5524 results for "*oma"

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• Predictive value of genomic, transcriptomic and epigenetic biomarkers in patients with recurrent and/or metastatic HNSC treated with PD-1/PD-L1 inhibitors

  Immune checkpoint inhibitors have improved survival in several solid tumors, including head and neck squamous cell carcinoma (HNSCC). However, current use of PD-1/PD-L1 inhibitors relies on PD-L1 expression, which does not reliably predict patient response. Therefore, better predictive biomarkers are needed to identify which patients benefit from immunotherapy. Previous studies suggest that genomic and transcriptomic features may help predict treatment response. This study aims to integrate genomic, transcriptomic, and methylomic data from 31 patients with recurrent/metastatic HNSCC to identify new biomarkers of resistance to anti-PD-1/PD-L1 therapy.

  Study EGAS50000001746

• A tumor-associated photoreceptor signature unifies distinct central nervous system malignancies

  Pineoblastoma is a clinically aggressive childhood brain tumor composed of distinct molecular subgroups with divergent driver genes, demographics, and clinical outcomes. To identify developmental origins and mechanisms governing disease pathogenesis, we derive single-cell transcriptomes from pineal parenchymal tumors, aligning malignant cells with our atlas of pineal gland development to retrace cellular origins. Integrative computational analyses maps pineoblastoma origins to transient cycling pinealocyte progenitors during development. Lineage-specific perturbation of suspected drivers in the early pineal gland yields preclinical models representative of consensus molecular subgroups. Multi-omic characterization of patient tumors and these models uncovers a tumor-associated photoreceptor signature common to pineoblastoma, retinoblastoma, and Group 3 medulloblastoma. Transcriptional activity of this signature within respective cellular origins establishes a developmental basis for molecular similarities between entities. Photoreceptor signature constituents are selective dependencies across these anatomically distinct central nervous system malignancies, motivating future studies evaluating developmentally encoded programs of malignancy as potential therapeutic liabilities.

  Study EGAS50000001457

• ecDNA copy number heterogeneity

  Neuroblastoma exhibits significant inter- and intra-tumour genetic heterogeneity and varying clinical outcomes. Here, we used DNA and RNA sequencing from the same single cells in cell lines and neuroblastoma patients to investigate these effects. We reveal extensive intercellular ecDNA copy number heterogeneity. We also provide direct evidence of how this heterogeneity influences the expression of cargo genes, including MYCN and its downstream targets, and the overall transcriptional state of neuroblastoma cells.

  Study EGAS50000000509

• Single cell RNA sequencing of relapsed/refractory multiple myeloma

  Study EGAS00001004805

• Whole-exome sequencing of HPV-negative HNSCC to identify pathway alterations

  This study applies whole-exome sequencing (WES) to characterize genomic alterations in HPV-negative head and neck squamous cell carcinoma. Tumors were analyzed to derive pathway-level alteration scores, enabling stratification into Hedgehog-high and Hedgehog-low groups. The genomic data were integrated with imaging, transcriptomic, and functional analyses to investigate tumor-intrinsic Hedgehog signaling. The study aims to identify molecular features associated with biologically distinct tumor subgroups.

  Study EGAS50000001550

• Multi-omics datasets (WES, RNA-seq) of mesothelioma MIST2 study, a phase II CDK4/6 (abemaciclib) clinical trial

  This study comprises 26 mesothelioma patients with whole exome and RNA sequencing, to to assess potential sensitivity to CDK4/6 inhibition in p16ink4A-negative mesothelioma.

  Study EGAS50000001823

• Multi-omics datasets (WES, RNA-seq) of mesothelioma NERO study, a phase II PARP inhibitor clinical trial

  Niraparib Efficacy in Patient With Unresectable Mesothelioma, NERO, this randomised phase II trial is designed to evaluating the efficacy of the PARP inhibitor Niraparib versus active symptom control.

  Study EGAS50000001825

• RNA sequencing dataset of of explants treated with PRX3 inhibitor thiostrepton in mesothelioma

  This dataset includes 66 RNA sequences datasets of mesothelioma explants under three conditions: baseline, untreated control and thiostrepton treatment.

