular variants in seed plants – a developmental perspective
<p>Over centuries of plant morphological research, biologists have enthusiastically explored how distinct vascular arrangements have diversified. These investigations have focused on the evolution of steles and secondary growth and examined the diversity of vascular tissues (xylem and phloem), including atypical developmental pathways generated through modifications to the typical development of ancestral ontogenies. A shared vernacular has evolved for communicating on the diversity of alternative ontogenies in seed plants. Botanists have traditionally used the term “anomalous secondary growth” which was later renamed to “cambial variants” by late Dr. Sherwin Carlquist (1988). However, the term “cambial variants” can be vague in meaning since it is applied for developmental pathways that do not necessarily originate from cambial activity. Here, we review the “cambial variants” concept and propose the term “vascular variants” as a more inclusive overarching framework to interpret alternative vascular ontogenies in plants. In this framework, vascular variants are defined by their developmental origin (instead of anatomical patterns), allowing the classification of alternative vascular ontogenies into three categories: (1) <strong>procambial variants</strong>, (2) <strong>cambial variants</strong> and (3) <strong>ectopic cambia</strong>. Each category includes several anatomical patterns. Vascular variants, which represent broader developmental-based groups, can be applied to both extant and fossil plants, and thereby offer a more adequate term from an evolutionary perspective. An overview of the developmental diversity and phylogenetic distribution of vascular variants across selected seed plants is provided. Finally, the evolutionary implications of vascular variants are discussed.</p>
Validation of a SARS-CoV-2 surrogate neutralization test detecting neutralizing antibodies against the major variants of concern
<p>SARS-CoV-2 infection and/or vaccination elicit a broad range of neutralizing antibody responses against the different variants of concern (VOC). We established a new variant-adapted surrogate neutralization test (sVNT) and assessed the neutralization activity against the ancestral B.1 (WT) as well as VOC Delta, Omicron BA.1, BA.2 and BA.5. Performances were compared to the reference virus neutralization test (VNT) against the respective VOC using three different cohorts collected during the COVID waves. Pre-COVID samples confirmed 100% specificity of the sVNT. Correlation analyses showed moderate to strong correlation for Omicron sub-variants (Spearman’s r=0.7081 for BA.1, r=0.7205 for BA.2 and r=0.6042 for BA.5), and for WT (r=0.8458) and Delta-sVNT (r=0.8158), respectively. Comparison of the WT-sVNT performance with two CE-IVD commercial kits “Icosagen SARS-CoV-2 Neutralizing Antibody ELISA kit” and “Genscript cPass kit” revealed an overall good correlation ranging from 0.8673 to -0.8773 and a midway profile between both commercial kits with 87.76% sensitivity and 90.48% clinical specificity resulting in a Youden Index of 78.24. This midway trend was further confirmed on 100 double-vaccinated individuals. The BA.2-sVNT performance was similar to that of the Genscript test. Finally, sVNT ability to assess neutralizing antibodies against Omicron BA.5 was validated on a double-vaccinated cohort (n=100) and an Omicron-breakthrough infection cohort (n=91). Correlation analysis revealed a strong association (r=0.8583) between BA.5-sVNT and VNT. Accurate classification was confirmed by receiving operating characteristic (ROC) analysis reporting an area under the curve (AUC) of 0.9543. In conclusion, the sVNT allows for efficient prediction of immune protection against the various VOCs.</p>
Inflammatory responses induced by the monophasic variant of Salmonella typhimurium in pigs play a role in the high shedder phenotype and fecal microbiota composition
<p>Pigs infected with <em><span>Salmonella</span></em> may excrete large amounts of <em><span>Salmonella</span></em>, increasing the risk of spread of this pathogen in the food chain. Identifying <em><span>Salmonella</span></em> high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with <span>Salmonella</span>. Immune response was studied through total blood cell counts, production of anti-<em><span>Salmonella</span></em> antibodies and cytokines, and gene expression quantification. Total <em><span>Salmonella</span></em> shedding for each pig was estimated and hierarchical clustering was used to cluster pigs into high, intermediate, and low shedders. Gut microbiota compositions were assessed using 16S rRNA microbial community profiling. Comparisons were made between control and inoculated pigs, then between high and low shedders pigs. Prior to infection, high shedders had similar immunological profiles compared to low shedders. As soon as 1 day postinoculation (dpi), significant differences in the cytokine production level and on the expression level of several host genes related to a proinflammatory response were observed between high and low shedders. Infection with <em><span>Salmonella</span></em> induced an early and profound remodeling of the immune response in all pigs, but the intensity of the response was stronger in high shedders. In contrast, low shedders seroconverted earlier than high shedders. Just after induction of the proinflammatory response (at 2 dpi), some taxa of the fecal microbiota were specific to the shedding phenotypes. This was related to the enrichment of several functional pathways related to anaerobic respiration in high shedders. In conclusion, our data show that the immune response to <em><span>Salmonella</span></em> modifies the fecal microbiota and subsequently could be responsible for shedding phenotypes. Influencing the gut microbiota and reducing intestinal inflammation could be a strategy for preventing <em><span>Salmonella</span></em> high shedding in livestock.</p>
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.