5495 results for "*oma"

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• Molecular Characterization of Large Cell Neuroendocrine Carcinoma of the Lung by Multilayered Omics Analysis

  Large cell neuroendocrine carcinoma (LCNEC) is a rare lung cancer type with a very poor prognosis. The underlying molecular features remain unclear. Here, we conducted a multi-omics analysis of 27 LCNEC cases along with 7 small cell lung carcinoma and aimed to propose new classification by extracting genomic and transcriptomic features in LCNEC, leading to the elucidation of the therapeutic approaches.

  Study JGAS000832

• Genetic, epigenetic and fragmentomic profiling of plasma cell-free DNA in cancer patients

  The primary goal of the study is to explore the temporal changes in cfDNA profiles in liver cancer patients undergoing therapeutic treatment. Serial blood collection and plasma cfDNA analysis were performed in patients with liver cancer, including patients with primary hepatocellular carcinoma, or those with secondary liver metastasis. Various molecular features of cfDNA were studied, including tumor fraction, epigenetic and fragmentomic analysis.

  Study EGAS50000002022

• Ex vivo therapy-driven selection of glioblastoma stem-like cells models resistance evolution

  Glioblastoma (GBM) remains lethal, creating an urgent need for experimental models of therapy- specific resistance evolution. Within-patient GSC models were developed by parallel ex-vivo selection under temozolomide (TMZ-GSC) or ionizing radiation (IR-GSC), alongside untreated controls (CTRL- GSC). • O6-methylguanine-DNA methyltransferase (MGMT) expression was confirmed as a determinant of primary TMZ resistance and was maintained during GSC evolution. • In MGMT-negative GSCs, primary TMZ sensitivity evolved into stable secondary resistance through mismatch-repair gene inactivation, recapitulating patient findings, or was retained along with a newly identified drug-tolerant phenotype. • Primary radioresistance was commonly observed, while its further evolution was associated with more efficient DNA double-strand-break repair and enrichment of homologous- recombination and checkpoint-control transcriptional programs. • In GSCs emerging after either TMZ or IR, broad transcriptional patient-specific programs and classification-relevant subtypes were largely preserved. • Across treatments, GSC evolution was accompanied by shared genome-maintenance and mitotic chromosome-segregation transcriptional programs and increased RTK expression and activity, collectively promoting recovery after genotoxic stress.

  Study EGAS50000002011

• Dataset related to ""Ex vivo therapy-driven selection of glioblastoma stem-like cells models resistance evolution"

  RNA-seq and NGS target panel dataset related to "Ex vivo therapy-driven selection of glioblastoma stem-like cells models resistance evolution"

  Dataset EGAD50000002898

• The Precision Medicine in Liver Cancer across an Asia-pacific NETwork (PLANET) – HCC recurrence cohort

  Hepatocellular carcinoma (HCC) is a highly fatal cancer marked by significant intra-tumor heterogeneity (ITH). Given 50% to 70% of HCC patients experience recurrence, understanding the origins and progression of recurrence is crucial. To address this, we assembled a multi-sector, paired HCC recurrence cohort of 24 patients, including comprehensive whole genome sequencing and transcriptome samples. Through this longitudinal cohort, we aimed to trace the origins of recurrence and identify molecular features associated with early recurrence. These insights may improve predictions of early HCC recurrence and inform potential therapeutic strategies.

  Study EGAS50000000869

• Single-nuclei RNAseq of normal human choroid and uveal melanoma

  Single-nuclei RNAseq of normal human choroid and uveal melanoma

  Study EGAS00001004955

• Single-nuclei RNAseq of normal human choroid and uveal melanoma

  Single-nuclei RNAseq of normal human choroid and uveal melanoma. Libraries were prepared using the Chromium Single Cell 3' Reagent Kits v3,. Paired-end libraries were sequenced on a NovaSeq X instrument (Illumina).

  Dataset EGAD50000002941

• A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

  Abstract: Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. We identify that glioblastoma heterogeneity is driven by spatially-patterned transitions of cancer cells from developmental-like states towards those defined by a glial injury response and hypoxia. This cancer cell trajectory regionalizes tumours into distinct tissue niches and manifests in a conserved manner across tumours as well as genetically distinct tumour subclones. Moreover, using a new deep learning framework to jointly map cancer cell states and clones in situ, we show that tumour subclones are finely spatially intermixed through glioblastoma tissue niches. Finally, we show that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments. Our findings define a stereotyped trajectory of cancer cells in glioblastoma and unify glioblastoma tumour heterogeneity into a tractable cellular and tissue framework.

  Dataset EGAD00001015516

• Transcriptional alterations induced by BET inhibitor and Omaveloxolone combination in acute myeloid leukemia cells

  Kasumi-1 and OCI-AML3 cells treated for 24h with BETi and Oma in hypoxia (1% O2) or normoxia (20% O2) were used for RNA extraction and hybridization on microarrays.

