15028 results for "cancer studies using rna-seq"

in 18.56 milliseconds.

• Non_Tumour_Renal_Cell_Line_Sequencing

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from commomon epithelial cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000205

• BCRC-ICGS (Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, Univ. of Birmingham) Data Access Committee

  Dac EGAC00001001982

• OICR PANCREATIC CANCER DATASET

  OICR PANCREATIC CANCER DATASET

  Dataset EGAD00001000262

• Degradation of Cyclin K/CDK12 is a druggable vulnerability of colorectal cancer (H012)

  Study EGAS00001004517

• Secondary Resistance to Anti-EGFR Therapy by Transcriptional Reprogramming in Patient-Derived Colorectal Cancer Models (hipo_B012)

  Study EGAS00001005320

• Copy number profiling of circulating cell-free DNA from high grade serous ovarian cancer patients

  Study EGAS00001004670

• Residual ctDNA after treatment predicts early relapse in patients with early-stage non-small cell lung cancer

  Study EGAS00001005967

• OICR-DAC, Ontario Institute for Cancer Research; Biliary Tract Cancer

  Next Gen Sequencing data from Biliary Tract Cancers

  Dac EGAC50000000528

• Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

  Study EGAS00001008218

• Neoantigens in bladder cancer

  Detection of spontaneous anti-neoepitope T-cell responses in non-metastatic bladder cancer patients

  Dac EGAC50000000740

• Breast Cancer Association Consortium Data Access Coordinating Committee

  Data access committee for the Breast Cancer Association Consortium (BCAC).

  Dac EGAC50000000824

• Cancer Research UK Cambridge Institute

  A department of the University of Cambridge and Cancer Research UK funded Institute

  Dac EGAC50000000683

• High Density SNP Association Analysis of Lung Cancer

  This research builds upon an extensive resource of a case-control study that has been ongoing at the UT MD Anderson Cancer Center since 1991. To identify risk variants for lung cancer, we conducted a genome-wide association study. Cases are newly diagnosed, histologically-confirmed patients presenting at MD Anderson Cancer and who had not previously received treatment other than surgery. Controls are healthy individuals seen for routine care at Kelsey-Seybold Clinics, the largest physician group-practice plan in the Houston Metropolitan area. This lung GWAS led to the identification of a susceptibility locus for lung cancer at 15q25.1. We used data from 315,450 tagging SNPs in 1,154 current and former (ever) smoking cases of European ancestry and 1,137 frequency-matched, ever-smoking controls from Houston, Texas in the discovery followed by the replication of the ten SNPs most significantly associated with lung cancer in an additional 711 cases and 632 controls from Texas and 2,013 cases and 3,062 controls from the UK. Two SNPs, rs1051730 and rs8034191, were significantly associated with risk of lung cancer with combined analysis yielded odds ratios of 1.32 (P < 1X10-17) for both SNPs. These two SNPs mapped to a region of strong linkage disequilibrium within 15q25.1 containing PSMA4 and the nicotinic acetylcholine receptor subunit genes CHRNA3 and CHRNA5. (Nat Genet. 2008 May;40(5):616-22. PMID:18385676)

  Study phs000753

• Transcriptome and TCR Sequencing of T Cells from Metastectomies

  T cells were sorted from metastatic tumors (colon, rectal, breast, anal, melanoma primary histologies) following tumor dissociation and single-cell sequencing was performed (RNAseq and TCRseq). For samples from tumors that had been previously studied, cells were analyzed comparing known neoantigen-reactive TCR-expressing cells to other T cells. For samples without previously identified neoantigen reactivity, TCRs were predicted on the basis of T cell transcriptomic states. To determine candidate neoantigen screening, exome and RNA sequencing were performed on fragments of matched tumors from which T cells were sequenced   

  Study phs002748

• Identification of Putative Neoantigens in Stage III Melanoma

  This study of three metastatic melanoma patients utilized exome sequencing and RNA sequencing to help identify putative neoantigen peptides that could be further validated by standard immunological assays before design of a personalized vaccine. For each set of neoantigens identified and verified by standard assays, we designed GMP peptides that correspond to the top neoantigens, then used these to condition dendritic cell isolates from each patient. The conditioned dendritic cells were used as the vaccine in three rounds of vaccination, followed by monitoring for T cell memory response to each of the neoantigens.

  Study phs001005

• Genomic and transcriptomic characterization of chordoma

  In this study, we performed paired tumor/normal whole exome and shallow long insert whole genome sequencing, as well as tumor RNAseq, from archival chordoma specimens collected from four patients at the Barrow Neurological Institute in Phoenix, AZ. The purpose of this analysis was to identify potential therapeutic targets. In three patients, we observed that although different DNA and RNA changes were present in each tumor, alterations fell on converging pathways. In the fourth patient, constitutional DNA demonstrated potentially pathogenic alterations that may have predisposed the patient to chordoma.

