10117 results for "cancer rna-seq"

in 62.91 milliseconds.

• BC WGS Dataset 3

  Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Dataset EGAD00001001351

• BC WGS Dataset 4

  Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Dataset EGAD00001001353

• Global Anaplastic Thyroid Cancer Initiative

  Raw whole genome sequence data(fastq) for the GATCI project

  Dataset EGAD00001003236

• EXOME_ARRAY_ANALYSIS

  EXOME ARRAY ANALYSIS OF ADVERSE REACTIONS TO FLUOROPYRIMIDINE-BASED THERAPY FOR GASTROINTESTINAL CANCER

  Dataset EGAD00010001499

• Whole Genome Sequencing of Gingivo-buccal Cancer: ICGC-India Project_YR03

  Dataset EGAD00001004478

• methylation_tnbc

  Raw methylation data from triple negative breast cancer.

  Dataset EGAD00010002077

• RNAseq

  RNAseq of pancreatic cancer organoids.

  Dataset EGAD00001010834

• OICR-DAC, Ontario Institute for Cancer Research

  Dac EGAC00001000591

• OICR-DAC, Ontario Institute for Cancer Research

  Dac EGAC00001000710

• Identification of molecule relationship between intravenous leiomyomatosis and uterus myoma

  Up to now, there are two hypothesis about the pathogenesis of the relationship of intravenous leiomyomatosis and uterine myoma. One theory suggests that the IVL comes from the smooth muscle cell in the vessel wall.The other theory indicates that the IVL derives from the uterine myometrium. However, limited to the technology, few studies have been deeply explore the underlying relation. In this study, we employ the RNA sequencing to explore the molecule relationship between IVL and uterus myoma. In order to identify the molecule relationship between IVl and uterine myoma we conducted transcriptome sequencing and bioinformaitc analysis

  Dataset EGAD00001003356

• Tumor Thrombus Dataset

  the dataset contains Exome and RNA fastq files of Renal Cell Carcinoma patients, which belongs to "Integrated genomic analysis of tumor thrombus"/

  Dataset EGAD00001008010

• Orthotopic murine Group 3 medulloblastoma in C57Bl/6 mice treated with saline, cyclophosphamide or gemcitabine

  Mice with medulloblastoma (Group 3) were treated with saline, cyclophosphamide, or gemcitabine as described by Abbas et al (2020). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen), library preparation (SureSelect, Agilent), rRNA depletion (Ribo-Zero Plus, Illumina) and sequencing were carried out by GenomicsWA or Australian Genome Research Facility. Libraries were sequenced on NovaSeq 6000 S1 flow cells as paired-end 150bp reads (Illumina).

  Dataset EGAD00001008511

• TK-EPN862 - Patient-derived xenograft model of Posterior Fossa A Ependymoma - RNAseq

  In Vivo Loss of Tumorigenicity in a Patient-Derived Orthotopic Xenograft Mouse Model of Ependymoma. Whitehouse et al. 2023 Frontiers in Oncology. We describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Patient and PDOX tumors were analyzed using RNA sequencing. RNAseq data (paired end) provided here correspond to Primary tumour, two metastatic lesions (one spinal, one cranial), and a patient-derived xenograft derived from the patient.

  Dataset EGAD00001009870

• RNA-sequencing of N-ERD patients with Dupilumab therapy

  Transcriptomic profiles of Non-steroidal anti-inflammatory drug-exacerbated respiratory disease (N-ERD) patients before and after aspirin challenge during 24 weeks of Dupilumab therapy. To investigate the dynamics of nasal mediators during aspirin provocation in N-ERD patients before and twenty-four weeks after therapy with the IL-4 receptor alpha-blocking antibody dupilumab.

  Study EGAS50000000386

• Identification of neoantigen from MSI-CRC patient derived organoids and its application for targeting by autologous T cells

  Targeting neoantigens expressed only by tumor cells enable tumor destruction without unexpected damages to healthy tissues. Here, we identified neoantigens from microsatellite instable (MSI) colorectal cancer (CRC) patient-derived organoids by genomics and immunopeptidomics approches. The neoantigens in this study were predicted from frame-shift mutation by whole-genome sequencing and confirmed its presentation on organoids surface class I HLA molecules by mass spectrometry. We utilized these neoantigens to isolate neoantigen-specific CD8 T cells from autologous PBMC, and proved tumor organoids killing ability of the CD8 T cells, whereas it did not attack normal organoids. This study provides a platform to identify neoantigen from patient-derived cancer organoids and a model to validate T cell recognition, which could be useful for adoptive CD8 T cell transfer treatment for MSI-CRC patient.

