Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2,880
datasets available to search
ShareScore release 0.9.0
Dataset results
2,880 results for “variant”
DAVI: A Dataset for Automatic Variant Interpretation
<p><span>The analysis of an individual’s genetic material may uncover genetic variants, which can be classified as disease-causing (pathogenic) or benign. Identifying pathogenic variants among millions of variants relies on the research of evidence in support of or against variant pathogenicity, a process regulated by the American College of Molecular Genetics (ACMG) guidelines, which leverages data from the scientific literature. Despite recent improvements towards automation, searching shreds of evidence for pathogenicity in the literature still requires manual curation, a time-consuming process, due to the ever-growing number of published papers. </span></p> <p><span>In this work, we built DAVI (Dataset for Automatic Variant Interpretation), a reliable, manually curated dataset comprising 1239 sentences extracted from 311 (variant, article) associations </span><span>for a pool of 41 variants. 597 sentences </span>contain (positive) evidence activating two opposing ACGM criteria, namely PS3 and BS3, while the remaining 642 do not contain (negative) evidence activating either of the two considered ACGM criteria. (variant, article) associations containing<span> at least one positive sentence are classified as positive, while (variant, article) associations containing any positive sentence are negative. Therefore DAVI also contains 154 positive and 157 negative (variant, article) associations. </span></p> <p> </p>
IMPACT OF HUMAN IMMUNOGLOBULIN GENETIC VARIANTS ON THE EXPRESSED ANTIBODY REPERTOIRE
<p>Tables related to the PhD thesis of Eric Engelbrecht, mentored by Corey T. Watson</p>
Primary SARS-CoV-2 variant of concern infections elicit broad antibody Fc-mediated effector functions and memory B cell responses
<p><span>Neutralization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by human sera is a strong correlate of protection against symptomatic and severe Coronavirus Disease 2019 (COVID-19). The emergence of antigenically distinct SARS-CoV-2 variants of concern (VOCs) and the relatively rapid waning of serum antibody titers, however, raises questions about the sustainability of serum protection. In addition to serum neutralization, other antibody functionalities and the memory B cell (MBC) response are suggested to help maintaining this protection. In this study, we investigate the breadth of spike (S) protein-specific serum antibodies that mediate effector functions by interacting with Fc-gamma receptor IIa (<span>FcγRIIa) and FcγRIIIa,</span> and of the receptor binding domain (RBD)-specific MBCs, following a primary SARS-CoV-2 infection with the D614G, Alpha, Beta, Gamma, Delta, Omicron BA.1 or BA.2 variant. Irrespectively of the variant causing the infection, the breadth of S protein-specific serum antibodies that interact with <span>FcγRIIa and FcγRIIIa and the RBD-specific MBC responses </span>exceeded the breadth of serum neutralization, although the Alpha-induced B cell response seemed more strain-specific<span>. Between VOC groups, both quantitative and qualitative differences in the immune responses were observed, suggesting differences in immunogenicity. Overall</span>, this study contributes to the understanding of protective humoral and B cell responses in the light of emerging antigenically distinct VOCs, and highlights the need to study the immune system beyond serum neutralization <span>to gain a better understanding of the protection against emerging variants. </span></span></p>
A joint embedding of protein sequence and structure enables robust variant effect predictions
<p>Data related to the GitHub repository KULL-Centre/_2023_Blaabjerg_SSEmb, which is also stored on Zenodo here: <span><span><a href="../doi/10.5281/zenodo.13765792" target="_blank" rel="noopener noreferrer">https://zenodo.org/doi/10.5281/zenodo.13765792</a>.</span></span></p>
18S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory
