4984 results for "*oma"

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• Longitudinal analysis of bone marrow heterogeneity reveals the co-evolution of malignant B cells and their T-cell niche supporting follicular lymphoma persistence

  Follicular Lymphoma (FL) is an indolent lymphoid malignancy characterized by cycles of remission and relapse, reflecting the inability of current therapies to fully eradicate tumor cells. Our hypothesis is that rare cancer precursor/persister cells (CPCs) evade treatment by homing to a protective tumor microenvironment, particularly within the bone marrow (BM), and/or by adopting specific cellular states, and form a rare reservoir of residual cells seeding lymphoma recurrence. To adress this, we collected paired BM samples at diagnosis and one year post-therapy from a clinical trial (FLIRT trial, NCT02303119) and applied multi-modal single-cell analysis to dissect the transcriptomics determinants of rare drug-tolerant persister cells and their surrounding T-cell niche.

  Study EGAS50000001295

• Multiplexed biomarkers dynamically detect heterogeneous residual neuroblastoma cell clone activity in the bone marrow niche

  Our objective was to develop a patient-specific, genomics-informed minimal residual disease (MRD) monitoring strategy for pediatric high-risk neuroblastoma using individualized multiplexed mediator-probe PCR (MP-PCR) assays. Tumor-specific somatic mutations or structural variants were identified through hybrid-capture panel sequencing. We examined tumor material from 8 patients, including 11 primary tumor samples, 3 of which represent spatially distinct primary tumor samples and 2 samples obtained at relapse. Provided are FASTQ data files, bam and bambai files, as well as breakpoint spanning and encompassing read (enspan) bam and bambai files. Sequencing bam data files are aligned to GRCh37.p13 reference genome (processed). Sequencing data were aligned to the GRCh37.p13 reference genome and processed using validated pipelines.

  Study EGAS50000001581

• Osteosarcoma 3D patient derived cultures to test genome-informed personalized treatment options; a feasibility study

  Background: Improving osteosarcoma treatment beyond conventional (neo)adjuvant chemotherapy and resection remains challenging. An urgent need for novel therapeutic options, particularly personalized and targeted approaches, has emerged due to high inter-patient molecular heterogeneity. A lack of representative in vitro and in vivo models impedes therapeutic development, therefore we aimed to create 3D in vitro long term culture models directly from patient material. Methods: Tumour cells from seven osteosarcoma patients were propagated in monolayer or collagen hydrogels, while whole-exome sequencing of corresponding primary tumour tissue was performed to identify potential drug targets. Established cultures were subsequently used to assess efficacy of the identified personalized treatment options. Results: Three out of seven hydrogel cultures harboured the same genetic alterations as the corresponding primary tumours. Among these, the L6565 patient line exhibited homozygous CDKN2A loss with retained Rb expression, rendering tumour cells sensitive to CDK4/CDK6 inhibition via palbociclib. This patient line was used to evaluate genome-informed therapy and to compare cell culture models of increasing complexity. Our findings demonstrate feasibility of establishing long-term patient-derived osteosarcoma cultures with a success rate of 14%. Tumour heterogeneity was reflected in advanced culture methods producing more variability in treatment response. Conclusion: These results highlight the potential of genome-informed therapies in osteosarcoma and the importance of refining culture techniques to enhance translational research and therapeutic outcomes.

  Study EGAS50000001583

• Single-cell Analysis of Neoplastic Plasma Cells Identifies Myeloma Pathobiology Mediators and Potential Targets

