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109 results for “primary central nervous system lymphoma”
The genomic and transcriptional landscape of primary central nervous system lymphoma
<p>Primary lymphomas of the central nervous system (PCNSL) are mainly diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). Despite extensive research, the molecular alterations leading to PCNSL have not been fully elucidated. In order to provide a comprehensive description of the genomic and transcriptional landscape of PCNSL, we here performed whole-genome and transcriptome sequencing and integrative analysis of 51 lymphomas presenting in the CNS, including 42 EBV-negative PCNSL, 6 secondary CNS lymphomas (SCNSL) and 3 EBV+ CNSL and matched controls. The results were compared to an independent validation cohort of 31 FFPE CNSL specimens (PCNSL, n = 19; SCNSL, n = 9; EBV+ CNSL, n = 3) and 36 systemic DLBCL cases outside the CNS.</p> <p>This repository contains tab separated value text files:</p> <p>- Radke_et_al_supplementary_somatic_CNVs.tsv (somatic copy number variations predicted by ACEseq)<br> - Radke_et_al_supplementary_somatic_indels.tsv (somatic indels predicted by the DKFZ platypus workflow)<br> - Radke_et_al_supplementary_somatic_indels_exonic.tsv (somatic exonic indels predicted by the DKFZ platypus workflow)<br> - Radke_et_al_supplementary_somatic_mutations_integrated.tsv (table of gene by patients, stating which mutations were observed) <br> - Radke_et_al_supplementary_somatic_mutations_integr_integrated_including_kataegis_counts.tsv (table of gene by patients, stating which mutations were observed, including the count of mutations falling into kataegis hotspots) <br> - Radke_et_al_supplementary_somatic_SNVs.tsv (somatic SNVs predicted by the DKFZ mpileup workflow)<br> - Radke_et_al_supplementary_somatic_SNVs_exonic_functional.tsv (somatic exonic SNVs predicted by the DKFZ mpileup workflow)<br> - Radke_et_al_supplementary_somatic_SNVs_rescued_by_TiNDA (mutations initially classified as germline, but likely tumor mutations based on VAF modelling by TiNDA)<br> - Radke_et_al_supplementary_somatic_SVs.tsv (somatic structural variations predicted by the DKFZ Sophia workflow)<br> - Radke_et_al_supplementary_RNAseq_numReads_CNSLs.tsv (RNAseq read counts calculated by the DKFZ RNAseq workflow)</p> <p>This repository contains the raw unedited images from the manuscript:</p> <p>- Radke_et_al_Main_Figure_1c_BCL6.tif (raw unedited image for Main Figure 1c - BCL6)<br> - Radke_et_al_Main_Figure_1c_CD10.tif (raw unedited image for Main Figure 1c - CD10)<br> - Radke_et_al_Main_Figure_1c_MUM1.tif (raw unedited image for Main Figure 1c - MUM1)<br> - Radke_et_al_Supplementary_Figure_1a_CD20.tif (raw unedited image for Supplementary Figure 1a - CD20)<br> - Radke_et_al_Supplementary_Figure_1a_EBV.tif (raw unedited image for Supplementary Figure 1a - EBV)<br> - Radke_et_al_Supplementary_Figure_1a_HE_(FFPE).tif (raw unedited image for Supplementary Figure 1a - HE (FFPE))<br> - Radke_et_al_Supplementary_Figure_1a_HE_(frozen)_1.tif (raw unedited image for Supplementary Figure 1a - HE (frozen) 1)<br> - Radke_et_al_Supplementary_Figure_1a_HE_(frozen)_2.tif (raw unedited image for Supplementary Figure 1a - HE (frozen) 2)<br> - Radke_et_al_Supplementary_Figure_1a_HE_(frozen)_3.tif (raw unedited image for Supplementary Figure 1a - HE (frozen) 3)<br> - Radke_et_al_Supplementary_Figure_1a_Ki67.tif (raw unedited image for Supplementary Figure 1a - Ki67)<br> - Radke_et_al_Supplementary_Figure_1b_EBV_PCR.pptx (raw unedited image for Supplementary Figure 1b - EBV PCR )<br> - Radke_et_al_Supplementary_Figure_1c_CDKN2A_FISH_1.jpg (raw unedited image for Supplementary Figure 1c - CDKN2A FISH 1)<br> - Radke_et_al_Supplementary_Figure_1c_CDKN2A_FISH_2.jpg (raw unedited image for Supplementary Figure 1c - CDKN2A FISH 2)<br> - Radke_et_al_Supplementary_Figure_7h_PD-L1_LS-033.tif (raw unedited image for Supplementary Figure 7h - PD-L1 LS-033)<br> - Radke_et_al_Supplementary_Figure_7h_PD-L1_LS-031.tif (raw unedited image for Supplemnetary Figure 7h - PD-L1 LS-031)</p>
Processed Vectra images for primary central nervous system lymphoma (PCNSL) patients
<ul> <li>FFPE materials</li> </ul> <p>Formalin-fixed paraffin-embedded (FFPE) tumor samples and clinical data were obtained from PCNSL patients enrolled in the HOVON105/ALLG NHL 24 intergroup, multicenter, open-label, randomized phase 3 study (NTR2437 and ACTRN12610000908033) through the HOVON Pathology Facility and Biobank. </p> <ul> <li>Muiltiplex imaging</li> </ul> <p>Multiplex immunofluorescence was performed on 4-µm-thick formalin-fixed, paraffin-embedded whole tissue sections using the Opal 7-color fluorescence immunohistochemistry (IHC) kit (Akoya biosciences, USA), as previously described. In brief, slides were deparaffinized and rehydrated, followed by a blocking step for endogenous peroxidase using 0.3% H<sub>2</sub>O<sub>2</sub>/methanol and fixation with 10% neutral buffered formalin (Leica Biosystems, Germany). Slides were washed in Milli-Q water and 0.05% Tween20 in 1x Tris-Buffered Saline (TBS-T). Antigen retrieval was done by placing the slides in 0.05% ProClin300/Tris–EDTA buffer pH 9.0 in a microwave at 100% power until boiling, followed by 15 min at 30% power. Slides were cooled in Milli-Q water, washed in 1x TBS-T and blocked with Antibody Diluent (Agilent, USA). The slides were then incubated with primary antibody diluted in Normal Antibody Diluent, followed by incubation with the broad spectrum HRP from the SuperPicture Polymer Detection Kit (Life Technologies, USA). Next, the slides were incubated with Opal TSA fluorochromes diluted in an amplification buffer (Akoya biosciences, USA). The primary and secondary antibody complex was stripped by microwave treatment with 0.05% ProClin300/Tris–EDTA buffer at pH 9.0. Finally, DAPI working solution (Akoya biosciences, USA) was applied and the slides were mounted with Prolong Diamond Anti-fade mounting medium (#P36965; Life Technologies).</p> <ul> <li>Image processing</li> </ul> <p>Stained slides were scanned using the Vectra Polaris Automated Quantitative Pathology Imaging System (Akoya biosciences, USA). From each slide, representative tumor regions and regions at the junction of tumor and surrounding cerebral tissue were selected and multispectral imaging (MSI) images were acquired at 40x resolution. After image capture, the images were spectrally unmixed and analyzed, using supervised machine learning algorithms within Inform 4.2.2. (Akoya biosciences). Cells were assigned into ten different phenotype categories: “PAX5+PD-L1-”, “PAX5+PD-L1+”, “CD163+PD-L1-”, “CD163+PD-L1+”, “CD3+CD8-PD-1-”, “CD3+CD8+PD-1-”, “CD3+CD8-PD-1+”, “CD3+CD8+PD-1+”, “other PD-L1+” or “other”, based on the size of the cells and positivity of markers in the panel. </p> <p> </p>
Rituximab and Combination Chemotherapy in Treating Patients With Primary Central Nervous System Lymphoma
ClinicalTrials.gov study NCT00335140. IPD Sharing: YES. Countries: 1. Publications: 1.
