5272 results for "*oma"

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• Single-cell multi-omic analysis of control and glioblastoma samples from the brain and border regions.

  Single-cell RNA-sequencing. Some samples were analyzed using CITE-Seq and samples were multiplexed and run on the same 10X reaction

  Dataset EGAD50000000045

• Methylome profiling of Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) and a patient derived cell-line model

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1 using the twist human methylome panel.

  Dataset EGAD50000000040

• Evaluating potential drug candidates for the treament of Henamgiopericytoma on patient derived cell line models

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1. Potential drug candidates that could be repurposed for the treatment of SFT/HPC were screened. Screening was performed through RNA-Seq

  Dataset EGAD50000000039

• Whole genome sequencing of Sinonasal hemangiopericytoma and patient derived cell line model

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. In this study, a novel SFT/HPC was characterized using whole genome sequencing.

  Dataset EGAD50000000038

• Efficacy of two different FGFR-inhibitors in a patient with extrahepatic cholangiocarcinoma harboring an FGFR2 mutation

  Cholangiocarcinomas (CCAs) is a type of cancer with few effective systemic therapies. Elucidation of the molecular landscape of the disease from genomic studies based on next generation sequencing (NGS) has contributed to the introduction of new targeted therapies. One of these treatments consists of a class of small molecules that target members of the FGFR family of receptor tyrosine kinases. These drugs are effective and have been approved for cholangiocarcinomas with fusions or rearrangements of FGFR genes. In contrast, the role of these inhibitors in cholangiocarcinomas with mutations in FGFR genes is less well defined. We report here a patient with a cholangiocarcinoma bearing a FGFR2 p.Ser252Trp mutation. The patient was treated with two different FGFR inhibitors, as the first caused ocular toxicity. She obtained clinical benefit from both. This case illustrates the efficacy of FGFR inhibitors on cholangiocarcinoma with specific point mutations. This is the first case to report the clinical benefit of these drugs in FGFR2 p.Ser252Trp mutation. Clinical benefit can be sustained, as seen in our patient. Our case also shows that FGFR inhibitors-induced adverse effects, such as ocular toxicities, may not recur after re-challenge with an alternative drug of the same class.

  Dataset EGAD50000000021

• Methylation Array data for: Three-dimensional patient-derived models of glioblastoma retain intra-tumoral heterogeneity

  3 sets of matched patient-derived-organoids (PDOs),  -neurospheres (PDNs), and parent glioblastoma tissue (9 samples total) underwent methylation array analysis. 200ng of each sample DNA extracted via a commercial kit (Qiagen) and loaded onto the Illumina EPIC v2.0 array. Data is provided as raw red and green .idat files.

  Dataset EGAD00010002745

• N2M2 methylation array data

  Methylation profiling of 228 samples, using the approach described in "Molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed glioblastoma without MGMT promoter hypermethylation (N2M2/NOA-20 phase I/IIa umbrella trial)"

  Dataset EGAD00010002747

• Methylation profiling of CDS and ES tumor samples

  Methylation profiling of 9 CDS and ES tumor samples, using the approach described in "Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target

  Dataset EGAD00010002760

• EpS_methylation_850K

  Methylation profile (array data using EPIC_850K) from tumour samples (epithelioid sarcoma)

  Dataset EGAD00010002571

• OncoScan SNP data set for systemic follicular lymphoma (sFL)

  122 unpaired initial tumor samples (122 FFPE samples) of sFL patients measured with OncoScan SNP microarrays, Affymetrix CEL intensity data file types (Thermo Fisher Scientific, Waltham, Massachusetts, USA)

  Dataset EGAD00010002592

• OncoScan SNP data set for localized follicular lymphoma (lFL)

  149 unpaired initial tumor samples (133/149 FFPE and 16/149 fresh frozen samples) of lFL patients measured with OncoScan SNP microarrays, Affymetrix CEL intensity data file types (Thermo Fisher Scientific, Waltham, Massachusetts, USA)

  Dataset EGAD00010002593

• Lymphoma_CN_Array

  CN Array samples from lymphoma patient tumours on Affymetrix platforms

  Dataset EGAD00010002235

• Myeloma methylation

  Myeloma methylation data

  Dataset EGAD00010002259

• RP1759 AYA sarcoma methylation array

  Raw methylation array data for tumor samples from patients with newly diagnosed, recurrent intermediate or high-grade sarcoma.