  Multiple myeloma is a clonal plasma cell (PC) dyscrasia that arises from precursors and has been studied utilizing approaches focused on CD138+ cells. By combining single-cell (sc)RNA- with scB-cell receptor (BCR)-sequencing, we differentiate monoclonal/neoplastic from polyclonal/normal PCs, and find more dysregulated genes, especially in precursor patients, than by analyzing bulk PCs. To determine if this approach can identify oncogenes that contribute to disease pathobiology, MAD2L1 and MAT2A are validated as targets with drug-like molecules that suppress myeloma growth in pre-clinical models. Moreover, functional studies show a role of LAMP5, which is uniquely expressed in neoplastic PCs, in tumor progression and aggressiveness via interactions with c-MYC. Finally, a monoclonal antibody recognizing cell-surface LAMP5 shows efficacy as an antibody-drug conjugate and in a chimeric antigen receptor-guided T-cell format. These studies provide additional insights into myeloma biology and identify potential targeted therapeutic approaches that can be applied to reverse myeloma progression.

  Study EGAS50000000802

• Molecular profiling reclassifies adult astroblastoma into known and clinically distinct tumor entities with frequent MAPK pathway alterations

  Study EGAS00001003798

• PTEN homozygous deletion is a negative prognostic factor in Tumor Treating Fields-treated glioblastoma, IDH wildtype patients

  This study investigates genomic determinants of outcome in glioblastoma, IDH-wildtype patients treated with Tumor Treating Fields (TTFields) in addition to standard radiochemotherapy. Tumor tissue from primary glioblastoma at initial diagnosis was profiled using the Illumina TruSight Oncology 500 (TSO500) targeted sequencing panel to characterise somatic alterations. The overarching goal is to provide exploration of genomic determinants of survival and treatment response in TTFields-treated glioblastoma, IDH-wildtype.

  Study EGAS50000001469

• Small molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma (RNAseq dataset)

  Study EGAS00001004748

• Cell-free DNA methylome and fragmentome analysis for disease relapse monitoring in patients with Ewing Sarcoma

  We conducted whole-genome and methylome sequencing of cfDNA from 87 serial samples of 23 patients with EwS and 3 patients with CIC-rearranged sarcoma (CIC). With EwingSign, a new machine learning model, we identified EwS or CIC in a test set for 11 out of 16 patients at diagnosis and 15 out of 18 clinically confirmed relapse events. 0 out of 24 non-cancer controls were detected positive with EwingSign.

  Study EGAS50000001415

• A single-cell atlas of meningioma.

  In this study, we examined the breadth of cell types and states in meningioma using the largest single-cell cohort of meningioma by generating more than 7.5 million total cells from meningioma and surrounding dura, profiled using single-nuclear RNA sequencing and high-resolution spatial transcriptomics.

  Study EGAS50000001589

• Discovery and validation of an ancillary genomic test of malignancy for primary melanocytic tumors

  Background:Pathological diagnosis of melanocytic tumors can be difficult and prone to error. More accurate and reliable ancillary investigations than those currently available are required to improve diagnostic accuracy. Goals: (1) to generate a genomic model for distinguishing benign (nevi) from malignant (melanoma) melanocytic skin tumors, developed from a customized gene panel evaluated on a cohort of 250 nevi and melanomas. (2) To evaluate the performance of the genomic model in melanocytic tumors of uncertain diagnosis/behavior. Details: The cohort of 250 melanomas and naevi was split into a discovery set and a validation set. Our genomic model obtained an area under the curve of 95% in the discovery cohort and 96% for the validation cohort. Based on a Youden index threshold, the resulting classifier shows high specificity (>95% in the discovery and validation cohorts), with sensitivities >80% in the discovery and validation cohorts. Evaluation of the genomic model on a cohort of 110 melanocytic tumors identifies key driver mutations in agreement with the likely pathway of origin of the tumors. The probability of melanoma (p=0.02) from the genomic model was significantly associated with pathology-based estimates of malignancy for melanocytic tumors lacking pathway-defining genomic aberrations (conventional tumors). The genomic model identified 8/36 (22%) conventional tumors with unresolved malignancy to have a high probability of melanoma, with 7/8 of these cases showing negative/non-aberrant results with either fluorescent in-situ hybridization, PRAME and/or p16 immunostains. Furthermore, no evidence of malignant behavior based on the genomic model was seen in 4 conventional borderline tumors with more than 1 year follow-up. Conclusion: This genomic model can become a clinically useful ancillary tool that is highly specific for differentiating melanomas from nevi.