  Dataset EGAD50000002650

• Transcriptome profiling of HNSCC treated with PD1/PDL1

  Immune checkpoint inhibitors have improved survival in several solid tumors, including head and neck squamous cell carcinoma (HNSCC). However, current use of PD-1/PD-L1 inhibitors relies on PD-L1 expression, which does not reliably predict patient response. Therefore, better predictive biomarkers are needed to identify which patients benefit from immunotherapy. Previous studies suggest that genomic and transcriptomic features may help predict treatment response. This study aims to integrate genomic, transcriptomic, and methylomic data from 31 patients with recurrent/metastatic HNSCC to identify new biomarkers of resistance to anti-PD-1/PD-L1 therapy.

  Dataset EGAD50000002506

• Transcriptomic profiling of Hedgehog-high and Hedgehog-low HPV-negative HNSCC

  This study investigates transcriptomic differences between Hedgehog-high and Hedgehog-low HPV-negative head and neck squamous cell carcinoma (HNSCC). Tumors were stratified based on pathway-level genomic alteration scores and imaging-associated Hedgehog activity. RNA sequencing was performed on archival FFPE tumor samples to assess pathway activation and transcriptional programs associated with Hedgehog signaling. The dataset supports integrative radiogenomic and functional analyses of tumor-intrinsic signaling pathways.

  Study EGAS50000001549

• Anaplastic Large Cell Lymphoma Tumor Gene Expression Profiling

  Anaplastic large cell lymphoma tumor RNA-Seq

  Study EGAS50000001011

• Anaplastic Large Cell Lymphoma Gene Expression

  Anaplastic Large Cell Lymphoma Gene Expression Study

  Dataset EGAD50000001478

• Mayo Anaplastic Large Cell Lymphoma Gene Expression

  Dac EGAC50000000633

• scRNAseq data of primary and metastatic melanoma samples

  Paired-end 10x single-cell RNA sequencing data from 13 melanoma samples. Sequencing was performed on the Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single-Cell 5 Reagent Kits v2.

  Dataset EGAD50000000665

• Comprehensive Genomic Profiling of a National Cohort of Pediatric Papillary Thyroid Carcinoma in Hungary

  Pediatric papillary thyroid carcinoma (PTC) is a rare childhood malignancy with increasing incidence and distinct clinicopathological features, including high rate of locoregional metastases and different molecular background compared to adult cases. Traditional treatments (surgery, radioactive iodine) are effective but pose long-term risks, prompting the exploration of targeted therapies. We performed comprehensive genomic profiling on 21 pediatric PTC patients utilising the Illumina TruSight Oncology 500 platform and detected mutations, gene fusions, copy number variations and revealed tumor mutational burden.

  Study EGAS50000001833

• Comprehensive Genomic Profiling of a National Cohort of Pediatric Papillary Thyroid Carcinoma in Hungary

  Pediatric papillary thyroid carcinoma (PTC) is a rare childhood malignancy with increasing incidence and distinct clinicopathological features, including high rate of locoregional metastases and different molecular background compared to adult cases. Traditional treatments (surgery, radioactive iodine) are effective but pose long-term risks, prompting the exploration of targeted therapies. We performed comprehensive genomic profiling on 21 pediatric PTC patients applying Illumina TruSight Oncology 500 platform and detected mutations, gene fusions, copy number variations and revealed tumor mutational burden.

  Dataset EGAD50000002659

• WGS - germline - oral squamous cell carcinoma

  We conducted a retrospective, single-center Canadian cohort study of patients who underwent primary surgery for OSCC between 2010 and 2024. Nucleic acid quality was assessed using the 4150 TapeStation System (Agilent) prior to library preparation. WGS was performed on germline DNA, following Genome Analysis Toolkit’s (GATK) Best Practices and procedures, with a target of 30X deduplicated coverage per sample, using an Illumina NovaSeq 6000 instrument.

  Dataset EGAD50000002608

• WES and RNA sequencing of mesothelioma patients from CONFIRM clinical trial

  CONFIRM is a placebo controlled, double-blind randomised phase III clinical trial designed to investigate the efficacy of the anti-PD1 inhibitor nivolumab in patients with relapsed mesothelioma. This study applied the whole exome sequencing and transcriptomic sequencing to uncover determinants of efficacy in patients exhibiting the most extreme response outcomes.

  Study EGAS50000001814

• Multi-omics datasets (WES, RNA-seq) of mesothelioma MIST4 study, a phase II PD-L1/VEGF blockage clinical trial

  This study comprises 26 mesothelioma patients with whole exome and RNA sequencing, designed to examine the efficacy and correlates of response to dual inhibition of programmed death-ligand 1 and vascular endothelial growth factor inhibition.

