14989 results for "cancer studies using rna-seq"

in 19.35 milliseconds.

• The_identification_of_genetic_vulnerabilities_in_head_and_neck_cancers_for_the_development_of_novel_therapies

  CRISPR/Cas9 lethality screens in a set of Asian head and neck cancer cell lines to identify novel targets.

  Study EGAS00001002204

• In_Situ_Transcription_whole_genome_sequencing

  Whole genome sequencing of multifocal breast cancer regions. Intention to use this data to inform in-situ transcription analysis.

  Study EGAS00001001971

• Targeting the bicarbonate transporter SLC4A4 overcomes immunosuppression and immunotherapy resistance in pancreatic cancer

  Targeting the bicarbonate transporter SLC4A4 overcomes immunosuppression and immunotherapy resistance in pancreatic cancer

  Study EGAS00001006334

• Linking the epigenetic landscape in chronic lymphocytic leukemia to deregulated chromatin networks

  Aberrant chromatin features and epigenetic signaling emerge as an important part of the tumor disease state in chronic lymphocytic leukemia (CLL). However, an integrative analysis of the malignant chromatin landscape is currently missing. Here, we mapped DNA-methylation, nucleosome position, 7 histone modifications, ATAC-seq and the transcriptome in primary CD19+ sorted B-cells from the peripheral blood of CLL patients in comparison to non-malignant lymphocytes of healthy donor reference samples. On the > 50 kb scale we identified global differences with respect to DNA methylation, nucleosome positioning and histone modifications in CLL. Furthermore, a chromatin state annotation was developed to identify deregulated chromatin features of promoters and enhancers in CLL. By integrating these findings with an ATAC-seq based transcription factor binding analysis we identified a set of promoters and enhancers specific to CLL that were enriched in certain transcription factors binding motifs and genes of the BCR signaling pathway. Thus, our study provides an in-depth map of the CLL chromatin landscape and links chromatin state changes at promoters and enhancers to deregulated pathways.

  Study EGAS00001002518

• A Single-cell Atlas of Progressive TKI Resistance in Chronic Myeloid Leukemia

  High-dimensional scRNA seq and CyTOF were used to identify features predictive of treatment outcome at diagnosis. An optimal TKI response was characterised by erythroid lineage skewing of the CD34+ HSPC compartment. While TKI-resistant CP was reminiscent of a BC-like state, where HSPCs were enriched for inflammation, stemness and quiescence. We designed a machine-learning approach which assessed the prognostic potential of all 32 sub-populations of our scRNA seq dataset. LSCs and NK populations harboured the highest prognostic power at diagnosis. Within the LSCs, erythroid lineage priming and MYC activation were features of an optimal and poor TKI responses, respectively. With the NK cell compartment, apart from a higher abundance of NK cells in TKI optimal responders, a memory-like HLA-DR+ adaptive NK and KLRC1+ NK populations were hallmarks of an optimal and poor TKI responses, respectively. Mechanistically, both cell intrinsic and extrinsic mechanisms contributed towards the higher sensitivity of EPs to TKI therapy. In summary, our high-dimensional single-cell atlas of TKI resistance highlights pivotal transcriptional features associated with TKI-resistance disease, some of which have the potential to be exploited as biomarkers.

  Study EGAS00001005509

• Low T cell diversity is associated with poor outcome in bladder cancer - Bulk TCRseq data

  T cells are crucial effector cells in the endogenous defense against cancer, yet the clinical impact of their quantity, diversity, and dynamics remains underexplored. In this study we performed bulk TCRseq on tumor and serial blood samples from patients with muscle invasive (n patients = 119) or non-muscle invasive bladder cancer (n patients = 30). The goal was to investigate the clinical relevance of the blood and tumor TCR repertoire in patients with bladder cancer.

  Study EGAS50000000940

• WGS of breast cancer diagnosed during pregnancy and matched control

  The aim of this study was to compare the mutational landscape of breast cancer diagnosed during pregnancy (BCP) and breast cancer from age/stage non-pregnant patients (controls). We present whole genome sequencing data (Illumina HiSeq X ten platform) of tumor and matched normal tissues from 35 BCP patients and 20 controls. This work provides important novel biological insights and a unique resource to study the biology of breast cancer in young women and how pregnancy could modulate tumor biology.

  Study EGAS00001002685

• Whole genome analysis of mutation hotspots in gastric cancer

  Tissue-specific driver mutations in non-coding genomic regions remain undefined for most cancer types. In this study, we unbiasedly analysed 212 gastric cancer whole genomes to identify recurrently mutated non-coding regions in gastric cancer. Applying comprehensive statistical approa- ches to accurately model background mutational processes, we observe significant enrich- ment of non-coding indels (insertions/deletions) in three gastric lineage-specific genes. We further identify 34 mutation hotspots, of which 11 overlap CTCF binding sites (CBSs).

  Study EGAS00001002872

• Enabling sensitive and precise detection of ctDNA through somatic copy number aberrations in breast cancer

  Cell-free DNA (cfDNA) extracted from peripheral blood has emerged as a crucial biomarker source in oncology research. To enhance the detection of somatic copy number alterations (SCNAs) and circulating tumor DNA (ctDNA), we developed eSENSES, a 2Mb breast cancer-targeted NGS panel. It includes 15,000 genome-wide SNPs, 500 focal SNPs in breast cancer driver regions, and exons from 81 commonly altered genes, alongside a custom computational approach. eSENSES provides a reliable, powerful and cost-effective tool for monitoring disease progression and guiding therapeutic decisions in breast cancer patients.