  Study EGAS50000000887

• Tumor Profiler Ovarian Study

  The Tumor Profiler Study is an observational trial combining a prospective diagnostic approach to assess the relevance of in-depth tumor profiling to support clinical decision-making with an exploratory approach to improve the biological understanding of the disease. Technologies used are digital pathology, targeted NGS, single-cell RNA, single-cell DNA, bulk RNA, bulk proteotyping, single-cell CyTOF, imaging mass cytometry, pharmacoscopy, 4i Drug Response Profiling, and cell-free DNA. These technologies were applied to 240 tumor samples collected over 3 years across three cancer indications: metastatic melanoma, metastatic epithelial ovarian cancer, and acute myeloid leukemia (AML). Here, we publish the scRNA and scDNA data of the ovarian cancer cohort.

  Study EGAS50000000885

• Raw RNA sequencing of hepatoblastoma PDX cell line HB-303-LEF

  Raw RNA sequencing of hepatoblastoma PDX cell line HB-303-LEF

  Study EGAS50000000928

• Mutational Profile in Newly Diagnosed Diffuse Large B-Cell Lymphoma: GAINED Study

  The GAINED study (NCT01659099) is a randomized phase 3 trial comparing obinutuzumab (G) to rituximab (R) in combination with ACVBP or CHOP14 induction, followed by PET-guided consolidation. This post-hoc analysis focuses on primary mediastinal B-cell lymphoma (PMBL) patients, confirmed through expert pathological review and characterized using gene-expression profiling (GEP) and Next-Generation Sequencing (NGS)

  Study EGAS50000000929

• High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Molecular characterization of high-grade B-cell lymphoma, not otherwise specified (HGBCL-NOS), is hindered by its rarity, evolving definition, and poor diagnostic reproducibility. To address this challenge, we analyzed 92 HGBCL-NOS tumors collected across Lymphoma/Leukemia Molecular Profiling Project sites. These tumors were profiled using whole-genome sequencing (WGS) or whole-exome sequencing (WES) to identify somatic mutations, WGS or low-pass WGS to detect copy number alterations, targeted capture sequencing to assess MYC and BCL2 structural variants, and RNA sequencing. The genetic features of HGBCL-NOS were compared to those of diffuse large B-cell lymphoma (DLBCL-NOS) and EBV-negative adult Burkitt lymphoma (BL). DLBCL-NOS tumors underwent targeted capture sequencing using a panel of 125 genes recurrently mutated in aggressive B-cell lymphomas. BL biopsies were drawn from the Burkitt Lymphoma Genome Sequencing Project and had available WGS (dbGaP Study Accession: phs000527.v18.p6).

  Study EGAS50000000932

• Optimized large-scale longitudinal biorepository of gastroesophageal adenocarcinoma patient-derived organoids

  To enable translation studies we created patient derived models to assess biomarkers, target validation, and patient response. To evaluate that the PDOs retain the genomic characteristics of the primary tumours we performed (WES) sequencing of 11 matched primary tumours and their matched organoid samples (total n=22). Libraries were sequenced using Illumina NovaSeq technology. Reads were aligned with BWA alignment to hg38. Files were processed following GATK best practices (version GATK 4.2.3.0). Variants were called using Mutect2. The dataset contains the alignmnent files (.bam) and the called mutations (.vcf).

  Study EGAS50000001614

• Genomic landscape of poorly differentiated thyroid carcinoma

  Poorly differentiated thyroid carcinoma (PDTC) is a rare and aggressive subtype of thyroid cancer with limited molecular characterization. This study aims to define the somatic mutational landscape of PDTC using whole-genome sequencing. Paired tumour and matched normal blood samples were collected from six patients undergoing surgery. The overarching goal is to identify recurrent mutations, structural variants, and other genomic alterations associated with tumour aggressiveness and poor clinical outcomes.