  Study EGAS50000001818

• WES dataset of mesothelioma MIST4 study

  This dataset includes bam files from WES of 20 tumor samples and 18 matched normal samples.

  Dataset EGAD50000002633

• RNA sequencing dataset of mesothelioma MIST4 study

  This dataset includes BAM files from RNA-seq of 20 tumor samples.

  Dataset EGAD50000002634

• Multiple Myeloma treated with anti-BCMA T-cell-redirecting therapy (1st Batch)

  Bone marrow samples were collected from patients treated with either anti-BCMA CART and/or anti-BCMA TCE. All samples were sorted using the StemCell EasySep Human CD138 positive selection kit II (StemCell, Cambridge, MA). The positive CD138+ were submitted for WGS, using peripheral blood mononuclear cells as normal matched. WGS was carried out by the Molecular Genomics Core Facility at Moffitt Cancer Center contingent on the availability of high-quality pre-treatment samples. Germline DNA was obtained from peripheral blood mononuclear cells, while tumor DNA was extracted from CD138-enriched bone marrow aspirate specimens using magnetic bead-based selection. Genomic DNA was isolated using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). For library preparation, 100 ng of genomic DNA was fragmented using the Covaris ML230 focused ultrasonicator (Covaris, Inc.), followed by library construction with the TruSeq DNA Nano Library Prep Kit (Illumina) in accordance with manufacturer instructions. Library quality and fragment size distribution were assessed via Agilent TapeStation, and quantification was performed using the Kapa Library Quantification Kit (Roche). Sequencing was conducted on the Illumina NovaSeq 6000 system using S4-300 reagent kits with a 2×150 bp paired-end configuration. Tumor samples were sequenced to a median coverage of 60×, and matched germline controls to 30×. Reference Genome: GRCh38.

  Dataset EGAD50000002632

• SV-based ctDNA detection in soft tissue sarcoma

  33 patients with localized soft tissue sarcoma consented for ctDNA tracking in the peri-operative and surveillance periods. WGS at a target of 15x coverage was performed from DNA extracted from FFPE of localized soft tissue sarcoma. Structural variants were identified from WGS and ddPCR assays were designed for tumor informed tracking of SV for ctDNA.

  Study EGAS50000001811

• SV Based ctDNA detection in localized soft tissue sarcoma

  WGS from FFPE for "Detecting ctDNA Using Personalized Structural Variants to Forecast Recurrence in Localized Soft Tissue Sarcoma." study. 33 patients had whole genome sequencing through the Illumina platform at an average depth of 15x. Tumor informed structural variants were identified and ddPCR assays were designed for individualized structural variant-based ctDNA detection.

  Dataset EGAD50000002614

• Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics

  Epithelioid sarcoma (EpS) is an aggressive sarcoma, characterized by the loss of SMARCB1 expression. EpS is traditionally classified as distal or proximal according to clinicopathological features, but its molecular characteristics remain largely unknown. To establish an EpS molecular classification and uncover determinants of inter- and intra-patient heterogeneity in EpS, we used multi-omics profiling and integrated the genomic, transcriptional and methylome landscapes with single-cell RNA sequencing on fresh samples as well as spatial transcriptomics. We identified two molecular subtypes of EpS: “distal-like” and “proximal-like”, which were distinct from the histological subtypes. Distal-like tumors include all morphological distal subtypes and a subset of proximal and hybrid EpS. They express a specific molecular single-cell derived epithelial-to-mesenchymal transition signature, which associates with improved patient survival and includes Desmoglein 2 (DSG2), which we identify as a potential routine immunohistochemical biomarker to improve diagnosis. Distal-like EpS also display increased peri-tumoral CD8+ T cell infiltrates and specific tumor-immune cell interactions. Conversely, proximal-like EpS harbor a higher inter-tumoral molecular heterogeneity with some cases resembling other SMARCB1-deficient tumors by DNA methylation profiling, and increased intra-tumoral pro-tumoral macrophage infiltrates. Our study introduces a novel molecular classification of EpS with prognostic value, associated diagnostic biomarkers and distinct tumor immune microenvironments, which extends beyond traditional clinicopathological classification. This paves the way for precision medicine-based therapeutic strategies for patients with EpS.

  Dac EGAC50000000552