  Study EGAS00001006633

• Screening_for_human_epigenetic_variation_at_CpG_islands

  Many human characteristics, including susceptibility to disease, are determined genetically. An unexplored alternative to such genetic determination concerns epigenetic mechanisms such as DNA methylation. CpG islands (CGIs) are generally constitutively hypomethylated, however there are circumstances in which they become heavily methylated and, when coincident with a gene promoter, this invariably causes transcriptional silencing. CGI methylation occurs in normal tissues during processes such as X-inactivation, but abnormal patterns of methylation have also been implicated in disease. The vast majority of evidence relates to cancer, where silencing of multiple genes in this way appears to be a causal contributor to the cancer state. To address the role and extent of CGI methylation in ‘normal’ and diseased cells we applied MBD-affinity purification in conjunction with next generation sequencing in a panel of human brain autopsy samples. These samples represent a panel of individuals as well as specific brain regions and neurological pathologies.

  Study EGAS00001000074

• Pharmacogenomic landscape of patient-derived cells informs precision oncology therapy

  Outcomes of anticancer therapy vary dramatically among patients, which may be caused by the specific molecular alterations in each patient’s tumor. Precision oncology aims to apply optimal therapies for each tumor based on its molecular characteristics. We have established a resource reporting the genomic and transcriptomic profiles of 462 patient tumor-derived cells (PDCs) across 14 cancer types, together with responses to 60 targeted agents. Compared with long-term cultured cancer cell lines, PDCs better recapitulate the molecular profiles of the original tumors. Among other unreported associations, we identify molecular factors inducing resistance to EGFR inhibitors in glioblastoma, and we suggest repurposing ibrutinib (currently used in hematological malignancies) for EGFR-specific therapy in gliomas. Lastly, using a retrospective clinical study, we find that PDC-derived sensitivities can be used to predict patient responses.

  Study EGAS00001002515

• Patient-derived organoids model treatment response of metastatic gastrointestinal cancers (targeted and whole-genome sequencing)

  Patient-derived organoids (PDOs) have recently emerged as robust pre-clinical models, however, their potential to predict patient clinical outcomes remain unclear. We report a living biobank of PDOs from metastatic, heavily-pretreated colorectal and gastroesophageal cancer patients recruited in phase I/II clinical trials. Phenotypic and genotypic profiling of PDOs showed a high-degree of similarity to the original patient tumor. Molecular profiling of tumor organoids was matched to drug screening results, suggesting PDOs could complement existing approaches in defining cancer vulnerabilities and improving treatment responses. We compared ex vivo organoid responses to anticancer agents, and PDO-based orthotopic mouse tumor xenograft models to the response of the patient in clinical trials. Our data suggest that PDOs can recapitulate patient responses in the clinic, and have the potential to be implemented in personalized medicine programs.

  Study EGAS00001002784

• Genetic makeup of agnospheres

  Agnospheres are cultures of cancer stem cells isolated from tissue biopsies from patients with Cancer of Unknown Primary (CUPs). The latter is a lethal malignancy (median survival <1 year), representing approximately the 3% of all cancers, and characterized by metastatic dissemination in the absence of a primary tumor recognizable by a standardized protocol including thorough body imaging and histopathological analysis. Agnospheres are long-term propagated in culture and, after subcutaneous injection into immunocompromised mice, they display high tumorigenicity and quickly reproduce the clinical presentation of the original tumor, featuring a multi-organ metastatic pattern and poorly differentiated histology. The goal of the project is to analyse the mutational profile of agnospheres in detail, as to verify its correspondance with that of the original tumors. Genetic information will be exploited to investigate the genetic drivers of the CUP phenotype, in particular the hypermetastatic ability and the differentiative block.

  Study EGAS00001004868

• ctDNA monitoring using patient-specific sequencing and integration of variant reads - Breast cohort

  Circulating tumor-derived DNA (ctDNA) can be used to monitor cancer dynamics noninvasively. Detection of ctDNA can be challenging in patients with low-volume or residual disease, where plasma contains very few tumor-derived DNA fragments. We show that sensitivity for ctDNA detection in plasma can be improved by analyzing hundreds to thousands of mutations that are first identified by tumor genotyping. We describe the INtegration of VAriant Reads (INVAR) pipeline, which combines custom error-suppression methods and signal-enrichment approaches based on biological features of ctDNA. With this approach, the detection limit in each sample can be estimated independently based on the number of informative reads sequenced across multiple patient-specific loci. We applied INVAR to custom hybrid-capture sequencing data from 176 plasma samples from 105 patients with melanoma, lung, renal, glioma, and breast cancer across both early and advanced disease. By integrating signal across a median of >105 informative reads, ctDNA was routinely quantified to 1 mutant molecule per 100,000, and in some cases with high tumor mutation burden and/or plasma input material, to individual parts per million. This resulted in median Area Under the Curve (AUC) values of 0.98 in advanced cancers, and 0.80 in early stage and challenging settings for ctDNA detection. We generalized this method to whole-exome and whole-genome sequencing, showing that the INVAR may be applied without requiring personalized sequencing panels, so long as a tumor mutation list is available. As tumor sequencing becomes increasingly performed, such methods for personalized cancer monitoring may enhance the sensitivity of cancer liquid biopsies.