  Dataset EGAD00010002275

• NanoString Cancer

  RCC files of 17 Cartridges from metastatic melanoma

  Dataset EGAD00010002432

• Methylation profiling of sarcoma and TFCP2-rearranged rhadomyosarcoma samples

  Methylation profiling of 345 sarcoma and TFCP2-rearranged rhadomyosarcoma samples, using the approach described "Genomic, transcriptomic, functional, and mechanistic characterization of rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusions"

  Dataset EGAD00010002451

• Quantitative analysis of a novel DNA hypermethylation panel using bronchial specimen for lung cancer diagnosis

  The dataset includes IDAT raw files for 10 samples and the analyzed DMP file which describes the differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. The histological type of the five lung cancer cases is adenocarcinoma and squamous cell carcinoma.

  Dataset EGAD00010002465

• PDX_HTA2.0_Guergen2022

  GeneChip HTA 2.0 data of primary renal cell carcinoma (RCC) and RCC metastases related to Guergen et al, Front Oncol 12:2022 889789. Microarrays were normalized individually using the SCAN method from the R package SCAN.UPC (version 2.34.0). Probe sets were summarized on the Entrez GeneID level using the annotation provided by BrainArray (version 25).

  Dataset EGAD00010002392

• MB_450k_methylation

  450k methylation arrays of primary and relapse tumor of a single case of sonic hedgehog medulloblastoma with Li-Fraumeni syndrome

  Dataset EGAD00010002370

• Oncoscan CNV FFPE SNP-arrays (Affymetrix, Thermo Fisher Scientific) for the study "Molecular profiling of EBV associated diffuse large B-cell lymphoma"

  Dataset EGAD00010002363

• Methylation array data of thymic epithelial tumors (TC, NET, THYM)

  Methylation microarray data (Illumina 850K) of 52 thymic epithelial tumors. 13 patients with thymoma A and B, 32 thymic carcinoma (TC) and 7 neuroendocrine tumors of the thymus (NET).

  Dataset EGAD00010002355

• RCC_HTA2.0_Buettner2022

  GeneChip HTA 2.0 data of primary renal cell carcinoma (RCC) related to Buettner et al, Genome Med 2022. Microarrays were normalized individually using the SCAN method from the R package SCAN.UPC (version 2.26.0, R version 3.6.1). Probe sets were summarized on the Entrez GeneID level using the annotation provided by BrainArray (version 23).

  Dataset EGAD00010002353

• RCC_HTA2.0_Reustle2022

  GeneChip HTA 2.0 data of primary renal cell carcinoma (RCC) related to Reustle et al., Clin Transl Med 12:2022 e883. Microarrays were normalized individually using the SCAN method from the R package SCAN.UPC (version 2.26.0, R version 3.6.1). Probe sets were summarized on the Entrez GeneID level using the annotation provided by BrainArray (version 23).

  Dataset EGAD00010002352

• Quantitative Exploratory Proteomics Analysis of Glioblastoma in Initial and Recurrent Tumors

  Shotgun Proteomics; Glioblastoma samples from 11 patients were obtained at initial and recurrent tumor stages. Proteins were extracted, identified and quantified via tandem mass spectrometry based on a TMT isobaric labelling approach. Quatitative proteomics reveals 146 differentially abundant proteins using a patient-matched statistical modelling. Analysis of proteolytic processing reveals differential proteolytic patterns in recurrent tumors. Proteogenomics reveals the presense of 30 single-amino acid variants present in glioblastoma tumor and 1 of those as increased in recurrent tumor.

