5524 results for "*oma"

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• Targeted DNA sequencing of 60 non-Hodgkin lymphoma biopsies using a custom gene panel for hematological malignancies: raw (FASTQ) data

  Targeted DNA sequencing was performed on 60 non-Hodgkin lymphoma (NHL) samples using a custom next-generation sequencing panel targeting the coding regions of 190 genes recurrently mutated in hematological malignancies. Libraries were sequenced on an Illumina NovaSeq 6000 platform using 2 × 150 bp paired-end reads. The dataset includes the raw sequencing data (FASTQ files) for all 60 samples.

  Dataset EGAD50000002845

• scRNAseq and spatial transcriptomics data of melanoma samples

  Paired-end 10x single-cell RNA sequencing and Visium spatial transcriptomics data from samples derived from 11 melanoma patients. Sequencing was performed on the Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single-Cell 5 Reagent Kits v2 or 10xGenomics Visium Gene Expression kit.

  Dataset EGAD50000002902

• Impact of Mutated CTCF DNA binding sites of Topologically associating domains on nearby Cancer Gene Regulation: A Multi-Omics Analysis

  Cutaneous squamous cell carcinoma (cSCC) is the most common lethal malignancy world-wide. Due in most part to the extremely high mutational burden (TMB) in cSCC, making sense of it’s non-coding and regulatory regional genomic variation has lagged that of other far less common cancers. This study presents the first investigation of mutations at CCCTC-binding factor binding sites (CTCFbs) of Topologically associating domains (TAD) across defined cSCC progression stages—primary non-metastatic (PNM), primary metastat-ic (PM), and lymph node metastasis (LNM).

  Study EGAS50000001686

• CTCF Binding Site Mutations: Linking Topologically Associated Domains Dysregulation to Cutaneous Squamous Cell Carcinoma Progression

  Fresh tumor tissue from nodal metastases (n = 41) was harvested during surgery and immediately snap-frozen. A total of 72/75 cSCC, WGS samples were included in the analysis (refer to QC section), comprising primary tumors (both metastatic (PM (n = 16)) and non-metastatic (PNM (n = 15)), as well as lymph node metastases (LNM (n = 41)). The metastatic cohort included matched PM and LNM samples for 13 patients. The PNM group had to meet the following criteria: absence of metastases at > 24 months follow-up after resection of the primary or negative sentinel lymph node biopsy at time of resection or histologically negative neck dissection. Somatic variant analysis was performed using DRAGEN pipeline version 4.3.6 on the Illumina Connected Analytics (ICA) v2 environment using in house shell scripting. Tumor-normal paired analyses were carried out in three stages: alignment, variant calling, and integrative somatic analysis. Further information on the somatic calling is available at https://help.dragen.illumina.com/product-guides/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/somatic-mode.

  Dataset EGAD50000002416

• IMC-F106C-101 dose escalation

  Brenetafusp is an ImmTAC bispecific (PRAME×CD3) targeting the cancer testis antigen PRAME. In this phase 1 study (NCT04262466), 126 HLA-A*02:01+ patients with advanced solid tumors received weekly IV doses from 0.3-320 mcg. The primary objective was to identify the maximum tolerated dose (MTD) or recommended phase 2 dose (RP2D); additional objectives included pharmacokinetics, pharmacodynamics, and preliminary anti-tumor activity. Brenetafusp demonstrated manageable safety and preliminary efficacy in PRAME+ tumors. A phase 3 trial in metastatic cutaneous melanoma is ongoing

  Study EGAS50000001976

• RNA-seq for "A preinvasive regulatory T cell axis for lung cancer interception" paper

  Bulk RNA sequencing data generated from primary resected non-small cell lung cancer (NSCLC) tumour tissue collected through the ASCENT study (Analysis of Screen-Detected Lung Cancers’ Genomic Traits; NCT04204499). The dataset comprises tumour RNA-seq from 89 patients with CT screen-detected NSCLC, predominantly early-stage disease, including lung adenocarcinoma and lung squamous cell carcinoma. The RNA-seq data were used to characterise tumour-immune transcriptional programmes and were analysed alongside matched peripheral blood immune profiling and clinical follow-up data.

  Dataset EGAD50000002852

• LUAD RNAseq – LORD

  RNA-seq data from paired normal and adenocarcinoma lung samples obtained from 515 patients that underwent lung cancer surgery.