  Dataset EGAD00010002852

• 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

• IMMUcan Upstream SCCHN3 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients from the UPSTREAM trial, with squamous cell carcinoma of the head and neck (SCCHN) cancer which has spread (metastatic) or the tumour has come back after previous treatment (recurrent). Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001505

• IMMUcan SCCHN1 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with confirmed locally recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) who receive first-line treatment with immune checkpoint inhibitors (ICI) or ICI combined with chemotherapy. Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001533

• Whole-genome sequencing study of uveal melanoma

  Uveal melanoma is the most common primary intraocular cancer, characterized by metastasis-related mortality. Here, we explored whole-genome sequences from 40 primary uveal melanomas to illustrate the landscape of genomic mutations and investigate their association with prognosis.

  Study EGAS50000001603

• Evaluation Of The Role Of Tumor Mutational Burden As A Prognostic Biomarker In Follicular Lymphoma

  In this study, we have evaluated TMB through a 409-gene panel in 135 patients with FL or transformed FL (tFL) at presentation. We analyzed the association of TMB with prognosis and specific genetic alterations recurrent in FL, with the goal of identifying molecular markers that could improve prognostic assessment.

  Study EGAS50000001448

• A New CA19-9 Cut-Off Value Identifies Lewis Antigen Status and Refines Prognostic Stratification in PDAC

  This study investigates the clinical utility of serum CA19-9 levels in pancreatic ductal adenocarcinoma (PDAC), with a focus on identifying patients with Lewis antigen–negative status due to germline FUT3 variants. Using data from multicenter prospective cohorts in Taiwan, we analyzed CA19-9 classification, FUT2/FUT3 genotypes, and clinicopathological annotations. The goal of this study is to refine prognostic stratification and reduce false-negative interpretation of CA19-9 in PDAC patients. All participants provided informed consent, and the study was approved by the relevant institutional review boards.

  Study EGAS50000001575

• A Comparative Analysis of Illumina, Element Biosciences, and Ultima Genomics Platforms for Liquid Biopsy Applications in Pancreatic Ductal Adenocarcinoma

  This dataset contains ultra-deep targeted cfDNA sequencing from plasma samples of four patients with pancreatic ductal adenocarcinoma and 12 healthy controls. Libraries targeting 66 PDAC-associated genes were sequenced using Illumina NovaSeq X Plus, Element Biosciences AVITI, and Ultima Genomics UG 100 to compare platform performance for fragmentomic profiling and low-frequency variant detection.

  Study EGAS50000002029

• Count Matrix of Bulk RNA-sequencing of POLARIX Clinical Trial

  This dataset contains transcriptomic profiles (RNA-seq) derived from pretreatment formalin-fixed paraffin-embedded (FFPE) biopsies of treatment-naïve patients with Diffuse Large B-cell Lymphoma (DLBCL). These patients were enrolled in the POLARIX clinical study (NCT03274492), which compared the efficacy of Pola-R-CHP against R-CHOP. The data includes samples from the Pola-R-CHP arm (n = 331) and R-CHOP arm (n=334). These data were used in identifying lymphoma immune infiltration patterns.

  Dataset EGAD50000002479

• Whole-exome and RNA-seq sequencing of HCC of metastatic and de novo origin

  Multifocal hepatocellular carcinoma (mfHCC) arises via intrahepatic metastasis (IM) or multicentric occurrence (MO), We performed whole-exome and RNA-sequencing of 76 tumor biopsies from 22 HCC patients to determine their evolutionary origins.

  Study EGAS50000002057

• Raw sequencing data from a phase 2 trial of dasatinib in patients with relapsed/refractory nodal T-follicular helper cell lymphoma

  De-identified raw sequencing data, including scRNA-seq data from peripheral blood samples, snRNA-seq data from tumor tissues, and bulk RNA-seq data from tumor tissues.

  Study EGAS50000002081

• Comprehensive Characterization of Early Relapse and End-Stage Relapsed Refractory Multiple Myeloma (HIPO K08K/H067/H021+nonHIPO)

  Study EGAS00001007469

• RNA-sequencing of HCC of metastatic and de novo origin

  Dataset consists of tumors and matched non-tumor livers from 22 patients with multifocal hepatocellular carcinoma. Tissues were obtained from at least two distinct tumor nodules undergoing liver biopsies. Note: refer to the supplementary table of the manuscript for patient IDs and further clinical data.

  Dataset EGAD50000002957

• Whole-exome sequencing of HCC of metastatic and de novo origin

  Dataset consists of tumors and matched non-tumor livers from 22 patients with multifocal hepatocellular carcinoma. Tissues were obtained from at least two distinct tumor nodules undergoing liver biopsies. Note: refer to the supplementary table of the manuscript for patient IDs and further clinical data.

  Dataset EGAD50000002958

• Follicular Lymphoma Whole Genome and Transcriptome Sequencing

  Study EGAS00001006646

• Genomic and immune signatures predict clinical outcome in newly diagnosed multiple myeloma treated with immunotherapy regimens

  Study EGAS00001007404

• 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