  Study EGAS50000001134

• RNA sequencing of untreated head and neck cancer patient-derived xenografts (PDXs) and matched patient tumor tissue.

  RNA sequencing was performed on untreated patient tumor tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC). The aim of this analysis was to characterize the transcriptional landscape of the tumors in the in vivo setting.

  Study EGAS50000001595

• Phylogenetic analysis of paired breast carcinomas identifies genetic events associated with clonal recurrence and invasive progression

  Development of ipsilateral breast carcinoma following diagnosis of breast ductal carcinoma in situ (DCIS) has been assumed to represent recurrence of the primary tumour. However, this may not be the case and it is important to know how often recurrences are new tumours. Ipsilateral primary-recurrence pairs (n=78) were sequenced to test their clonal relatedness. Shared genetic events were identified from whole exome sequencing (n=54 pairs) using haplotype-specific copy number and phylogenetic analysis. The remaining pairs were sequenced by a targeted panel or low-coverage whole genome sequencing. We included 32 non-recurrent DCIS to compare recurrent and non-recurrent disease. We found that 7% of DCIS recurrences were non-clonal by whole exome sequencing, indicative of a new breast carcinoma. Lower resolution methods detected a higher non-clonality rate (29%). Comparing primary DCIS with their recurrences found that evolution of DCIS to invasive disease was associated with increased ploidy and copy number events. TP53 mutations were enriched in DCIS with clonal recurrence compared with non-recurrent DCIS. Our results verify that de novo “recurrent tumours” of independent origin occur in patients who may be at high risk. (https://www.biorxiv.org/content/10.1101/2024.05.19.594731v2.full)

  Study EGAS50000001298

• 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

• Common origin and somatic mutation patterns of composite lymphomas and leukemias

  When two lymphomas occur concurrently or sequentially in a patient, it is a major question whether they derive from the same lymphocyte or hematopoietic precursor cell or developed independently. We studied four composite classic Hodgkin lymphomas (HL) and other mature B-cell lymphomas, and two composite mature B- and T-cell neoplasias by whole exome sequencing (WES) and analyzed shared somatic mutations in the lymphomas of these clonally related composite lymphomas, indicating their derivation from a common, pre-malignant precursor. Most identified mutations were restricted to one or the other of these lymphomas, likely explaining how distinct lymphomas developed from a common ancestral B cell. In the two B-cell/T-cell lymphoma cases, and a composite clonally unrelated HL/chronic lymphocytic leukemia, the lymphoma partners did not share any somatic mutations. In three cases, we identified potentially oncogenic variants also in cells serving as constitutional controls.

  Study EGAS50000001017

• WES of sorted B lineage cells from patients with plasma cell neoplasms

  Whole-exome sequencing (WES) was conducted on cell populations isolated from each patient—diagnosed with either multiple myeloma (MM) or light-chain amyloidosis (AL) —including CD34⁺ hematopoietic progenitors, B-cell precursors, mature B cells, normal plasma cells, and clonal plasma cells. In the control cohort of healthy adults, the same target cell populations were analyzed, with the exception of clonal plasma cells, which were absent.

  Study EGAS50000001498

• WGS of Roma (Romani/Rroma) and European/Romanian individuals from Romania

  Study EGAS00001003624

• 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

• WES data from tumors and matching controls collected from 11 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates the progression of translocation renal cell carcinoma (tRCC) based on Whole Exome Sequencing (WES) data from 11 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. Tumor samples and their matched normal DNA were sequenced on the Illumina platform.

  Study EGAS50000000126

• Visium CytAssist Spatial Gene Expression analysis for FFPE glioblastoma samples

  This study used spatial transcriptomics to investigate gene expression patterns in FFPE glioblastoma tumor samples from four patients.

  Study EGAS50000001242