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Dataset results
203 results for “neoantigens”
pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection (Supp data)
<p>Supplemental tables for article: <strong>pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection </strong></p>
Supplementary data to: Detection of Neoantigen-specific T Cells Following a Personalized Vaccine in a Patient with Glioblastoma
<p>Supplemental Data for the patient described in the manuscript: "Detection of Neoantigen-specific T Cells Following a Personalized Vaccine in a Patient with Glioblastoma". Summary of somatic variant calls from DNA whole exome, gene FPKM from RNA sequencing, and neoantigen predictions for high-affinity (ic<sub>50</sub> <500 nM) candidates.</p>
Lack of shared neoantigens in prevalent mutations in cancer
<p><span>Tumors are mostly characterized by genetic instability, as result of mutations in surveillance mechanisms, such as DNA damage checkpoint, DNA repair machinery and mitotic checkpoint. Defect in one or more of these mechanisms causes additive accumulation of mutations. Some of these mutations are drivers of transformation and are positively selected during the evolution of the cancer, giving a growth advantage on the cancer cells. If such mutations would result in mutated neoantigens, these could be actionable targets for cancer vaccines and/or adoptive cell therapies. However, the results of the present analysis show, for the first time, that the most prevalent mutations identified in human cancers do not express mutated neoantigens. The hypothesis is that this is the result of the selection operated by the immune system in the very early stages of tumor development. At that stage, the tumor cells characterized by mutations giving rise to highly antigenic non-self mutated neoantigens would be efficiently targeted and eliminated. Consequently, the outgrowing tumor cells cannot be controlled by the immune system, with an ultimate growth advantage to form large tumors embedded in an immunosuppressive tumor microenvironment (TME). The outcome of such a negative selection operated by the immune system is that the development of off-the-shelf vaccines, based on shared mutated neoantigens, does not seem to be at hand.</span></p>
Molcular Dynamics Data for Therapeutic High Affinity T Cell Receptor Targeting a KRAS G12D Cancer Neoantigen
<p>This folder contains the starting structures and input scripts required to simulate the wild-type and G12D KRAS peptide bound TCR-pHLA complexes, as performed in this study.</p> <p><br> Starting_Structures - This folder contains the amber parameter/topology files used to simulate each system (.prmtop) and the coordinates of the starting structure both as amber coordinate file (.rst) and PDB file (.pdb).<br> MD_Inputs - This folder contains the amber MD inputs used to run the md simulations. <br> MMPBSA_inputs - This folder contains the input files for running MMPBSA with the MMPBSA.py script in amber. The mmpbsa.in script was used for calculating overall binding energy whereas the mmpbsa_decomp.in script was used for calculating the per-residue contribution to binding energy. </p>
Flow cytometry data and image data -A dendritic cell vaccine for both vaccination and neoantigen-reactive T cell preparation for cancer immunotherapy in mice
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A Phase I Study With a Personalized NeoAntigen Cancer Vaccine in Melanoma
ClinicalTrials.gov study NCT01970358. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Messenger RNA (mRNA)-Based, Personalized Cancer Vaccine Against Neoantigens Expressed by the Autologous Cancer
ClinicalTrials.gov study NCT03480152. IPD Sharing: NO. Countries: 1. Publications: 4.
Neoantigen-based Personalized DNA Vaccine in Patients With Newly Diagnosed, Unmethylated Glioblastoma
ClinicalTrials.gov study NCT04015700. IPD Sharing: NO. Countries: 1. Publications: 0.
Ability of a Dendritic Cell Vaccine to Immunize Melanoma or Epithelial Cancer Patients Against Defined Mutated Neoantigens Expressed by the Autologous Cancer
ClinicalTrials.gov study NCT03300843. IPD Sharing: NO. Countries: 1. Publications: 3.
Bispecific antibodies and CAR T cells targeting a TP53 mutation-associated neoantigen show discordant affinity requirements
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An mRNA-encoded, long-lasting Interleukin-2 restores CD8+ T cell neoantigen immunity in MHC class I-deficient cancers
<ul> <li><strong><span>Cd45Summit-IntgrAllgroups_finalUMAP_simplified_colorordered.RData </span></strong><span>contains all final result of the workflow (data integration and annotation) without subsetting the cell types into the different treatment groups.</span></li> <li><strong><span>Cd45Summit-IntgrAllgroups_finalUMAP_Only_CD8Tcells_subsetted.RData </span></strong><span>contains combined dataset of all present CD8+ T cell types (final UMAP, all annotated), which are subsetted into the four treatment groups.</span></li> <li><strong><span>Cd45Summit-IntgrAllgroups_finalUMAP_Only_ProlifMacros_subsetted.RData </span></strong><span>contains only the proliferating CD8+ T cells, which are subsetted into the four different treatment groups.</span></li> <li><strong><span>Cd45Summit-IntgrAllgroups_forJan_Macors_Gr1to4.RData </span></strong><span>contains only the combined macrophages of the dataset, subsetted into the four treatment groups.</span></li> </ul>
Molecular Dynamics of HLA-A 02:01 with neoantigen and wild-type peptides from AKP6 and ASTN1 genes.
<p>Molecular Dynamics simulations of 4 complexes :</p> <p>1. Protein HLA-A*02:01 with the wild-type peptide WLIDMESLV from AKP6 gene.</p> <p>2. Protein HLA-A*02:01 with the neoantigen peptide WLIDMKSLV from AKP6 gene.</p> <p>3. Protein HLA-A*02:01 with the neoantigen peptide KLYGLDWAEL from ASTN1 gene.</p> <p>4. Protein HLA-A*02:01 with the wild-type peptide KPYGLDWAEL from ASTN1 gene.</p>
Neoantigen Vaccines in Esophageal Squamous Cell Carcinoma
ClinicalTrials.gov study NCT06675201. IPD Sharing: NO. Countries: 1. Publications: 1.
Clinical Study of a Personalized Neoantigen Cancer Vaccine Combined With Anti-PD-1 and RFA in Patients With Solid Tumors
ClinicalTrials.gov study NCT04864379. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Treatment of Relapsed or Refractory t(8; 21) AML With Targeted AML1-ETO Neoantigen Cytotoxic T Cells (CTL)
ClinicalTrials.gov study NCT06499025. IPD Sharing: NO. Countries: 1. Publications: 6.
GNOS-PV02 Personalized Neoantigen Vaccine, INO-9012 and Pembrolizumab in Subjects with Advanced HCC
ClinicalTrials.gov study NCT04251117. IPD Sharing: NO. Countries: 2. Publications: 1.
Clinical Study of Personalized mRNA Vaccine Encoding Neoantigen in Patients With Advanced Digestive System Neoplasms
ClinicalTrials.gov study NCT03468244. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Individualized Neoantigen Therapy with Unusual Radiotherapy Enhancement (iNATURE)
ClinicalTrials.gov study NCT06314087. IPD Sharing: NO. Countries: 1. Publications: 1.
Clinical Trial on the Safety, Tolerance and Preliminary Efficacy of XH001 Injection Combined With Neoantigen Vaccine-induced Tumor-specific T-cell Injection in Advanced Gastric Cancer
ClinicalTrials.gov study NCT07298200. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
A Study of a Personalized Cancer Vaccine Targeting Shared Neoantigens
ClinicalTrials.gov study NCT03953235. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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.