  Study EGAS50000001705

• LUAD RNAseq - LORD

  The Lung Oncology Research and Discovery (LORD) program is a multi-omics translational initiative aimed at advancing precision medicine in lung cancer. It builds on a lung tissue biobank and leverages biological samples collected from patients who underwent lung cancer surgery at the IUCPQ-UL (Quebec City, Canada). LORD is therefore a single-site, retrospective, case-only study. Genomic profiling of biobanked samples is ongoing, with samples being analyzed sequentially in phases defined by sample type and omic modality. For this dataset, we provide RNA-seq data from paired normal and adenocarcinoma lung samples obtained from 515 patients.

  Dataset EGAD50000002450

• Projet LORD- LUAD RNAseq data

  RNAseq data from paired samples of non affected lung parenchyma and Lung adenocarcinoma (LUAD) from 515 patients surgically intervened at the Institut universitaire de cardiologie et de pneumologie de Québec- Université Laval

  Dac EGAC50000000846

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - pilot normal and pre/post-chemo

  Dataset EGAD00001000704

• Single-cell RNA sequencing of large B cell lymphoma relapsed after CAR T-cell therapy and in vitro serial killing models

  Relapsed/refractory large B-cell lymphoma (rrLBCL) following CAR T-cell therapy remains associated with a poor prognosis. Using single-cell RNA sequencing (scRNA-seq), we characterized the T-cell profiles in 7 post-CAR T rrLBCL and 5 CAR T-naïve rrLBCL, revealing dysfunctional transcriptional features in T cells after CAR T-cell therapy. In addition, the dataset includes T cell profiling of CAR T-cell products and samples obtained after serial killing assays in vitro, performed with or without supplementation with non-IL2Rα agonist pegenzileukin. These analyses demonstrated that IL-2 was the most depleted cytokine following the coculture assay.

  Study EGAS50000001982

• Single-cell RNA sequencing of large B cell lymphoma relapsed after CAR T-cell therapy and in vitro serial killing models

  Relapsed/refractory large B-cell lymphoma (rrLBCL) following CAR T-cell therapy remains associated with a poor prognosis. Using single-cell RNA sequencing (scRNA-seq), we characterized the T-cell profiles in 7 post-CAR T rrLBCL and 5 CAR T-naïve rrLBCL, revealing dysfunctional transcriptional features in T cells after CAR T-cell therapy. In addition, the dataset includes T cell profiling of CAR T-cell products and samples obtained after serial killing assays in vitro, performed with or without supplementation with non-IL2Rα agonist pegenzileukin. These analyses demonstrated that IL-2 was the most depleted cytokine following the coculture assay.

  Dataset EGAD50000002866

• MOSAIC Window Mesothelioma Data

  This dataset will include Spatial Transcriptomics from the 10x Genomics Visium SD technology, Single-Cell RNA-Seq from the 10x Genomics Chromium Flex protocol, Bulk RNA-Seq (sequenced on Illumina), WES (sequenced on Illumina), H&E, and Clinical data from 10 Mesothelioma patients. For Visium and Chromium data we are sharing the outputs of respectively Space Ranger and Cell Ranger. For Bulk RNA-Seq we are including processed files such as counts.tsv, FPKM.tsv, fusion_genes.tsv, TPM count matrix.tsv, DESeq2 count matrix.tsv, multiqc_report. For WES, we are sharing the presence or absence of single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variants (CNVs).* Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001706

• MOSAIC Window Glioblastoma Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 10 Glioblastoma (GBM) Cancer patients. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001352

• Mechanisms of resistance to pembrolizumab treatment in classical Hodgkin Lymphoma

  In this project we are applying whole exome sequencing (WES) on plasma-derived ctDNA samples to identify mutations that drive resistance to pembrolizumab treatment in classical Hodgkin Lymphoma

  Study EGAS50000001985

• Whole-exome sequencing (WES) data from a classical Hodgkin lymphoma patient obtained before pembrolizumab treatment and at relapse

  This dataset contains raw paired-end whole-exome sequencing (WES) FASTQ files generated from plasma-derived cell-free DNA (cfDNA) collected from a patient with classical Hodgkin lymphoma before pembrolizumab treatment and at the time of relapse, together with a matched normal sample. Libraries were prepared using a whole-exome capture kit and sequenced on the Element AVITI platform to generate 2 × 150 bp paired-end reads. The submitted data comprise the primary sequencing output in gzipped FASTQ format.

