11925 results for "cancer rna-seq"

in 19.36 milliseconds.

• Deep multi-region whole-genome sequencing reveals heterogeneity and gene-by-environment interactions in treatment-naive, metastatic lung cancer

  Our understanding of genomic heterogeneity in lung cancer is largely based on the analysis of early-stage surgical specimens. Here we used endoscopic sampling of paired primary and intrathoracic metastatic tumors from 11 lung cancer patients to map genomic heterogeneity inoperable lung cancer with deep whole-genome sequencing. Intra-patient heterogeneity in driver or targetable mutations was predominantly in the form of copy number gain. Private mutation signatures, including patterns consistent with defects in homologous recombination, were highly variable both within and between patients. Irrespective of histotype, we observed a smaller than expected number of private mutations, suggesting that ancestral clones accumulated large mutation burdens immediately prior to metastasis. Single-region whole-genome sequencing of from 20 patients showed that tumors in ever-smokers with the strongest tobacco signatures were associated with germline variants in genes implicated in the repair of cigarette-induced DNA damage. Our results suggest that lung cancer precursors in ever-smokers accumulate large numbers of mutations prior to the formation of frank malignancy followed by rapid metastatic spread. In advanced lung cancer, germline variants in DNA repair genes may interact with the airway environment to influence the pattern of founder mutations, whereas similar interactions with the tumor microenvironment may play a role in the acquisition of mutations following metastasis.

  Study EGAS00001003830

• PARADIGM: Combined ctDNA and serum PSA for dynamic monitoring of metastatic prostate cancer starting first-line treatment

  The prognosis of newly-diagnosed metastatic prostate cancer is highly variable. The PARADIGM prospective cohort study evaluated predictors of survival in blood collected at the start of each of the first six treatment cycles from 114 high-volume metastatic patients starting androgen deprivation therapy combined with docetaxel or an androgen receptor pathway inhibitor.

  Study EGAS50000001357

• Shallow whole genome sequencing of ctDNA samples from DETECT study

  A large-scale retrospective study in metastatic breast cancer patients using circulating tumour DNA and machine learning to predict treatment outcome and progression-free survival from the paper "A large-scale retrospective study in metastatic breast cancer patients using circulating tumour DNA and machine learning to predict treatment outcome and progression-free survival", by Beddowes et al. Mol.Onc.

  Study EGAS50000000911

• Cancer_Genome_Libraries_Tests

  Testing library production.Genomic libraries (500 bps) will be generated from total genomic DNA derived from commomon epithelial cancer samples and subjected to paired end sequencing on the llumina plateforms. 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 EGAS00001000208

• High intensity sequencing of plasma cfDNA and WBC gDNA

  We sought to define the technical feasibility of a high-intensity sequencing assay of cfDNA and matched white-blood cell (WBC) DNA covering a large genomic region (508 genes, 2Mb, 60,000x raw-depth) in a prospective study of 124 metastatic cancer patients, with contemporaneous matched metastatic tumor tissue biopsies, and age-matched 47 non-cancer controls.

  Study EGAS00001003755

• Cell-free DNA sequencing data of healthy control, atrophic gastritis, and gastric cancer patients’ blood

  Sample cohort (n=48) is consisted of healthy, atrophic gastritis and gastric cancer patients. Some of the gastric cancer patients samples are collected at the separate time points: -1 before the operation; -2 after the operation; -3 during the control visit. For the hybridisation capture of the genes unique 15 gastric cancer-related gene panel was developed and very deep sequencing using TruSight Oncology Unique Molecular Identifier (UMI) Reagents (Illumina) was used.

  Dataset EGAD00001011153

• A Comprehensive Catalogue of Somatic Mutations from a Human Cancer Genome

  A Comprehensive Catalogue of Somatic Mutations from a Human Cancer Genome

  Dataset EGAD00001000149

• Whole genome bisulfite sequencing of prostate cancer samples upon oral pimonidazole administration

  Whole genome bisulfite sequencing of prostate cancer samples upon oral pimonidazole administration

  Dataset EGAD50000000099

• APOBEC Breast Cancer Whole Genome

  Five tumor-normal human breast cancer cases driven by APOBEC mutagenesis, including normal tissue, primary, and metastatic samples for each patient.