  Dataset EGAD00010002350

• Chordoma_methylation

  Chordoma tumors DNA methylation profiling by genome tiling array

  Dataset EGAD00010002338

• RCC_HTA2.0_Reustle2020

  GeneChip HTA 2.0 data of primary renal cell carcinoma (RCC) related to Reustle et al, Genome Med 12:2020 32. Preprocessing of microarray data was performed using Robust Multi-array Average (RMA).

  Dataset EGAD00010002323

• Methylation

  Illumina EPIC arrays Naevus Melanoma Spitz Case

  Dataset EGAD00010002312

• UK_RCC_GWAS

  Renal cell carcinoma (RCC) cases comprised adult patients with histologically proven RCC were collected through two sources within the UK. First, 856 cases from SORCE, a MRC collection of surgically treated RCC cases ascertained through UK clinical oncology centres. Second, 189 RCC cases collected through the ICR and Royal Marsden NHS Hospitals Trust. Cases included 590 clear cell carcinomas (CCCs), 42 papillary carcinomas (PCs), 33 chromophobe carcinomas (CCs) and 19 mixed or other histological subtypes. DNA was extracted from EDTA-venous blood samples using the conventional methods and quantified using PicoGreen (Invitrogen). Cases were genotyped using the Human OmniExpress-12 BeadChip according to the manufacturer's recommendations (Illumina Inc, San Diego, CA, USA). After strict QC, 944 cases were retained. Data provided in plink format. Controls used were data from the Wellcome Trust Case Control Consortium 2 (WTCCC2) 1958 birth cohort and the UK Blood Service Control Group (available as EGAS00000000028). 

  Dataset EGAD00010002310

• NPC genome-wide human SNP array data for HongKong population

  nasopharyngeal carcinoma genome-wide human SNP array data for 423 NPC cases and 573 controls

  Dataset EGAD00010002298

• NPC genome-wide human SNP array data

  nasopharyngeal carcinoma genome-wide human SNP array data for 4083 NPC cases and 4811 controls

  Dataset EGAD00010002296

• Set_of_human_mesenchymal_CSA

  51 DNA methylation arrays of human samples initially diagnosed as mesenchymal chondrosarcoma. Microdissection of the cartilage and/or the small round cell component from the same sample may have occurred. As mentioned in the sample descriptions, the diagnoses of four samples have been revised. Additional molecular investigations were conducted for a subset of samples as described in the related publication.

  Dataset EGAD00010002515

• SNP Array data for: Three-dimensional patient-derived models of glioblastoma retain intra-tumoral heterogeneity

  4 sets of matched patient-derived-organoids (PDOs),  -neurospheres (PDNs), and parent glioblastoma tissue (12 samples total) underwent SNP array analysis. 200ng of each sample DNA extracted via a commercial kit (Qiagen) and loaded onto the Global Screening Array v2.0 array. Data is provided as raw red and green .idat files.

  Dataset EGAD00010002744

• colorectal_epigenome

  Three different types of samples were used: 19 normal adjacent, 17 adenoma and 19 colorectal tumor tissue samples. This included 10 pairs of colorectal cancer and normal samples and 1 pair of adenoma-normal samples of the same patient. Tissue specimens were formalin-fixed paraffin-embedded (FFPE). DNA was isolated using the QIAamp FFPE Tissue kit (Qiagen, Hilden, DE) according to the manufacturer’s instructions. The processed DNA was run on the Illumina Human MethylEPIC® v1.0 BeadChip array.

  Dataset EGAD00010002726

• ISA Nutrition 2015

  Comprehensive data on lifestyle-related modifiable factors, sociodemographic, anthropometric, economic, biochemical, and genetic markers related to the occurrence of cardiometabolic diseases as part of the observational cross-sectional survey (2015 Health Survey of Sao Paulo with Focus on Nutrition (2015 ISA-Nutrition), a population-based study. Data of 805218 SNPs for 841 individuals was genotyped using the Axioma 2.0 Precision Medicine Research Array in the Thermo Fisher Scientific laboratory (Affymetrix Inc, Santa Clara, CA).

