5032 results for "*oma"

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• Clinical Outcomes of 344 Diffuse Large B-Cell Lymphoma patients

  This study examines clinical outcomes of patients with diffuse large B-cell lymphoma (DLBCL). We analyzed a cohort of 344 patients from the German High-Grade Non-Hodgkin Lymphoma Study Group (DSHNHL). To protect patient confidentiality, all samples were pseudonymized. The dataset includes clinical key characteristics, such as patient age at diagnosis, sex, ECOG performance status, disease stage, serum lactate dehydrogenase levels, bulky disease, bone marrow involvement, extranodal involvement, and B-symptoms. We used these data alongside proteomic and transcriptomic profiles to explore relationships between clinical features and molecular signatures, reconstructing regulatory networks. Insights from this integrative analysis aim to identify key pathological drivers and biomarkers of DLBCL progression, ultimately informing improved risk stratification and targeted therapeutic approaches.

  Study EGAS50000001054

• RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial

  Study on RNA-seq data from tumor tissue samples of primary tumors of advanced clear cell renal cell carcinoma patients enrolled in the NIVOREN GETUG-AFU-26 trial who consented to and participated in the translational program. The goal of this study was to assess previously published gene expression signatures and evaluate their association with the benefit and/or resistance to nivolumab, as well as their association with circulating soluble factors.

  Study EGAS50000001057

• Investigation of BK Polyomavirus (BKPyV) and Molecular Signatures in UC specimens from Taiwan

  Urothelial carcinoma (UC) is the most prevalent cancer of kidney transplant recipients in some regions. The integration of BK polyomavirus (BKPyV) genome into the human genome is observed in some cases of UC. The prevalence of aristolochic acid (AA) mutational signatures in urothelial carcinoma is high in the general population of Taiwan. To better understand the mechanisms of UC carcinogenesis in kidney transplant recipients, 19 UC specimens were analyzed by whole genome sequencing (WGS) and Hybrid Sequencing.

  Study EGAS50000001063

• MorphoITH: A Framework for Deconvolving Intra-Tumor Heterogeneity Using Tissue Morphology

  This study introduces MorphoITH, a framework for deconvolving intra-tumor heterogeneity (ITH) in clear cell renal cell carcinoma (ccRCC) based on tissue morphology from histopathological slides. The study tested MorphoITH's ability to capture different aspects of morphology and to reflect genetic ITH. The data deposited here is derived from a morphology guided multi-regional sequencing dataset used to study the relationship between morphology and genetic evolution. This dataset consists of whole exome sequencing of tumor from multiple sites and adjacent normal samples which were collected from two patients treated in affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital.

  Study EGAS50000001064

• CDK4/6 inhibition in advanced chordoma: final results of the NCT PMO-1601

  Background. Chordoma is a rare bone tumor with no approved systemic therapy. Inactivation of the tumor suppressor p16 (encoded by CDKN2A) leads to aberrant cyclin D-CDK4/6-RB pathway activity, which can be inhibited by palbociclib in chordoma cell lines. Patients and Methods. We conducted a phase II single-arm, open-labeled trial on palbociclib in adult patients with advanced chordomas with p16 loss (by immunohistochemistry) or CDKN2A loss (by genomic analysis) and CDK4/6 and RB1 presence (by immunohistochemistry or RNA-Sequencing). Patients received 125mg palbociclib once daily for 21 days in a 28-day cycle. The study used a Simon optimal 2-stage design. The primary endpoint was disease control rate after six cycles. Response was evaluated according to Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. Secondary endpoints included progression-free survival, overall survival, and biomarker analysis. The study was considered positive if 25% of patients reached the primary endpoint. Results. Between December 2017 and April 2023, 28 patients (median age 60 years, range 31-84) were enrolled. After a median follow-up of 28 months, the disease control rate was 39%, with 11 out of 28 patients achieving stable disease. No objective responses were observed. The median progression-free survival was 5.6 months, and the median overall survival was 24.6 months. Treatment was well tolerated without new safety signals. CDKN2A deletions were the most common genomic alterations underlying p16 loss and were accompanied by MTAP co-deletion. There was no correlation between responder phenotypes by immunohistochemistry and outcome. RNA-based analysis showed heterogeneous pathways deregulation at study entry suggesting underlying primary resistance mechanisms Conclusion. This trial met its primary endpoint with a 39% disease control rate, though antitumor activity was modest. Molecularly tailored combination therapies should be considered to improve efficacy. (ClinicalTrials.gov number, NCT03110744).

