14989 results for "cancer studies using rna-seq"

in 25.45 milliseconds.

• Dataset for white blood cell and cell-free DNA analyses for detection of residual disease in gastric cancew

  The dataset for white blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer includes 169 bam files from targeted deep sequencing on the Illumina HiSeq2500. The samples analyzed include genomic DNA from white blood cells and cell-free DNA from longitudinal blood collections of patients with gastric cancer.

  Dataset EGAD00001005750

• Memorial Sloan Kettering Cancer Center - Human Oncology & Pathogenesis Program (HOOP) - Data Access Committee

  Dac EGAC00001000305

• Functional Genomics Laboratory, Kolling Institute of Medical Research DAC - TP53 mutation data in ovarian cancer

  Dac EGAC00001000589

• The data access committee for genome-wide cell-free DNA fragmentation in patients with cancer

  Dac EGAC00001001180

• Somatic pathogenic variants in the normal mammary gland of sporadic breast cancer patients.

  Dac EGAC00001002391

• DAC Molecular heterogeneity and commonalities in pancreatic cancer precursors with gastric and intestinal phenotype

  Dac EGAC00001002978

• NPY methylated ctDNA is a promising biomarker for treatment response monitoring in metastatic colorectal cancer

  Dac EGAC00001003001

• EGAD00010000526

  SNP 6.0 arrays of small cell lung cancer

  Dataset EGAD00010000526

• Microbiome confounders and quantitative profiling challenge established microbial targets in colorectal cancer developmental stages

  Study EGAS00001007413

• Genomic validation of the revised Bethesda criteria in terms of pathogenesis and oncologic significance

  Study EGAS00001003959

• Accurate mutation detection in leukemia by re-sequencing a cancer gene set

  Study EGAS00001000268

• Activation of IL7RA signalling in human B-lymphoid precursors induces pre-leukemia

  Study EGAS00001003979

• Biological and Therapeutic Implications of a Unique Subtype of NPM1 Mutated AML

  Study EGAS00001004872

• Minor intron splicing efficiency increases with the development of lethal prostate cancer

  Study EGAS00001005546

• Serum Proteome Profiling Identifies Early Markers of Therapeutic Response to Neoadjuvant Chemotherapy of Breast Cancer

  Study EGAS00001006228

• Genomics characterization of BRAF-V600E colorectal cancer patients treated with anti-BRAF/EGFR

  Study EGAS00001006247

• Induction Failure in Childhood and Young Adult T-cell Acute Lymphoblastic Leukemia

  Study EGAS00001006411

• 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

• Integration of intra-sample contextual error modeling for improved detection of somatic mutations

  Study EGAS00001003806

• IRCCS Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori" Italian Cancer Center Data Access Committee

  Dac EGAC00001003223

• IRCCS Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori" Italian Cancer Center Data Access Committee

  Dac EGAC00001003227

• St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project Steering Committee

  Dac EGAC00001000045

• Data access policy for PDTX Breast Cancer data from Bruna et al (2016), Cell.

  Dac EGAC00001000540

• DAC for "A Functional Network of Gastric-Cancer-Associated Splicing Events Controlled by Dysregulated Splicing Factors"

  Dac EGAC00001000675

• DAC for study: "Circulating tumour DNA abundance and potential utility in de novo metastatic prostate cancer"

  Dac EGAC00001001099

• The University of Hong Kong Colon Cancer Organoids Genomics Study Data Access Committee

  Dac EGAC00001001405

• Treatment-mediated selection of lethal prostate cancer clones defined by copy number architectures

  Dac EGAC00001002865

• Whole exome sequencing of metastatic breast cancer

  Dataset EGAD00001000836

• Nanostring_nCounter_BreastCancer360

  hormone receptor-positive early breast cancer by Nanostring BC360 panel

  Dataset EGAD00010001994

• The landscape of somatic mutations in epigenetic regulators across 1000 pediatric cancer genomes

  Study EGAS00001000449

• Identification of mutations and structural rearrangements in plasma DNA form metastatic prostate cancer patients

  Study EGAS00001000453

• Single cell sequencing: Capturing the origin and dynamics of chromosomal copy-number heterogeneity

  Study EGAS00001003812

• STM4 - Mouliere et al, 2018. Enhanced detection of circulating tumor DNA by fragment size analysis

  Study EGAS00001004418

• BRCA2, ATM, and CDK12 defects differentially shape prostate tumor driver genomics and clinical aggression

  Study EGAS00001004800

• IG-MYC rearrangement defines a high-risk subgroup of B-cell precursor acute lymphoblastic leukaemia

  Study EGAS00001005111

• Genomic Analysis of Focal Nodular Hyperplasia with Associated Hepatocellular Carcinoma Unveils its Malignant Potential

  Study EGAS00001005313

• Evaluating CRISPR-based Prime Editing for cancer modeling and CFTR repair in organoids

  Study EGAS00001005358

• Genomic profiling of metastatic basal cell carcinoma reveals candidate drivers of disease and therapeutic targets

  Study EGAS00001006148

• Mechanism of action and resistance to Trastuzumab Deruxtecan in patients with metastatic breast cancer

  Study EGAS00001007372

• CUPiD, a cfDNA methylation-based tissue-of-origin classifier for Cancers of Unknown Primary

  Study EGAS00001007445

• The WID-EC test for the detection and risk prediction of endometrial cancer

  Study EGAS00001005033

• The DNA methylome of cervical cells and risk of ovarian cancer

  Study EGAS00001005045

• Characterization of UV DNA damage in B-cell precursor acute lymphoblastic leukemia

  Study EGAS00001008128

• The data access committee for "Validation of cfDNA fragmentome analyses for early detection of liver cancer"

  Dac EGAC00001003543

• An Integrated Approach to Patient Stratification and Therapy Selection in Acute Myeloid Leukemia

  Study EGAS00001004655

• A renal cell carcinoma tumorgraft platform to advance precision medicine

  Study EGAS00001005516

• Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia (HIPO, H005)

  Study EGAS00001006361

• Angiosarcoma_whole_exome

  Extension of angiosarcoma whole genome sequencing study

  Study EGAS00001000588