  Dataset EGAD50000001275

• SNP data for Ovarian cancer PRS (controls)

  SNP data of 28 sites required for the Ovarian cancer PRS (controls)

  Dataset EGAD00001008145

• Single Cell RNAseq of blood and tumor from renal cancer patients

  Single Cell RNAseq of blood and tumor from renal cancer patients

  Dataset EGAD00001005977

• Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients

  Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients

  Dataset EGAD00001001421

• Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008271

• SCLC tumor sequencing

  In this study we have sequenced the tumor of 28 Small Cell Lung Cancer patients.

  Study EGAS00001003985

• PEACE (Posthumous Evaluation of Advanced Cancer Environment) whole exome sequencing data

  PEACE (Posthumous Evaluation of Advanced Cancer Environment) whole exome sequencing data

  Dataset EGAD00001015763

• The genetic evolution of precursor lesions in pancreatic cancer

  Mapping genetic evolution of pancreatic cancer precursor lesions such as IPMNs and PanINs.

  Dataset EGAD00001002232

• WES data of serially passaged TIC-enriched spheres of colorectal cancer

  WES data of serially passaged TIC-enriched spheres of colorectal cancer (CRC)

  Dataset EGAD00001006266

• Bulk transcriptomic analyses of monocyte-derived dendritic cells treated with CES1i

  The data published here contains bulk RNA-sequencing (RNAseq) data as obtainedfrom monocyte-derived dendritic cells in treated with/without LPS and with/without CESi (WWL113). Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000344

• Small RNA sequencing of human oocytes and early embryos

  This dataset contains single-end fastq files for human oocytes (n=12), zygotes (n=5), and early embryos (n=10) sequenced with Illumina NextSeq500. The sequencing libraries were prepared from single oocytes, zygotes, and embryos in two batches.

  Dataset EGAD50000000227

• Single-nucleus RNA-sequencing of normal adrenal cortex and adrenocortical tumors

  This study reports a single-nucleus transcriptome atlas of steroid, stromal and immune cells in 38 human normal adrenals and adrenocortical tumors.

  Study EGAS50000000585

• Integrated Multiomics Uncovers Distinct Macrophage Alterations in Human Metabolic dysfunction-Associated Steatohepatitis Progression

  We report single-nuclei RNA sequencing data (n=18) from human livers in metabolic dysfunction-associated steatotic liver disease (MASLD) patients. there are 5 MASH, 4 MASL, 5 control obese and 4 control lean samples.

  Dataset EGAD50000001129

• Kidney tumour_DNA (2018-09-19)

  This is a bulk DNA and RNA sequencing study of human renal tumours . This dataset contains all the data available for this study on 2018-09-19.

  Dataset EGAD00001004346

• Data set for pan.met study

  The dataset referenced by EGA Study ID EGAS00001004208 includes 20 human exome sequencing data and 11 human RNA sequencing data from tumor or normal tissues. Each sequencing data includes two pair-end short read files in fastq format.

  Dataset EGAD00001005957

• Whole transcriptome profiling of osteosarcoma

  This dataset contains 86 osteosarcoma samples and their matched normals that underwent RNA sequencing using size fractionation, NuGEN Ovation Ultralow Library System V2 preparation, and paired-end sequencing on Illumina HiSeq 2000.

  Dataset EGAD00001008436

• Sequencing data for oesophageal / related samples - Foley, Shorthouse et al (RNA)

  Data supporting: "SMAD4 and KCNQ3 Alterations are Associated with Lymph Node Metastases in Oesophageal Adenocarcinoma" RNAseq (FASTQ files) 6 samples

  Dataset EGAD00001011065

• Whole transcriptome profiling of osteosarcoma

  This dataset contains 86 osteosarcoma samples and their matched normals that underwent RNA sequencing using size fractionation, NuGEN Ovation Ultralow Library System V2 preparation, and paired-end sequencing on Illumina HiSeq 2000.

  Dataset EGAD00001008435

• Comparative transcriptome of CD34+ hematopoietic progenitors from myeloproliferative patients and control donors

  Comparative transcriptome of CD34+ hematopoietic progenitors from 4 myeloproliferative patients (MPN) and 4 control donors performed by RNA-Sequencing.

  Dataset EGAD00001007531

• Transcriptome Analysis of CLL patient samples

  This dataset includes Illumina RNA Sequencing Data for 59 chronic lymphocytic leukemia patient samples. 57 samples are single end, 2 samples are paired end sequencing.