Buparlisib (BKM120) In Patients With Recurrent/Refractory Primary Central Nervous System Lymphoma (PCNSL) and Recurrent/Refractory Secondary Central Nervous System Lymphoma (SCNSL)
ClinicalTrials.gov study NCT02301364. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Safety and Feasibility Study of Combination of State of Art Chemoimmunotherapy, Intensive Central Nervous System Prophylaxis and Scrotal Irradiation to Treat Primary Diffuse Large B-cell Lymphoma of T
ClinicalTrials.gov study NCT00945724. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Combination Chemotherapy, Monoclonal Antibody, and Radiation Therapy in Treating Patients With Primary Central Nervous System Lymphoma
ClinicalTrials.gov study NCT00068250. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Combined Immunochemotherapy Followed By Reduced Dose Radiation Therapy (RT) for Patients With Newly Diagnosed Primary Central Nervous System Lymphoma
ClinicalTrials.gov study NCT00594815. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Trial for Patients With Newly Diagnosed Primary Central Nervous System (CNS) Lymphoma
ClinicalTrials.gov study NCT01011920. IPD Sharing: Not stated. Countries: 4. Publications: 2.
Phase II Trial of Sequential Chemotherapy and Radiotherapy for AIDS-Related Primary Central Nervous System Lymphoma
ClinicalTrials.gov study NCT00000801. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Ibrutinib With Rituximab and Lenalidomide for Patients With Recurrent/Refractory Primary or Secondary Central Nervous System Lymphoma (PCNSL/SCNSL)
ClinicalTrials.gov study NCT03703167. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Orelabrutinib,Rituximab and Methotrexate in Newly Diagnosed Primary Central Nervous System Lymphoma
ClinicalTrials.gov study NCT05600660. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of Tirabrutinib vs Rituximab/Temozolomide for Relapsed/Refractory Primary Central Nervous System Lymphoma (PCNSL)
ClinicalTrials.gov study NCT07104032. IPD Sharing: NO. Countries: 1. Publications: 0.
Chemotherapy and Whole-Brain Radiation Therapy in Treating Patients With Primary Central Nervous System Non- Hodgkin's Lymphoma
ClinicalTrials.gov study NCT00002676. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Efficacy of Lenalidomide With Rituximab in Refractory or Relapse of Primary Central Nervous System Lymphoma
ClinicalTrials.gov study NCT01956695. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Rituximab,Methotrexate and Lenalidomide in Newly Diagnosed Primary Central Nervous System Lymphoma
ClinicalTrials.gov study NCT04934579. IPD Sharing: NO. Countries: 1. Publications: 1.
Bruton's Tyrosine Kinase (BTK) Inhibitor, Ibrutinib, in Patients With Newly Diagnosed or Refractory/Recurrent Primary Central Nervous System Lymphoma (PCNSL) and Refractory/Recurrent Secondary Central
ClinicalTrials.gov study NCT02315326. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Cranial Radiotherapy or Intensive Chemotherapy With Hematopoietic Stem Cell Rescue for Primary Central Nervous System Lymphoma in Young Patients
ClinicalTrials.gov study NCT00863460. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Improving Safety and Accuracy of Stereotactic Brain Biopsies in Primary Central Nervous System Lymphoma.
ClinicalTrials.gov study NCT06263361. IPD Sharing: NO. Countries: 1. Publications: 9.
Temsirolimus in Recurrent Primary Central Nervous System (CNS) Lymphoma
ClinicalTrials.gov study NCT00942747. IPD Sharing: Not stated. Countries: 1. Publications: 6.
A Prospective Clinical Study of BTK Inhibitor, PD-1 and Formustine in the First-line Treatment of Primary Central Nervous System Lymphoma
ClinicalTrials.gov study NCT04831658. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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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.
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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.