  Study EGAS00001007985

• Diversity of U1 small nuclear RNAs and Evaluation of Diagnostic Methods for their Mutations

  U1 small nuclear RNA (snRNA) mutations are recurrent non-coding alterations found in various malignancies, including medulloblastoma, yet their identification has proven challenging due to their repetitive nature. To establish a robust DNA-based, and RNA-based method for detecting U1 snRNA mutations, we performed targeted DNA sequencing using our original gene panel for medulloblastoma and RNA-sequencing. As an RNA-based method, we developed a random forest classifier employing splicing patterns which were massively altered as a result of U1 snRNA mutations. By using both methods, we successfully detected U1 snRNA mutation in five DNA samples and four RNA samples.

  Study EGAS50000000693

• Exploring the evolution of atypical fibroxanthoma to pleomorphic dermal sarcoma: a genomic and pharmacological insight

  The study includes an integrated genomic and pharmacological analysis of atypical fibroxanthoma (AFX) and its progression to pleomorphic dermal sarcoma (PDS), two rare cutaneous mesenchymal tumors with overlapping clinical and histological features but distinct prognostic profiles. The findings will shed light on the molecular mechanisms underlying this progression and provide preliminary evidence for potential therapeutic vulnerabilities, particularly in the context of targeted and immune-based approaches.

  Study EGAS50000001741

• Personalized analysis of ctDNA for detection of molecular residual disease and recurrence in a cohort of surgically treated patients with head and neck squamous cell carcinoma

  Despite advances in multimodal treatment, survival for patients with advanced head and neck squamous cell carcinoma (HNSCC) has improved only modestly. The recent advent of tumor-informed assays capable of detecting circulating cell-free tumor DNA (ctDNA) has enabled early detection of molecular residual disease (MRD) and recurrence following curative therapy. We assessed ctDNA in plasma from 76 and saliva from 54 HNSCC patients, respectively, who received primary curative-intent surgery.

  Study EGAS50000001018

• Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma

  This depository contains the raw BAM/CRAM files used in the manuscript "Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma" Steemers et al. (2026). This includes: - 332 PTA-based single-cell WGS samples (~15X depth) - 7 bulk tumour samples (~30X depth) with matched germline samples (~30X depth) - 14 bulk tumour samples seqeunced by the Princess Maxima Centre diagnostics department (~105X depth) with matched germline samples (~35X depth)

  Study EGAS50000001681

• Development and first-in-human CAR T therapy targeting the pathognomonic MiT-fusion driven protein GPNMB

  Summary: CAR T therapy for solid tumors is constrained by the scarcity of safe, uniformly expressed cell-surface targets. Here we identify GPNMB, a MiT fusion-driven protein, as highly, homogeneously, and stably expressed in primary and relapsed translocation-positive alveolar soft part sarcoma (ASPS) and renal cell carcinoma (tRCC). We develop a GPNMB-directed CAR T cell product, GCAR1, which demonstrates potent activity against patient-matched cells, organoids and xenograft models. In a first-in-human treatment of two patients with relapsed/refractory, metastatic ASPS, GCAR1 is well tolerated and induces stable disease for up to 6 months, accompanied by resolution of many non-target lesions. GCAR1 T cells expand in peripheral blood as a polyclonal population and remain detectable for up to 6 months. Spatial transcriptomics identify multiple immunosuppressive niches adjacent to T cells infiltrating treatment-resistant lesions; biological PDL1 blockade or PD1 and TIGIT double knockout overcomes this resistance and shows synergistic activity with GCAR1 in xenograft models. Taken together, these data provide clinical proof-of-concept for treating solid tumors with CAR T cells targeting a surface antigen driven by an oncogenic gene fusion.