  Dataset EGAD00010002678

• MB_COMICS_Methylome

  Medulloblastoma (MB) is the most common malignant brain tumor in children. It is a neuroectodermal tumor located in the cerebellum. International consensus recognizes four distinct subgroups of MBs including Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4) with distinct molecular characteristics, prognoses, and mortality rates in patients. Here, we have compiled and evaluated a large international MB cohort for which we generated methylome data for 369 primary MB patient samples.

  Dataset EGAD00010002669

• A5_SDHB_PCPG_Methylation

  Illumina Infinium MethylationEPIC Array profiling of 93 pheochromocytoma and paraganglioma tumours with and a germline SDHB mutation

  Dataset EGAD00010002667

• Pleural_mesothelioma

  EPIC methylation data of pleural mesothelioma samples and healthy pleura samples

  Dataset EGAD00010002657

• Healthy_pleura

  EPIC methylation data of pleural mesothelioma samples and healthy pleura samples

  Dataset EGAD00010002656

• Illumina Infinium MethylationEPIC Array IDAT files generated from 11 glioma patient samples

  This dataset includes IDAT files from 6 IDH-mutant, 5 IDH-wild-type glioma patient samples of unmatched initial and recurrent timepoints profiled using the Illumina Infinium MethylationEPIC Array.

  Dataset EGAD00010002157

• Illumina BeadArray SNP arrays

  SNP measurement. Illumina BeadArray SNP arrays for the study "Molecular characteristics in Burkitt lymphoma over age groups"

  Dataset EGAD00010002137

• Genotype-Multiple-Myeloma-case

  Genome-Wide Human SNP Array 6.0 or the CytoScan HD array, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) now part of Thermo Fisher Scientific (Thermo Fisher Scientific, Inc.)

  Dataset EGAD00010002102

• SNP array karyotyping of upper urinary tract urothelial carcinoma

  Genome-wide copy number analysis of upper urinary tract urothelial carcinoma using GeneChip Human Mapping 250K Nspl

  Dataset EGAD00010002098

• Methylation array of upper urinary tract urothelial carcinoma

  Genome-wide methylation analysis of upper urinary tract urothelial carcinoma using Infinium MethylationEPIC BeadChip Kit

  Dataset EGAD00010002096

• A novel orthotopic patient-derived xenograft model of radiation-induced glioma following medulloblastoma

  DNA methylation arrays were performed to molecularly subtype these samples based on Capper D, Jones DTW, Sill M, et al. DNA methylation-based classification of central nervous system tumours. Nature. 2018;555(7697):469-474. doi:10.1038/nature26000

  Dataset EGAD00010002017

• T Cell Receptor Sequencing

  The T cell Receptor Sequencing dataset contains 84 files related to T cell receptor sequences obtained using ImmunoSeq by Adaptive Biotechnologies and phenotype metadata from 23 patients enrolled on a phase II clinical trial of neoadjuvant immune checkpoint blockade in high-risk resectable melanoma at MD Anderson Cancer Center (NCT02519322). Included are data on baseline and on-treatment samples from tumor and blood.

  Dataset EGAD00010001608

• AI_NF1glioma_DNAmeth

  DNA methylation of NF1-glioma

  Dataset EGAD00010001610

• Anaplastic meingioma methylation

  Methylation of anaplastic meningiona samples

  Dataset EGAD00010001629

• Glioma GWAS summary statistics

  Meta-analysis association statistics from case-control analysis (includes imputed SNPs)

  Dataset EGAD00010001657

• Methylation

  Meningioma Methylation

  Dataset EGAD00010001687

• Gene Expression Profiling for study EGAS00001004165

  Gene Expression Profiling from 44 Mantle Cell Lymphoma cases

  Dataset EGAD00010001842