  Dataset EGAD00001006293

• Exome sequencing of early and late passage Patient Derived Xenogratf Tumoroids with matched Patient Derived Xenogratfs and matched normal liver

  The breadth and depth at which cancer models are interrogated contribute to successful translation of drug discovery efforts to the clinic. In colorectal cancer (CRC), model availability is limited by a dearth of large-scale collections of patient-derived xenografts (PDXs) and paired tumoroids from metastatic disease, the setting where experimental therapies are typically tested. XENTURION is a unique open-science resource that combines a platform of 129 PDX models and a sister platform of 129 matched PDX-derived tumoroids (PDXTs) from patients with metastatic CRC, with accompanying multidimensional molecular and therapeutic characterization. This specific dataset is focused on a comparison of early and late passage tumoroids transcriptomes. In this study we focused our attention on early (passage 3) and late (passage 8-12) PDXTs with their matched PDXs and normal liver

  Study EGAS50000000185

• Establishment of xenogfafts and cultured cell lines from clinical samples

  The purpose of the present study was to clarify the presence or absence of alterations in the molecular properties of patient-derived xenografts (PDXs) with up to eight passages in endometrial carcinomas. Alterations in the proportion of immunohistochemically positive/negative cells for PAX8, estrogen receptor, PAX2, and PTEN were observed in established PDXs of endometrioid carcinomas and carcinosarcomas, whereas proportions of cells with AE1/AE3, TP53, ARID1A PMS2, and MSH6 were maintained. Variants of cancer-associated genes in PDX compared to those in the parental tumors were examined in two cases, a frameshift deletion in BRCA1 was observed in the parental tumor tissue, and additional genomic alterations were found in the PDXs of this case. Genomic and phenotypic alterations in endometrial carcinoma PDXs relative to the parental tumors were observed and were partly associated with endometrial cancer-specific characteristics in cellular differentiation and gene mutations.

  Study JGAS000585

• Genome Sequencing of Pancreatic Ductal Adenocarcinoma at The Human Genome Sequencing Center of Baylor College of Medicine (HGSC-BCM)

  Pancreatic ductal adenocarcinomas (PDAC) is the 11th most common cancer in the USA but the 4th in fatalities. The onset and progression of cancer is driven by extensive rearrangement and mutation of the genome. We combined our capability to capture and enrich exome DNA with the next generation sequencing capacity to allow us to detect and characterize the somatic mutation profile of 24 patients with PDAC. Patient samples were collected by the Elkins Pancreatic Center in the Baylor College of Medicine Department of Surgery. Sequencing of the pancreatic ductal adenocarcinoma is one of the NHGRI Center Initiated Projects in progress in the Human Genome Sequencing Center at Baylor College of Medicine. These data are also contributed to an ICGC study and will be published with the ICGC collaborators.

  Study phs000516

• Dynamics of Genomic and Immune Responses During Primary Immunotherapy Resistance in Mismatch Repair Deficient Tumors

  We study a patient with dMMR lung cancer refractory to immunotherapy. Post-treatment tumor demonstrated compound heterozygous frameshift deletions located upstream of the kinase domain in the gene encoding JAK1 protein, downregulation of JAK1 and mediators of its signal transduction, and total loss of JAK1 phosphorylation. Importantly, one of the JAK1 mutations, despite not being detected in the pre-treatment tumor, was found at low variant allele frequency in the pre-treatment circulating tumor DNA, suggesting clonal selection of the mutation. This report provides the most detailed look yet of defective JAK1 signaling in the context of dMMR and immunotherapy-resistance. Together with observations of JAK1 frameshift indels being enriched in dMMR compared with MMR-proficient tumors, our findings demonstrate the critical function of JAK1 in immunological surveillance of dMMR cancer.

  Study phs002089

• Genome-wide Association Study and Meta-Analysis of Ewing Sarcoma

  We combined a set of 122 French Ewing sarcoma (EWS) cases from the Institut Curie, 19 EWS cases from the National Cancer Institute (NCI) Center for Cancer Research (CCR), and 29 EWS cases from the NCI Bone Disease and Injury Study. All EWS cases were confirmed by medical record review and the presence of a specific EWSR1-ETS translocation were noted when data was available. Each participant provided informed consent and each participating study was approved by the Institutional Review Boards of their study center. DNA was extracted using standard methods from blood, saliva (Oragene), or buccal cells. All de novo genotyping of EWS cases was performed at the NCI CGR on the Illumina OmniExpress-24 v1.1 array. Genotyping was performed according to manufacturer's guidelines using the Infinium HD Assay automated protocol.

  Study phs001549