  Study EGAS50000001696

• Transcriptomic profiling of myeloid cells from secondary lymphoid organs (lymph nodes and tonsils) from lymphoma patients and controls.

  Despite their recognized impact on the pathogenesis and prognosis of B-cell lymphoma, tumor-associated macrophages (TAM) have not been extensively explored in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). We investigated mononuclear phagocyte (MNP) heterogeneity using single cell RNA sequencing (scRNAseq) in B-cell lymphoma lymph nodes compared to reactive secondary lymphoid organs (lymph nodes and tonsils).

  Study EGAS50000001135

• Sequencing data for Clinical Trial

  This study is a tri-institutional Phase 1/randomized Phase 2 trial, bevacizumab-naïve rHGA patients were randomized to either LITT (laser interstitial thermal therapy) plus pembrolizumab (LITT+PEM) or non-LITT surgery plus pembrolizumab (NLS+PEM). Randomization ceased after 21 patients when emerging data showed limited adjuvant ICI (immune checkpoint inhibitors) benefit, and the next 24 patients all received LITT+PEM. The goal of the trial is to use LITT, a minimally invasive cytoreductive approach, to prime these “cold” tumors for enhanced ICI response. rHGA= high-grade astrocytoma

  Study EGAS50000001144

• RNA-seq data in hMPC, MSC_Pat and EWIma

  Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic and epigenetic hallmarks of EwS.

  Study EGAS50000001173

• IDH-wildtype untreated human glioblastoma samples (GB-UK cohort), published in Noorani & Haughey et al 2025.

  Extrachromosomal DNA (ecDNA) oncogene amplification is associated with treatment resistance and shorter survival in cancer. Currently, the spatial dynamics of ecDNA, and their evolutionary impact, are poorly understood. Here, we investigate the spatiotemporal evolution of ecDNA by integrating computational modeling with samples from 94 treatment-naive human IDH wild-type glioblastoma patients. Random ecDNA segregation combined with ecDNA-conferred fitness advantages induce distinct spatial ecDNA copy number patterns which depend on ecDNA oncogenic makeup. EGFR-ecDNAs often reach high copy numbers and confer strong fitness advantages. In contrast, PDGFRA-ecDNAs reach lower copy numbers and confer weaker fitness advantages. EGFR structural variants occur exclusively on ecDNA, arise from and are intermixed with wild-type EGFR-ecDNAs. Computational modeling suggests wild-type and variant EGFR-ecDNAs often accumulate before clonal expansion. Using a genetically engineered mouse model, we confirm that the accumulation of oncogenic ecDNA prior to clonal expansion under strong positive selection is observable both in vivo and in vitro in mouse neural stem cells. Intermixed wild-type and variant ecDNAs remain prevalent at diagnosis, as less fit wild-type ecDNAs hitchhike on strongly selected variant EGFR-ecDNAs. A dN/dS analysis in the Genomics England cohort further suggests positive selection of variants on EGFR-ecDNAs but not PDGFRA-ecDNAs in glioblastoma. Overall, our results suggest ecDNA oncogenic makeup determines unique evolutionary trajectories in glioblastoma. New concepts like ecDNA tumor clonality, ecDNA heteroplasmy and multi-species ecDNAs require a refined evolutionary interpretation of genomic data in a large subset of glioblastoma patients and likely other solid cancers.

  Study EGAS00001008126

• Non_Hodgkin_lymphoma_project___mutational_burden_of_chemotherapy_in_normal_blood

  his study aims to further investigate the mutational burden induced by chemotherapy in the normal stem and progenitor cell of individuals treated for Non -hodgkins lymphoma. Single cell derived progenitor colonies have been grown and DNA extracted. 5-10 colonies from a number of individuals exposed to chemotherapeutic regimens for lymphoma will undergo whole genome sequencing to address the question of the extent of mutational impact of these different regimens.

