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223
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ShareScore release 0.9.0
Dataset results
223 results for “retinoblastoma”
Comprehensive identification of pathogenic variants in retinoblastoma by long- and short-read sequencing
<p>Retinoblastoma (RB) is the most common intraocular malignancy in childhood. The causal variants in RB are mostly characterized by previously used short-read sequencing (SRS) analysis, which has technical limitations in identifying structural variants (SVs) and phasing information. Long-read sequencing (LRS) technology has significant advantages over SRS in detecting SVs, phased genetic variants, and methylation. In this study, we comprehensively characterized the genetic landscape of RB using combinatorial LRS and SRS of 16 RB tumors and 16 matched blood samples. We detected a total of 232 somatic SVs, with an average of 14.5 SVs per sample across the cohort. We identified 20 distinct pathogenic variants, including <span>three</span> novel small variants and <span>five</span> <span>somatic</span> SVs. Furthermore, our analysis shows that the vast majority (93.8%) of <em>RB1</em>-disrupted patients fit the two-hit hypothesis through diverse types, including the biallelic hypermethylated promoter as well as small and large compound heterozygous mutations which were missing in SRS analysis. By constructing the evolutionary history of all genetic variants, we reveal the evolution trends that <em>RB1</em> disruption early and followed by copy number changes, including amplifications of Chr2p, and deletions of Chr16q, during RB tumorigenesis. Altogether, we characterize the comprehensive genetic landscape of RB, providing novel insights into the genetic alterations and mechanisms contributing to RB initiation and development. Our work also establishes a framework to analyze genomic landscape of cancers based on LRS data. <br><br>We took IGV screenshots of SV and SNV/indels. The IGV naming conventions for SV is: sample name, chromosome 1, start, chromosome 2, end, SV type, SV length, SV breakpoint. The IGV naming convention for SNV/indels is: sample name, chromosome, position, reference allele, alternate allele.</p>
Explainable AI for Retinoblastoma Diagnosis: Interpreting Deep Learning Models with LIME and SHAP
<p>Retinoblastoma is a rare and aggressive form of childhood eye cancer that requires prompt diagnosis and treatment to prevent vision loss and even death. Deep learning models have shown promising results in detecting retinoblastoma from fundus images, but their decision-making process is often considered a "black box" that lacks transparency and interpretability. In this project, we explore the use of LIME and SHAP, two popular explainable AI techniques, to generate local and global explanations for a deep learning model based on InceptionV3 architecture trained on retinoblastoma and non-retinoblastoma fundus images. We collected and labeled a dataset of 400 retinoblastoma and 400 non-retinoblastoma images, split it into training, validation, and test sets, and trained the model using transfer learning from the pre-trained InceptionV3 model. We then applied LIME and SHAP to generate explanations for the model's predictions on the validation and test sets. Our results demonstrate that LIME and SHAP can effectively identify the regions and features in the input images that contribute the most to the model's predictions, providing valuable insights into the decision-making process of the deep learning model. In addition, the use of InceptionV3 architecture with spatial attention mechanism achieved high accuracy of 97\% on the test set, indicating the potential of combining deep learning and explainable AI for improving retinoblastoma diagnosis and treatment.</p>
Pharmacological induction of translational readthrough of nonsense mutations in the retinoblastoma (RB1) gene
<p>Original blot images and qRT-PCR data.</p>
Study of Treatment for Patients With Cancer of the Eye -Retinoblastoma
ClinicalTrials.gov study NCT00186888. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Intra-arterial Chemotherapy for the Treatment of Intraocular Retinoblastoma
ClinicalTrials.gov study NCT01293539. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Combination Chemotherapy, Autologous Stem Cell Transplant, and/or Radiation Therapy in Treating Young Patients With Extraocular Retinoblastoma
ClinicalTrials.gov study NCT00554788. IPD Sharing: Not stated. Countries: 6. Publications: 1.
