8213 results for "canc*"

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• PARADIGM: Combined ctDNA and serum PSA for dynamic monitoring of metastatic prostate cancer starting first-line treatment

  The prognosis of newly-diagnosed metastatic prostate cancer is highly variable. The PARADIGM prospective cohort study evaluated predictors of survival in blood collected at the start of each of the first six treatment cycles from 114 high-volume metastatic patients starting androgen deprivation therapy combined with docetaxel or an androgen receptor pathway inhibitor.

  Study EGAS50000001357

• 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

• MIBC NAC2020 cohort RNA sequencing

  The dataset contains RNA sequencing data from N=48 transurethral resections of bladder tumours (TURBTs) from N=48 patients with muscle-invasive bladder cancer. All TURBTs originate from formalin-fixed paraffin embedded tissue. We used the Illumina TruSeq RNA exome kit, previously known as the TruSeq RNA Access Library Prep Kit. This kit converts total RNA into template molecules of known strand origin, followed by sequence-specific capture of coding RNA. All samples were run in an Illumina NovaSeq6000 instrument. Paired FASTQ files from all 48 patients are provided.

  Study EGAS50000000741

• 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

• Patient-specific CAR T cell barriers in colorectal cancer identified by phenotypic screening of tumor organoids

  This study used CAR-T cells in coculture with patient-derived organoids to model patient-specific responses to CAR-T cell therapy. Heterogeneous killing efficiencies together with downstream analysis revealed tumor-intrinsic drivers of CAR-T resistance. In addition, drug library screens for synthetic lethality identified possible targets for combinatorial treatment strategies.

  Study EGAS50000002034

• DKTK Organoid Platform: A multicentric living biobank for functionalizing patient-derived organoids and model clinical outcomes

  To enable the generation of harmonized and well annotated PDTO cohorts across national institutions, the German Cancer Consortium (DKTK) has established the Strategic Initiative Organoid Platform. For the MetPredict cohort, individual PDTOs were generated from spatially distinct liver metastases of colorectal cancer. To study the molecular inter-metastatic heterogeneity, samples were submitted to whole exome sequencing.

  Study EGAS50000002045

• Bladder Cancer Genomics Data Access Committee – Erlangen–Bonn Collaboration

  The Bladder Cancer Genomics Data Access Committee (DAC) represents the collaborative bladder cancer research program between the Institute of Pathology, Universitätsklinikum Erlangen; the Department of Urology and the Institute of Experimental Oncology, Universitätsklinikum Bonn. The DAC comprises representatives from each participating institution, including Prof. Dr. med. Dr. rer. biol. hum. Markus Eckstein (Universitätsklinikum Erlangen) and PD Dr. med. Niklas Klümper (Universitätsklinikum Bonn). The committee is responsible for reviewing and approving requests for access to controlled-access bladder cancer genomic and associated clinical datasets generated through this collaboration deposited in the European Genome-phenome Archive (EGA). The committee reviews requests from qualified researchers to determine whether the proposed use of the data is consistent with the participants' informed consent, applicable ethical approvals, institutional data access policies, and relevant data protection regulations before granting access.

  Dac EGAC50000001118

• Bulk RNA Sequencing of 112 Bladder Cancer Tumor Samples Using Lexogen QuantSeq 3′ mRNA-Seq

  Bulk RNA sequencing dataset comprising tumor samples from 112 bladder cancer patients. Gene expression profiling was performed using the Lexogen QuantSeq 3′ mRNA-Seq library preparation protocol, which generates strand-specific 3′ end transcript libraries for digital gene expression quantification. The dataset provides transcriptomic profiles for molecular characterization of bladder cancer and supports studies of tumor biology, biomarker discovery, and clinical outcome associations.

  Study EGAS50000002032

• Raw Bulk QuantSeq 3′ mRNA Sequencing Data from 137 Bladder Cancer Tumor Samples

  This controlled-access dataset comprises raw single-end FASTQ files generated from 137 bladder cancer tumor samples collected from 112 patients using the Lexogen QuantSeq 3′ mRNA-Seq protocol on the Illumina NovaSeq 6000 platform. Access is governed by the Bladder Cancer Genomics Data Access Committee (DAC) and the associated controlled-access policy.

  Dataset EGAD50000002920

• Processed Gene-Level Expression Counts from 137 Bladder Cancer QuantSeq 3′ RNA-seq Samples

  This controlled-access dataset contains processed gene-level expression counts generated from 137 bladder cancer tumor samples collected from 112 patients. Gene expression quantification was performed using the nf-core/rnaseq workflow with Salmon, and transcript-level abundance estimates were aggregated to gene-level counts. Access is governed by the Bladder Cancer Genomics Data Access Committee (DAC) and the associated controlled-access policy.

