14978 results for "cancer studies using rna-seq"

in 18.76 milliseconds.

• Measuring minimal residual disease in acute myeloid leukemia with MASQ

  Study EGAS00001003732

• Whole exome sequencing of chemotherapy-resistant muscle-invasive urothelial bladder cancer

  Study EGAS00001004231

• Association of DNA-methylation profiles with immune responses in breast cancer patients

  Study EGAS00001004211

• Genetics and transcriptomics of human acute erythroid leukemia

  Study EGAS00001004203

• Selective Elimination of Immunosuppressive T cells in Patients with Multiple Myeloma

  Study EGAS00001004915

• Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

  Study EGAS00001005472

• Initial cohort of 500 solid tumors screened for Basket of Baskets

  Study EGAS00001005893

• Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells

  Study EGAS00001007091

• Genomic Landscape of Follicular Lymphoma Across a Wide Spectrum of Clinical Behaviors

  Study EGAS00001007105

• Multi-omics analysis of an individual with multiple pancreatic neuroendocrine tumours (panNETs)

  Study EGAS00001006722

• CGP_CORE_CELL_LINES___RNA_seq

  Graham to complete

  Study EGAS00001000828

• Using NGS to Sequence Whole Genomes to Identify Genes Underlying ALS

  Our ALS Consortium - a partnership of clinicians, basic scientists, geneticists, and computational biologists from 48 institutions (4 of which are industry partners) across 5 countries - establishes a framework to apply whole genome sequencing (WGS) and functional genomics to the study of amyotrophic lateral sclerosis (ALS). Because ALS-causing mutations tend to be of moderate impact and are relatively rare in the population (reviewed in Al-Chalabi et al., 2017, PMID: 27982040), identification of new mutations require several thousand samples, which need to be obtained from multiple sites (even the busiest ALS clinics see only 200-400 patients per year). ALS Consortium is using genomics technologies to study the causes and mechanisms underlying neurodegenerative disease, and the contribution of various cell types within the brain and spinal cord. Much of this work is done and continues to be done in collaboration with the members of the NYGC ALS Consortium.

  Study phs003067

• Targeted Mutational Analysis of Intestinal T-cell Lymphomas, Using a Customized Targeted Amplicon Panel on the Ion Torrent PGM

  Intestinal T-cell lymphomas (ITCL) are rare, aggressive T-cell lymphomas that are composed primarily of enteropathy-associated lymphomas Type 1 and type 2, and a small fraction of cases not classifiable as EATL that are classified as peripheral T-cell lymphoma, not otherwise classifiable. The molecular pathogenesis of these rare lymphomas is largely unknown. We studied a series of 34 ITCL cases using a combination of amplicon based targeted next generation sequencing and pyrosequencing for mutations in 34 genes previously reported to be mutated in other types of T-cell lymphomas and other genes known to have significant roles in normal T-cell proliferation. We identified a high percentage of cases with mutations in JAK/STAT signaling pathway members, and also in RAS family members. Notably, we did not detect GNAI-2 mutations in our North American cases of EATL type 2 by targeted pyrosequencing, which had been reported previously in Asian cases.

  Study phs001126

• PCR-free shallow whole genome sequencing for chromosomal copy number detection from plasma of cancer patients is an efficient alternative to the conventional PCR-based approach

  Somatic copy number alterations (SCNAs) can be detected in tumor cell-free DNA (cfDNA) by shallow whole genome sequencing (sWGS). Polymerase chain reaction (PCR) is typically included in library preparations, but a PCR-free method could be an effective alternative for research and diagnostics. Peripheral blood samples (n=22) were collected in EDTA-containing tubes from non-small cell lung cancer patients (n=10) and healthy donors (n=12). PCR and PCR-free library preparations underwent sWGS and the following metrics were compared: mapping quality, proportion of duplicate reads, genome coverage, sequencing read length and copy number profiles. The PCR-free method was further evaluated on archived plasma samples (n=33) of varying pre-analytical quality collected in EDTA or lithium heparin tubes. Archived samples were from acute myeloid leukaemia (n=15) and B-cell lymphoma (n=18) patients. The percentage of unique reads was significantly higher for the 22 samples analysed by PCR-free (95.7%) compared to PCR (84%). PCR-free libraries from 33 archived samples produced data of a comparable quality, with 95.4% unique reads. All other evaluated metrics were highly comparable for PCR and PCR-free library preparations. We conclude that SCNA detection can be performed by PCR-free sWGS on cfDNA from cancer patients and is feasible for diagnostic and archival plasma collected in EDTA- or lithium heparin-containing tubes. Our results pave the way for an automated cfDNA workflow for cancer plasma samples.