Global Retinoblastoma Presentation 2017 data, on behalf of the Global Retinoblastoma Study Group
<p>Data at time of diagnosis of retinoblastoma patients who were diagnosed during 2017 in treatment centers across the world.</p>
Cyclin F drives proliferation through SCF-dependent degradation of the retinoblastoma-like tumor suppressor p130/RBL2
Cell cycle gene expression programs fuel proliferation and are universally dysregulated in cancer. The retinoblastoma (RB)-family of proteins, RB1, RBL1/p107, and RBL2/p130, coordinately represses cell cycle gene expression, inhibiting proliferation, and suppressing tumorigenesis. Phosphorylation of RB-family proteins by cyclin-dependent kinases is firmly established. Like phosphorylation, ubiquitination is essential to cell cycle control, and numerous proliferative regulators, tumor suppressors, and oncoproteins are ubiquitinated. However, little is known about the role of ubiquitin signaling in controlling RB-family proteins. A systems genetics analysis of CRISPR/Cas9 screens suggested the potential regulation of the RB-network by cyclin F, a substrate recognition receptor for the SCF family of E3 ligases. We demonstrate that RBL2/p130 is a direct substrate of SCFcyclin F. We map a cyclin F regulatory site to a flexible linker in the p130 pocket domain, and show that this site mediates binding, stability, and ubiquitination. Expression of a mutant version of p130, which cannot be ubiquitinated, severely impaired proliferative capacity and cell cycle progression. Consistently, we observed reduced expression of cell cycle gene transcripts, as well a reduced abundance of cell cycle proteins, analyzed by quantitative, iterative immunofluorescent imaging. These data suggest a key role for SCFcyclin F in the CDK-RB network and raise the possibility that aberrant p130 degradation could dysregulate the cell cycle in human cancers.
Mutational Analysis of the RB1 Gene in Patients with Unilateral Retinoblastoma
<p><strong><span>Mutational Analysis of the RB1 Gene in Patients with Unilateral Retinoblastoma in Jordan</span></strong></p>
hERG Kv11.1 and Janus Kinase 2 interplay in retinoblastoma cell migration
<p>Docking poses, Molecular Dynamics simulation starting structures and MD trajectories</p>
A Study of Intra-Ophthalmic Artery Topotecan Infusion for the Treatment of Retinoblastoma
ClinicalTrials.gov study NCT01466855. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Severe and Transient Hypoxemia During Selective Intra-arterial Chemotherapy for Retinoblastoma in Children: Evaluation of the Right-sided Heart Function.
ClinicalTrials.gov study NCT03559894. IPD Sharing: NO. Countries: 1. Publications: 5.
A Study of the Effectiveness of a Local Injection of Chemotherapy for Retinoblastoma
ClinicalTrials.gov study NCT00857519. IPD Sharing: NO. Countries: 1. Publications: 2.
Intra-arterial Chemotherapy(Chemosurgery) for Retinoblastoma
ClinicalTrials.gov study NCT00901238. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Retinoblastoma Biomarker Study
ClinicalTrials.gov study NCT00342797. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Intra-arterial Chemotherapy With Melphalan for the Treatment of Retinoblastoma (RTB) in Advanced Intraocular Stage
ClinicalTrials.gov study NCT01393769. IPD Sharing: Not stated. Countries: 1. Publications: 21.
Phase I Trial of Periocular Topotecan in Retinoblastoma
ClinicalTrials.gov study NCT00460876. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Topotecan Episcleral Plaque for Treatment of Retinoblastoma
ClinicalTrials.gov study NCT04428879. IPD Sharing: NO. Countries: 1. Publications: 0.
Trial Comparing Two Carboplatin Doses in Groups C and D Intraocular Retinoblastoma
ClinicalTrials.gov study NCT00889018. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Adjuvant Chemotherapy for High-risk Retinoblastoma After Enucleation
ClinicalTrials.gov study NCT01906814. IPD Sharing: NO. Countries: 1. Publications: 1.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.