  Study EGAS00001006733

• Ultra-Low-Pass Whole Genome Sequencing of Cell-Free DNA for Large B-Cell Lymphoma

  While deep targeted DNA sequencing of liquid biopsies has shown prognostic utility in large B-cell lymphoma (LBCL), the routine clinical adoption of these assays remains limited due to their high costs. Here, leveraging a well-annotated cohort of encompassing both frontline and relapsed/refractory (R/R) LBCL, we profiled patient plasma samples with two complementary modalities – ultra-low-pass whole genome sequencing (ulpWGS) and deep targeted DNA sequencing, the former being a cost-effective method to profile large scale chromosomal abnormalities and estimate tumor burden. Our findings revealed a strong association of high cell-free tumor burden by both genomic profiling modalities with established measures of tumor burden and patient survival. Notably, the associations with survival remained statistically significant after accounting for international prognostic index scoring. Furthermore, we showed that del(17p) in circulating tumor DNA as detected by ulpWGS was strongly associated with TP53 mutation status and predicted for significantly inferior patient outcome in frontline but not R/R LBCL patients. Our study demonstrates that ulpWGS can provide robust prognostic biomarkers for both frontline and R/R LBCL, highlighting its broad applicability for risk stratification.

  Study EGAS50000001027

• Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  The mammalian SWI/SNF (mSWI/SNF) family of chromatin remodelers govern cell type-specific chromatin accessibility and gene expression and assemble as three distinct complexes: canonical BAF (cBAF), Polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF). ARID1A and ARID1B are paralog subunits that specifically nucleate the assembly of cBAF complexes and are frequently dual deleted in highly aggressive differentiated endometrial carcinomas (DECs). Here, in cellular models and primary human tumors, we find that ARID1A/B-mediated cBAF loss results in increased ncBAF and PBAF biochemical abundance and function genome-wide to maintain the DEC oncogenic signature. Further, treatment of ARID1A/1B-mutant cell lines and PDX models in vivo with a clinical-grade SMARCA4/2 ATPase inhibitor, FHD-286, markedly attenuates cell proliferation and tumor growth, and synergizes with carboplatin-based chemotherapy. Taken together, these findings reveal the oncogenic contributions of shifted of mSWI/SNF family complex abundance and chromatin-level gene regulatory functions and suggest therapeutic utility of mSWI/SNF complex small molecule inhibitors in dedifferentiated endometrial carcinoma and other cBAF-disrupted cancer types.

  Study EGAS50000001004

• Longitudinal Single-cell Genomic Analysis of Initial and Recurrent Meningioma

  This study investigates the genomic evolution of meningioma through single-cell whole genome sequencing analysis of paired tumor samples. We analyzed tumor tissues from initial and recurrent meningiomas from the same patients to understand clonal evolution and tumor progression. The research aims to characterize copy number alterations and genomic heterogeneity at single-cell resolution across different time points of tumor development.

  Study EGAS50000000860

• metastatic uveal melanoma tumour biopsies

  Tumour biopsies were obtained from uveal melanoma patients pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Study EGAS50000000864

• Clonal hematopoiesis in metastatic urothelial and renal cell carcinoma

  This study aimed to determine the prevalence and clinical relevance of clonal hematopoiesis in metastatic urothelial and renal cell carcinoma.