  Dataset EGAD50000002921

• Clinical Annotation and Survival Metadata for 137 Bladder Cancer Samples

  This controlled-access dataset contains curated clinical metadata associated with 137 bladder cancer tumor samples obtained from 112 patients. Variables include patient demographics, clinician-assigned phenotype, overall survival (OS), progression-free survival (PFS), and corresponding event status variables. Access is governed by the Bladder Cancer Genomics Data Access Committee (DAC) and the associated controlled-access policy.

  Dataset EGAD50000002922

• High grade serous ovarian cancer germline exome sequencing

  This cohort includes matched germline samples from the same patient cohort. Germline DNA was isolated from whole blood and normal tissue for whole exome sequencing.

  Study EGAS50000001730

• High grade serous ovarian cancer tumor exome sequencing

  Whole exome sequencing data generated from 25 human high grade serous ovarian cancer (HGSOC) specimens. These data were used to characterize somatic mutations, copy number alterations, and genomic features. Raw sequencing data are provided as BAM files.

  Study EGAS50000001731

• 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

• G4SCOPE identifies sequence features and epigenetic contexts of chromatin G-quadruplexes

  Cancer-associated epigenetic remodeling involves both DNA secondary structures and covalent cytosine modifications, yet predicting chromatin-constrained G-quadruplex (G4) folding remains challenging. Here, we develop G4SCOPE, a multi-task deep learning framework that predicts G4 occupancy and quantitative CUT&Tag signal directly from DNA sequence in isogenic human breast epithelial cells. Trained across wild-type, TP53-deficient, TP53/BRCA1-deficient and TP53/BRCA2-deficient backgrounds, the model integrates convolutional motif learning with transformer-based self-attention to capture local motifs and broader contextual sequence features without auxiliary epigenomic inputs. It distinguishes chromatin-associated G4s from GC-matched loci with in vitro G4-forming potential, captures quantitative variation in local CUT&Tag signal, and performs consistently across the four breast epithelial genotypes. Independent application in K562 cells further supports the portability of the framework to a distinct cellular context. Model-derived G4 representations also separate loci with distinct local 5-methylcytosine and 5-hydroxymethylcytosine profiles. Together, these results show that DNA sequence can predict chromatin G4 occupancy and quantitative CUT&Tag signal, and that the learned representations reflect differences in local cytosine-modification state.

  Study EGAS50000002094

• BCAC TIIC Data

  Data on spatially-resolved tissue infiltrating immune cells (TIICs) from 17,265 breast cancer patients of European descent, from studies participating in the Breast Cancer Association Consortium, together with linked clinical data.

  Study EGAS50000001477

• RNA sequencing to characterize ALK

  ALK fusions are present in 3–5% of patients with non-small cell lung cancer (NSCLC). These fusions promote ligand-independent dimerization, resulting in constitutive activation of downstream signaling pathways, including RAS–MAPK and PI3K–AKT3. Here, we report the identification and characterization of the ALK in biopsies from a patient with ALK-positive NSCLC progressing on first-line lorlatinib

  Study EGAS50000001779

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

  Study EGAS00001007469

• H021-Master Umbrella study2 (not to be released)

  Study EGAS00001005145

• Cord blood DNA duplex sequencing libraries using deepDLP

  As part of the DeepClone protocols paper we used three cord blood samples to validate the error rate of deepDLP duplex library preparation method. The FASTQs shared below correspond to these three cord blood samples. With this data we concluded that the error rate of the technology is between 1 and 3x10-8 errors per sequence basepair.

  Study EGAS50000002002

• High Grade Serous Ovarian Cancer Whole Exome Sequencing

  Whole exome sequencing (WES) was performed on genomic DNA (50–200 ng) extracted from high-grade serous ovarian cancer (HGSOC) tumor tissue and matched buffy coat or normal tissue. DNA was sheared using a Covaris E220 system to generate fragments of approximately 150–200 bp. Sequencing libraries were prepared using the Agilent SureSelect XT Low Input Library Preparation Kit with unique dual indices. Tumor libraries were enriched using a custom SureSelect V6 + UTR + OneSeq LowRes capture probe set, while germline libraries were enriched using the Agilent SureSelect Human All Exon V6 capture kit supplemented with custom probes. Libraries underwent initial quality control sequencing on the Illumina MiSeq platform, followed by pooled sequencing on the Illumina NovaSeq 6000 using a 300-cycle kit. Archived here are the BAM files for each sample.

  Dataset EGAD50000002488