  Dataset EGAD50000002869

• Familial Melanoma Sequencing

  In this experiment we have sequenced the exome of 15 individuals from eight families who have familial melanoma. By sequencing the exome we hope to be able to identify new genes that are associated with this disease.

  Study EGAS00001000017

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - WGS validation cohort

  This reposiroty contains bulk WGS data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere.

  Study EGAS50000001211

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - RNA validation cohort

  This reposiroty contains bulk RNA data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere.

  Study EGAS50000001212

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - WGS

  This reposiroty contains bulk WGS data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere. The dataset contains 11 tumor-normal sample pairs.

  Dataset EGAD50000001724

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - RNA

  This reposiroty contains bulk RNA data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere. The dataset contains RNAseq samples from bone marrows.

  Dataset EGAD50000001725

• Bulk RNA sequencing of 36 multi-region IPMN–PDAC tumours comprising 160 sequencing runs

  This dataset contains bulk RNA sequencing data generated from 36 multi-region tumour samples obtained from patients with intraductal papillary mucinous neoplasms (IPMN) and associated pancreatic ductal adenocarcinoma (PDAC). A total of 160 sequencing runs are included. Libraries were prepared from poly(A)-selected RNA and sequenced on an Illumina platform. The data are provided as raw sequencing files for downstream transcriptomic analyses.

  Dataset EGAD50000002215

• single-cell RNA-Seq data of Circulating immune profiling reveals impaired monocyte states and trajectories driving immunosuppression in glioblastoma

  This dataset contains single-cell RNA sequencing data generated from human PBMC obtained from 10 GBM patients and 5 healthy donors. The main objective of this study was to map the differentiation continuum and transcriptional landscape of peripheral blood mononuclear cells in primary glioblastoma patients at the single-cell level to identify specific systemic immune signatures. Libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM (10x Genomics, Pleasanton, CA, USA) and sequenced on an Illumina NextSeq 500/550 or an Illumina NovaSeq 6000 system. This dataset comprises raw FASTQ files and gene expression count matrices. Access to these data is controlled and managed by the Luxembourg Institute of Health (LIH) Data Access Committee (DAC).

  Dataset EGAD50000002932

• Spatial atlas of diffuse large B-cell lymphoma

  We leveraged highly multiplexed, single-cell–resolution spatial transcriptomics, bulk RNA sequencing, and tumor–germline paired whole-exome sequencing to profile 465 diffuse large B-cell lymphoma (DLBCL) tumors and define the assembly of 60 lymphoma microenvironment (LME) cell subsets and 5 tumor B cell states into conserved spatial niches and communities that resemble non-malignant lymphoid architecture. Three distinct LME-enriched communities were assembled from combinations of niches and reflected recently described LME archetypes with conserved spatial biology. Tumor B cells were enriched in three B communities harboring distinct, developmentally linked, transcriptional states associated with divergent cell-cell communication (CCC) pathways. Intratumoral heterogeneity in B communities was pervasive across patients and largely unlinked with molecular subtype. Combinations of B communities, rather than single states, were associated with patient outcome, implicating microenvironment-associated tumor B cell transcriptional plasticity in the biology and clinical behavior of DLBCL.

  Study EGAS50000002037

• Spatial atlas of diffuse large B-cell lymphoma

  We leveraged highly multiplexed, single-cell–resolution spatial transcriptomics, bulk RNA sequencing, and tumor–germline paired whole-exome sequencing to profile 465 diffuse large B-cell lymphoma (DLBCL) tumors and define the assembly of 60 lymphoma microenvironment (LME) cell subsets and 5 tumor B cell states into conserved spatial niches and communities that resemble non-malignant lymphoid architecture. Three distinct LME-enriched communities were assembled from combinations of niches and reflected recently described LME archetypes with conserved spatial biology. Tumor B cells were enriched in three B communities harboring distinct, developmentally linked, transcriptional states associated with divergent cell-cell communication (CCC) pathways. Intratumoral heterogeneity in B communities was pervasive across patients and largely unlinked with molecular subtype. Combinations of B communities, rather than single states, were associated with patient outcome, implicating microenvironment-associated tumor B cell transcriptional plasticity in the biology and clinical behavior of DLBCL.

  Study EGAS50000002036