  Study phs001643

• Single-Cell Analysis of the Multiple Myeloma Microenvironment after Gamma-Secretase Inhibition and CAR T-Cell Therapy

  We examined the effects of gamma-secretase inhibition (GSI) on the bone marrow microenvironment in multiple myeloma patients before anti-B-cell maturation antigen (BCMA) CAR T-cell therapy. Single-nuclei RNA and ATAC sequencing revealed significant changes in gene expression and chromatin accessibility, especially in monocytes and tumor cells, following exposure to GSI. The findings suggest that GSI influences not only BCMA signaling but also broader cellular interactions within the tumor microenvironment. De-identified sequencing data from the study is available through dbGaP.

  Study phs003741

• Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [time-course bulkRNAseq]

  Time-course bulk-RNA sequencing of brain organoids grown in four distinct growth protocols designed to generate dorsal (D) and ventral (V) forebrain, midbrain (M) and striatum (S) tissue at days 13 (for dorsal and ventral)/16 (for midbrain and striatum), 25, 40, 80 and 120. Per per cell line-protocol-timepoint combination three organoids (biological replicates) were grown. For reference, also three samples of the pluripotent stem cells across cell lines, not yet exposed to any protocol, were sequenced (day 0, pluripotent).

  Study EGAS50000000663

• Deciphering the complex clonal heterogeneity of polycythemia vera and the response to interferon alpha

  We integrated colony formation and differentiation assays with single-cell RNA sequencing and single-cell genotyping in PV patient-derived cells vs. healthy controls to dissect how IFNa targets diseased clones during erythroid differentiation. Our findings indicate that PV-derived clones either undergo apoptosis or pass through their typical differentiation cycle, contributing to the long-term exhaustion of mutant cells in the bone marrow. The pivotal roles of ribosomal genes and clonal prerequisites in the therapeutic mechanism of IFNa are underscored by our study.

  Study EGAS50000000904

• Transcriptomic profiling of fragile X syndrome unmethylated full mutation carriers

  Total RNA sequencing of fibroblasts from two unrelated FMR1 unmethylated full mutation carriers, a fragile X patient and a control individual. The existence of rare, unmethylated full mutation carriers who carry the mutation that causes fragile X syndrome but do not gain methylation at the locus offers a rare opportunity to study the mechanisms underlying fragile X syndrome. This study aims to compare the transcriptomes of these four individuals in order to elucidate the mechanism behind the methylation a the FMR1 CGG repeat expansion that causes Fragile X syndrome.

  Study EGAS50000000647

• Single cell transcriptome sequencing of the developing human embryonic meninges

  There are no effective medical therapies for meningiomas, partly due to our limited understanding of their cellular origin and composition For this purpose, we generated data to make a comprehensive reference single cell and spatial transcriptomic atlas of human fetal meninges. Samples of meninges from human embryos of post-conceptional week (PCW) 5.0-13.0 were dissected and subject to 10Xgenomics chromium single cell RNA sequencing with the purpose of identifying cell types and gene expression programs for normal meninges development, Furthermore, this dataset should help discover cells of origin for meningiomas.

  Study EGAS50000000980

• Gene expression data of 2D duodenum organoids with or without continuous flow

  We developed a monolayer culture system for small intestinal organoids, and then placed the culture plate on a rotator to generate a constant flow in the overlay medium. This mechanical stimulation facilitated the formation of villus-like structures from the monolayer of small intestinal organoids. We analyzed gene expression of 2D normal duodenum organoids with or without medium rotation. Total RNA was extracted from organoids with or without a four-day medium rotation, and after 0, 1, 2 or 4 days of medium rotation, and sequenced with HiSeq X Ten (Illumina).

  Study JGAS000256

• Genomic Landscape of Pediatric Myelodysplastic Syndromes

  Pediatric myelodysplastic syndromes (MDS) are a rare disease and unlike their adult counterpart, very little is known about their genomic landscape. We characterized a cohort of patients from a single institution by whole exome sequencing, as well as a subset of patients by whole genome sequencing, RNA-sequencing and targeted deep sequencing. We found a spectrum of mutations, both somatic and germline, that are distinct from those observed in adult MDS. In turn, we observed mutations commonly observed in other pediatric myeloid tumors.

  Study EGAS00001002202

• Alternative splicing isoforms in patient-derived hepatocellular carcinoma cells

  The aim of this study was to obtain a landscape of alternative splicing (AS) in human hepatocellular carcinoma (HCC). We applied hybrid sequencing by integrating Pacbio long-read and Illumina short-read RNA sequencing data from 8 patient-derived HCC cell lines, and used an immortalized hepatocyte cell line as reference. This study revealed features of annotated and novel splice variants in HCC cells, including transcript length, AS type and protein changes. We also identified novel isoforms and tumor specific isoforms, which may represent potential biomarkers and targets for therapeutic development.

  Study EGAS00001002697

• ImmunoAgeing_Longitudinal

  The objective is to establish whether immunosenescence is associated with the development of clonal haematopoiesis in a healthy ageing population. This will be addressed in collaboration with the European consortium running the ImmunoAgeing project (www.immunoageing.eu). Genomic DNA derived from the peripheral blood of 394 individuals at 3-5 time-points over a 20-year period will be analysed. RNA bait pulldown (Agilent) will be used to perform targeted sequencing of genes known to be recurrently mutated in myeloid malignancies The presence, size and nature of clonal haematopoiesis will be correlated with quantitative measures of immunosenescence.

  Study EGAS00001003183