  Study EGAS50000000870

• A Comprehensive Genetic Study of Classical Hodgkin Lymphoma Using Circulating Tumour DNA

  This study on classical Hodgkin lymphoma (cHL) used advanced methods to analyse circulating tumour DNA (ctDNA) in 297 cases, offering insights into its genetic landscape and linking it to disease pathophysiology and clinical progression. Key findings include the identification of whole genome duplication as a predictor of poor chemotherapy response. Additionally, a highly recurrent somatic expression quantitative trait locus of the BCL6 gene was discovered, implicating regulatory mutations in cHL pathophysiology and highlighting BCL6 as both a vulnerability and therapeutic target. Consensus clustering identified two cHL subtypes distinguished by the underlying mechanisms of genetic instability, rather than by specific genetic mutations or EBV infection. The study also linked the number and clonality of neoantigens with tumour microenvironment and response to checkpoint blockade. Finally, our results suggested ctDNA analysis as a tool to distinguish ambiguous PET/CT-positive lesions persisting after treatment, aiming to reduce unnecessary medical interventions.

  Study EGAS50000000873

• Bone marrow breakout lesions act as key sites for tumor-immune cell diversification and exhaustion in multiple myeloma

  Multiple myeloma is a disease characterized by the expansion of cancerous plasma cells in the bone marrow. The bone marrow microenvironment plays a pivotal role in supporting myeloma growth and modulating tumor immunity. As the disease progresses, myeloma cells may become independent of the bone marrow environment, leading to extramedullary disease associated with poor prognosis. However, the early processes associated with bone marrow independence and its implications for disease and immune control remain poorly understood. Here, we employed comprehensive single-cell and spatial mapping to identify the disruption of the cortical bone and subsequent expansion of myeloma cells in breakout lesions as a key event in multiple myeloma pathogenesis and tumor immunity. Breakout lesions harbor an adapted niche and a unique immune microenvironment conferred by sustained immune-tumor interactions. In particular, tumor-reactive T cells with a highly exhausted phenotype, alongside unique NK cell and macrophage subtypes, specifically expanded in breakout lesions. Spatially-resolved genomic, transcriptomic and cellular analyses uncovered extensive intra-lesion heterogeneity, suggesting a divergent co-evolution of genomic variation and locally confined T cell responses in distinct subregions. Ultra-high plex imaging revealed that tumor-reactive T cells, together with other immune-regulatory cells and dendritic cells, co-expand and exhaust upon sustained tumor interactions in locally confined immune islands. In contrast, immune-regulatory macrophage and NK cell subsets operate spatially separated within myeloma cell deserts. Jointly, our analyses uncover bone marrow breakout lesions as a hotspot for tumor-immune cell interactions, diversification and exhaustion, representing a key event in myeloma pathogenesis with significant therapeutic implications.

  Study EGAS50000000304

• Genetic and Microenvironmental Analysis of Peripheral T-cell Lymphoma

  This study enrolled 129 patients diagnosed with PTCL, comprising 94 cases of nTFHL and 35 cases of PTCL-NOS. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) were performed using DNA and RNA of sufficient quality extracted from their tumor specimens. WES was conducted for all 129 cases, while RNA-seq was performed on 57 tumor samples.

  Study EGAS50000001258

• Identification of putative multiple myeloma (MM) susceptibility genes

  We sought to identify novel MM susceptibility genes using a collection of families with multiple cases of MM/MGUS, including 189 affected individuals from 40 families, and index cases from an additional 88 families, along with 170 early-onset (EO) MM cases (≤ 55 years). We analyzed a total of 347 affected individuals using whole exome (N=321) and whole genome (N=26) sequencing. Samples were identified and collected through nation-wide efforts in France, Sweden and Greece. We focused on rare (MAF<0.5%) germline protein truncating and likely deleterious missense variants in genes harboring variants in at least two families showing variant-disease segregation, and in additional index (≥2) and/or early-onset (≥2) cases.

  Study EGAS50000001259

• SDR-seq_06_BCL

  Multiomic targeted scDNA-scRNA-seq (SDR-seq) of primary B-cell non-Hodgkin lymphomas. Aim is to link genomci variants to gene expression in single cells. Profiled two follicular lymphoma (FL) primary patient samples and one germinal center subtype diffuse large B-cell lymphoma (GCB) primary patient sample.

  Study EGAS50000000374