  Study EGAS50000000793

• Cancer Research UK Manchester Institute/ Cancer Research UK National Biomarker Centre Data Access Committee

  Cancer Research UK Manchester Institute/Cancer Research UK National Biomarker Centre Data Access Committee is created to • Review and approve data access requests. • Ensure data security and compliance with institutional and legal obligations. • Maintain accurate records of access decisions For questions or further information, please contact: Chair of the Data Access Committee: Caroline Wilkinson Email: dac@cruk.manchester.ac.uk

  Dac EGAC50000000795

• RRBS sequencing data of ovarian cancer, breast cancer, control tissues, and white blood cell DNA.

  The dataset comprises 8 breast cancer, 11 ovarian cancer, 1 benign tumour, 18 normal tissue, 2 endometrium, and 23 white blood cell samples. Genome wide methylation analysis was performed by Reduced Representation Bisulfite Sequencing (RRBS) on Illumina HiSeq 2500. Data is provided as FASTQ files

  Dataset EGAD00001003822

• The Genomic Landscape of Prostate Cancer Brain Metastases

  Study EGAS00001004557

• Cancer Research UK manchester Institute Cancer Biomarker Centre

  Dac EGAC00001001765

• Cancer-Restricted Cryptic Antigens Are Targets for T Cell Recognition

  Subjects included patients with pancreatic cancer, at least 18 years of age, who were recruited from outpatient clinics and inpatient units at Dana-Farber Cancer Institute and Brigham and Women's Hospital.Bulk and single-cell transcriptomic profiling of human pancreatic cancer patient samples (direct from tumor or profiling of patient-derived organoids) was performed. Patient-derived pancreatic cancer organoids were profiled in the presence or absence of interferon-gamma stimulation. Healthy-donor CD8 T lymphocytes were ex vivo primed and expanded with candidate non-canonical (cryptic) peptide antigens. Single-cell transcriptomic profiling with paired T cell receptor (TCR) sequencing and molecularly-barcoded HLA tetramers enabled deconvolution and identification of cryptic antigen-reactive TCRs.

  Study phs003887

• BRAF_and_MEK_resistant_cell_line_clones

  The Sanger Institute has the largest collection of genetically-characterised cancer cell lines world-wide (we have collected >1000 human cancer cell lines which are being screened against >400 cancer therapeutics (http://www.sanger.ac.uk/genetics/CGP/translation). These lines have been characterized to the level of gene copy number, gene expression and cancer gene mutation sequence data. This has enabled us to select melanoma lines with varying BRAF mutational status and that show sensitivity to a range of BRAF inhibitors. Sensitive lines are being used to generate resistant clones by serial exposure to increasing concentrations of BRAF and MEK inhibitors and these are being characterised by genome-wide copy number analysis as well as by whole exome sequencing.

  Study EGAS00001000172

• Global Endometrial DNA Methylation Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk and Endometrial Function

  Endometriosis is a common gynecological disorder affecting 11% of reproductive aged women and is a leading cause of pain and infertility. We investigated global DNA methylation (DNAm) profiles in endometrium associated with endometriosis, menstruation, and genetic variation. Endometrial samples were collected from 984 patients with confirmed endometriosis (n=637) and women without endometriosis (n=347). Patients were recruited through the University of California San Francisco, USA, University of Melbourne, Australia, Endometriosis CaRe Centre in Oxford, UK, and EXPPECT Centre, The University of Edinburgh, UK, using the World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project (WERF EPHect) standardized protocols for tissue collection and processing, and participant characteristics and clinical annotation. DNA was extracted from samples and was use to generate DNAm data using the Illumina Infinium MethylationEPIC Beadchip and genotype data using the Axiom Precision Medicine Research array. Estimates from this study suggest that 15.4% of the variation in endometriosis is captured by DNAm. DNAm analysis identified significant differences in DNAm profiles and DNAm networks, associated with endometriosis, endometriosis sub-phenotypes, and menstrual cycle phases. Integration of DNAm and genetic data in a DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis highlighting target genes contributing to disease risk. This study identified novel factors affecting epigenetic regulation in endometrium associated with endometriosis risk and disease heterogeneity and provides an important data resource for reproductive medicine. Genotype data generated as part of this study are available on dbGaP and methylation data are available on GEO.

  Study phs003307

• Myocardial Infarction Genetics Exome Sequencing Consortium: Precocious Coronary Artery Disease Study

  The Precocious Coronary Artery Disease (PROCARDIS) study is an international, multicenter case-control study aimed at discovering the genetic contributors to premature coronary artery disease. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000 or 2500.

  Study phs000883

• Ancient nuclear genomes enable repatriation of Indigenous human remains

  For many decades Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return of their ancient people. By sequencing ten ancient nuclear genomes of Aboriginal Australians and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1,540 yr BP) of known provenance we demonstrate the feasibility of successfully identifying the geographic origins of unprovenanced ancestral remains using genomic methods.

  Study EGAS00001003359

• Molecular profiling of DLBCL patients treated in the HOVON84 trial

  Using a comprehensive NGS assay for simultaneous screening of mutations, copy number alterations, and translocations, 5 biology-based risk profiles could be reproduced in a Dutch DLBCL population and validated for outcome prediction. This approach will enable application as a diagnostic tool to select DLBCL patients for risk adapted treatment and help to develop biomarker-driven clinical trials for personalized medicine.

  Study EGAS00001003949