<p>Illumina paired-end V9-18S raw reads (FASTQ format, 2 X 150 PE) were pre-processed with cutadapt and vsearch to remove primer sequences, trim low quality bases and unify mixed orientation reads produced in the ligation-based library preparation; the procedure was implemented in a custom bash script. Processed reads were then used to generate amplicon sequence variants (ASVs) using the DADA2 R library; the pipeline was adapted from the one described on the program website (<span><span><a href="https://benjjneb.github.io/dada2/tutorial.html" target="_blank" rel="noopener">https://benjjneb.github.io/dada2/tutorial.html</a></span></span>); no further quality filtering was implemented at this stage, except for discarding all reads with ambiguities (parameter maxN = 0 of function filterAndTrim). Filtered forward (F) and reverse (R) reads were used to train the error model and then denoised by applying the trained error model to generate ASVs. Finally, F and R reads were merged and checked for chimeras; allowing no mismatches in read merging (default parameter maxMismatch = 0 of function mergePairs). ASVs were then classified with BLAST against the PR2 v5.01 reference database, integrated with 1,293 sequences from GoN protist strains and fungi environmental sequences. Highest bit score matching with the best taxonomic resolution were then selected among the returned results.</p>
Missense Variant Collection from ClinVar (2023)
<p><span>All human missense variations submitted to the ClinVar as of April 2023. Variations with at least one</span><br><span>review star were selected and matched to entries in the UniProt Knowledge Base. Duplicate variations sharing the same</span><br><span>genomic coordinates were eliminated. Many sequence and structural features were computed for each variation,</span><br><span>discarding those for which any of the feature computation failed.</span></p>
Supplemental Material for "Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)"
<p>Supplemental materials to the manuscript.</p>
Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk (sequence model release)
<p>(This is the updated version that has been converted a standard pytorch model format)</p> <p>This is the deep learning sequence model used in </p> <p>Jian Zhou, Chandra L. Theesfeld, Kevin Yao, Kathleen M. Chen, Aaron K. Wong, and Olga G. Troyanskaya, Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk, Nature Genetics, 2018.</p> <p>Note the full software is available from https://github.com/FunctionLab/ExPecto and this release is created for the convenience of use and under the same non-commercial license. The model weights can be loaded with pytorch load_state_dict function (for an example please find <a href="https://github.com/FunctionLab/ExPecto/blob/master/chromatin.py">https://github.com/FunctionLab/ExPecto/blob/master/chromatin.py</a>). We also provide a web server for browsing mutations with strong predicted effects at https://hb.flatironinstitute.org/expecto/, which are currently limited to mutations within 1kb to TSS or are 1000 Genomes variants.</p> <p>Trivia: we code-named our models with whale names. This model has an unofficial codename DeepSEA "Beluga".</p>
Data from: Common variants in CLDN2 and MORC4 genes confer disease susceptibility in patients with chronic pancreatitis
A recent genome-wide association study (GWAS) identified association with variants in X-linked CLDN2 and MORC4, and PRSS1-PRSS2 loci with chronic pancreatitis (CP) in North American patients of European ancestry. We selected 9 variants from the reported GWAS and replicated the association with CP in Indian patients by genotyping 1807 unrelated Indians of Indo-European ethnicity, including 519 patients with CP and 1288 controls. The etiology of CP was idiopathic in 83.62% and alcoholic in 16.38% of 519 patients. Our study confirmed a significant association of 2 variants in CLDN2 gene (rs4409525—OR 1.71, P = 1.38 x 10-09; rs12008279—OR 1.56, P = 1.53 x 10-04) and 2 variants in MORC4 gene (rs12688220—OR 1.72, P = 9.20 x 10-09; rs6622126—OR 1.75, P = 4.04x10-05) in Indian patients with CP. We also found significant association at PRSS1-PRSS2 locus (OR 0.60; P = 9.92 x 10-06) and SAMD12-TNFRSF11B (OR 0.49, 95% CI [0.31–0.78], P = 0.0027). A variant in the gene MORC4 (rs12688220) showed significant interaction with alcohol (OR for homozygous and heterozygous risk allele -14.62 and 1.51 respectively, P = 0.0068) suggesting gene-environment interaction. A combined analysis of the genes CLDN2 and MORC4 based on an effective risk allele score revealed a higher percentage of individuals homozygous for the risk allele in CP cases with 5.09 fold enhanced risk in individuals with 7 or more effective risk alleles compared with individuals with 3 or less risk alleles (P = 1.88 x 10-14). Genetic variants in CLDN2 and MORC4 genes were associated with CP in Indian patients.