  Study EGAS00001004692

• Whole Exome Sequencing data of six chRCC tumors corresponding to three patients

  Mammalian target of rapamycin (mTOR) is a central regulator of mammalian metabolism and physiology. Aberrant hyperactivation of the mTOR pathway promotes tumor growth and metastasis, and can also promote tumor resistance to chemotherapy and cancer drugs; this makes mTOR an attractive cancer therapeutic target. mTOR inhibitors have been approved to treat cancer; however, the mechanisms underlying drug sensitivity remain poorly understood. Here, whole exome sequencing of three chromophobe renal cell carcinoma (chRCC) patients with exceptional mTOR inhibitor sensitivity revealed that all three patients shared somatic mutations in the deubiquitinase USP9X. The clonal characteristics of the mutations, which were amassed by studying multiple patients’ primary and metastatic samples from various years, together with the low USP9X mutation rate in unselected chRCC series, reinforced a causal link between USP9X and mTOR inhibitor sensitivity. Rapamycin treatment of USP9X-depleted HeLa and renal cancer 786-O cells, along with the pharmacological inhibition of USP9X, confirmed that this protein plays a role in patients’ sensitivity to mTOR inhibition. USP9X was not found to exert a direct effect on mTORC1, but subsequent ubiquitylome analyses identified p62 as a direct USP9X target. Increased p62 ubiquitination and the augmented rapamycin effect upon bortezomib treatment, together with the results of p62 and LC3 immunofluorescence assays, suggested that dysregulated autophagy in USP9X-depleted cells can have a synergistic effect with mTOR inhibitors. In summary, we show that USP9X constitutes a potential novel marker of sensitivity to mTOR inhibitors in chRCC patients, and represents a clinical strategy for increasing the sensitivity to these drugs.

  Study EGAS00001007104

• The University of Hong Kong Intestinal Metaplasia Organoids Study

  Background: Gastric intestinal metaplasia (IM) is a pre-cancerous stage spanning a morphological spectrum that is poorly represented by human cell line models. Objective: We aim to establish and characterize human IM cell models to better understand IM progression along the cancer spectrum. Design: A large human gastric IM organoid (IMO) cohort (n=28), their clonal derivatives and normal gastric organoids (n=42) for comparison were established. Comprehensive multi-omics profiling and functional characterization were performed. Results: Single-cell transcriptomes revealed IMO cells spanning a spectrum from hybrid gastric/intestinal to advanced intestinal differentiation. Their lineage trajectories connected different cycling and quiescent stem and progenitors, highlighting differences in gastric to IM transition and the potential origin of IM from STMN1 cycling isthmus stem cells. Hybrid IMOs showed impaired differentiation potential, high lineage plasticity beyond gastric or intestinal fates, and reactivation of a fetal gene program. Cell populations in gastric IM and cancer tissues were highly similar to those derived from IMOs and exhibited a fetal signature. Genomically, IMOs showed elevated mutation burden, frequent chromosome 20 gain, and epigenetic de-regulation of many intestinal and gastric genes. Functionally, IMOs were FGF10 independent and showed downregulated FGFR2. Several IMOs exhibited a cell-matrix adhesion independent (CMi) subpopulation that displayed chromosome 20 gain but lacked key cancer driver mutations, potentially representing the earliest neoplastic precursor of IM-induced gastric cancer. Conclusions: Overall, our IM organoid biobank captured the heterogeneous nature of IM, revealing mechanistic insights on IM pathogenesis and progression, offering an ideal platform for studying early gastric neoplastic transformation and chemoprevention.

  Study EGAS00001007899

• University of Sydney Thyroid Cancer Data Access Committee

  This Data Access Committee (DAC) manages access to genomic data generated by the Thyroid Cancer Research Group at the University of Sydney and Royal North Shore Hospital. The DAC will evaluate data access requests to ensure they align with participant consent and the conditions approved by the Northern Sydney Local Health District Human Research Ethics Committee. Requests will be reviewed for scientific validity, alignment with the original consent, and compliance with institutional and regulatory data governance policies.

  Dac EGAC50000000661

• Targeted Sequencing Data for RESOLVE Clinical Trial

  This is a Phase II clinical trial. This research study is studying a combination of targeted therapies as a possible treatment for estrogen-receptor positive (ER+) endometrial cancer and low-grade serous ovarian cancer. The drugs involved in this study are: - Abemaciclib (also known as Verzenio™) - Letrozole (also known as Femara®) - Metformin (also known as Glucophage®) - Zotatifin (also known as eFT226) - Gedatolisib (also known as PF-05212384)

  Dataset EGAD50000001711

• 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