  Dataset EGAD00001008320

• RNASeq read files of glioblastoma PDX samples

  This dataset contains 46 fastq files of paired-end RNA sequencing of an Illumina®️ TrueSeq stranded mRNA library of 23 glioblasoma PDX samples.

  Dataset EGAD00001010196

• Gene expression profile of mesothelial cells from peritoneal adhesion biopsies

  RNA-sequencing analysis was carried out on mesothelial cells isolated from peritoneal adhesion biopsies and compared to control human peritoneal mesothelial cells to identify a mesothelial-to-mesenchymal transition (MMT)-related gene signature in patients.

  Dataset EGAD00001008324

• Sequencing data for oesophageal / related samples - Kazachenka et al (RNA)

  Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" RNAseq for 279 samples

  Dataset EGAD00001011076

• Skin Fibroblast Transcriptome of Type 2 Diabetic Patients

  Comparative analysis of transcriptomes of skin fibroblasts in 17 Type 2 Diabetic individuals by RNA sequencing.

  Dataset EGAD00001004980

• Primary Lung Cancer whole genome study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. 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.

  Dataset EGAD00001000388

• Comprehensive genomic characterization of early stage bladder cancer - whole exome sequencing data

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed WES data from 438 patients. The dataset is composed of 876 BAM files: 438 tumor samples and 438 paired blood samples.

  Study EGAS50000000511

• Exome Recapture and Sequencing of Prospectively Characterized Clinical Specimens From Cancer Patients

  The study cohort comprises samples from patients whose tumors have been prospectively characterized as part of their care at Memorial Sloan Kettering Cancer Center. This includes a variety of distinct tumor type and molecular subtypes.

  Study phs001783

• The dataset for Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer

  The dataset for “Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer” includes 496 cram files from whole genome next-generation sequencing on the Illumina NovaSeq 6000. The samples analyzed include tumor tissue, matched buffy coat and longitudinal plasma samples from individuals with pancreatic cancer.

  Dataset EGAD50000001353

• Tumor gene project

  The study focuses on human tumor susceptibility as well as somatic cancer genomics. We use high-throughput sequencing approaches to achieve a comprehensive molecular characterization of tumors. Our goal is to better understand their genesis and management opportunities.

  Study EGAS50000000984

• Breast Cancer PDTX Encyclopaedia

  Molecular data from the collection of PDTX breast cancer models described in Bruna et al, 2016. Cell. It includes whole exome sequencing, shallow whole genome sequencing, expression arrays and reduced bisulfite representation sequencing (RRBS).

  Study EGAS00001001913

• BASIS_RNAseq

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000707

• Lung_Multi_site_Targeted_Sequence_Capture

  DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Study EGAS00001000436

• Breast_Cancer_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000210

• Harnessing_transposons_for_drug_resistance_gene_discovery_in_cancer

  This study involves a forward genetic screen to identify common insertion sites in drug resistant clones. We will be utilising piggybac transposon systems in order to generate multiple drug resistant clones in a range of human cancer cell lines.

  Study EGAS00001000468

• Multisite_Primary_Breast_Cancer

  DNA extracted from multiple biopsies taken from different areas of primary breast tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Study EGAS00001000891

• Genome and transcriptome sequence data from a metastatic serous ovarian cancer patient

  Genome and transcriptome sequence data from a metastatic serous ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004909

• Genome and transcriptome sequence data from a rectosigmoid adenocarcinoma (colorectal cancer) patient

  Genome and transcriptome sequence data from a rectosigmoid adenocarcinoma (colorectal cancer) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002567

• Genome and transcriptome sequence data from an adenocarcinoma of primary unknown cancer patient

  Genome and transcriptome sequence data from an adenocarcinoma of primary unknown cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002577

• Genome and transcriptome sequence data from a GI primary (prev breast cancer) patient

  Genome and transcriptome sequence data from a GI primary (prev breast cancer) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002979

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004923

• Genome and transcriptome sequence data from a large intestine-colon cancer patient

  Genome and transcriptome sequence data from a large intestine-colon cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005885

• Genome and transcriptome sequence data from a non-small cell lung cancer patient

  Genome and transcriptome sequence data from a non-small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001969