Illumina 1M-Duo v3 manifest for variant positions
<p>This file contains an archived version of Illumina Duo v3 manifest file that contains the variant information.</p>
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
<p>Supplementary Figure S4. SNP alignment of multiple high-quality genomes from Cameroon, available genomes of lineage B.1.620 as well as earliest and latest genomes of lineages B.1.1.7, B.1.351, P.1, B.1.526.2, B.1.177.60, B.1.177.57, and B.1.1.280. Only polymorphic SNPs within the alignment that are shared by at least eight B.1.620 are shown and lineage B.1.620 is outlined with a dashed line. Sites identical to the reference (GenBank accession NC_045512) are shown in grey, changes from the reference are indicated and coloured by nucleotide (green for thymidine, red for adenosine, blue for cytosine, yellow for guanine, dark grey for ambiguities, black for gaps). The first 100 and the last 50 nucleotides are not included in the figure but were used to infer the phylogeny. If mutation results in an amino acid change, the column label indicates the gene, reference amino acid, amino acid site, and amino acid change in brackets. The maximum-likelihood phylogeny on the right shows the relationships between depicted genomes and was rooted on the reference sequence.</p>
Terc Gene Cluster Variants Predict Liver Telomere Length in Mice
<p>Files are organized by experiment (see publication for more info)</p> <p>Excel files contain raw data. </p> <p>SPSS (.sav) files contain organized raw data in format used for analysis.</p> <p>Word document contains SPSS analysis parameters and output syntax.</p>
A collection of read depth profiles at structural variant breakpoints
<p><strong>SWaveform is a newly created open genome-wide resource for read depth signal in the vicinity of structural variant (SV) breakpoints aims to boost development of computational tools and new algorithms for discovery of genomic rearrangement events from long- or short read sequencing data. SVs encompassing insertions, deletions, duplications, inversions and translocations are a dominant force shaping genomes and substantially contributing to genetic diversity. Still, there are challenges in reliable and efficient genotyping of SVs from whole genome sequencing data, thus delaying translation into clinical applications, and wasting valuable resources. SWaveform includes a database containing ~15M of read depth profiles at SV breakpoints extracted from 911 sequencing samples generated by the Human Genome Diversity Project, generalised patterns of the signal at breakpoints and an interface to navigate and download the data. The data set can be of immense value to bioinformatics and engineering communities as it empowers smooth application of intelligent signal processing and machine learning techniques for discovery of genomic rearrangement events and thus opens the floodgates for development of innovative algorithms and software.</strong></p>
Dataset of 1000 random variants extracted from ClinVar
<p>Random selection of 1000 single amino polymorphisms in the ClinVar database</p>
Shinique Smith - Bale Variant No. 0023 (Totem)
Clothing, fabric, twine and wood 2014, this 3D scan 2014 Scanned at: Museum of Fine Arts, Boston Source: Objaverse 1.0 / Sketchfab
Gene Expression Profile and Inflammation Profile of Classic Asthma, Cough Variant Asthma and Eosinophilic Bronchitis
ClinicalTrials.gov study NCT02555345. IPD Sharing: Not stated. Countries: 1. Publications: 0.
LP-168 and Obinutuzumab for Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma (CLL/SLL) and Variants of This
ClinicalTrials.gov study NCT06978088. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
IL29 and IL28B Variants Associated With Periodontal Disease Pathogenesis
ClinicalTrials.gov study NCT02710903. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genetic Variants Affecting the Clinical Severity of Beta Thalassemia
ClinicalTrials.gov study NCT04918056. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genetic Variants and Iron Absorption
ClinicalTrials.gov study NCT02197624. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.