12345 results for "cancer rna-seq"

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• NOWAC blood-based breast cancer case-control study

  Tumor-host interactions extend beyond the local microenvironment and cancer development largely depends on the ability of malignant cells to hijack and exploit the normal physiological processes of the host. Although abnormalities in a host’s systemic immunity are associated with increased cancer susceptibility, the functional interplay between tumor cells and circulating immune cells in regulating tumorigenic responses is unclear. We employed the Norwegian Women and Cancer study, a large prospective population-based cohort study, to identify gene expression changes in blood cells that provide a robust and reproducible diagnostic signal specific to breast cancer patients. We further show that circulating blood cells in breast cancer patients are enriched in genes involved in systemic immunosuppression and the motility, metabolism, growth, and proliferation of immune cells. By mining of the cancer-associated blood transcriptome, we identified immune mediators or biomarkers that could permit early detection of breast cancer and open avenues to novel targeted immunotherapies.

  Study EGAS00000000134

• Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

  Somatic mutations are a hallmark of tumorigenesis and may be useful for non-invasive diagnosis of cancer. We analyzed whole-genome sequencing (WGS) data from 2,511 individuals in the Pan-Cancer Analysis of Whole Genomes (PCAWG) study as well as 489 individuals from four prospective cohorts and found distinct regional and mutation type specific frequencies in tissue and cell-free DNA (cfDNA) of cancer patients that were associated with replication timing and other chromatin features. A machine learning model using genome-wide mutational profiles combined with other features and followed by CT imaging detected >90% of lung cancer patients, including those with stage I and II disease. The fixed model was validated in an independent cohort, detected patients with cancer earlier than standard approaches, and could be used to monitor response to therapy. This approach lays the groundwork for non-invasive cancer detection using genome-wide mutation features that may facilitate cancer screening and monitoring.

  Study EGAS00001007248

• CLL_targeted_exome_sequencing

  Aim to characterise cancer gene landscape in CLL, particularly in cases with mutated POT1 gene. Treatment-naïve CLL cases will be interrogated by targeted exome sequencing using a cancer gene panel.

  Study EGAS00001001963

• Reference_DNA_standards_for_GCLP_pipeline

  The use of reference DNA standards generated from cancer cell lines sequenced in the Cancer Genome Project to establish the sensitivity, specificity, accuracy and reproducibility of the WTSI GCLP sequencing pipeline

  Study EGAS00001001173

• cfDNA methylation profiling in Metastatic Cancer and Cancer of Unknown Primary

  This study contains methyl-binding domain sequencing and shallow whole genome sequencing from circulating cell-free DNA (cfDNA) for 143 patients with metastatic cancer of known type, 41 patients with Cancer of Unknown Primary (CUP) and 27 non-cancer controls.

  Dataset EGAD00001011178

• Evolution of Structural Rearrangements in Prostate Cancer Intracranial Metastases

  Intracranial metastases in prostate cancer are uncommon but clinically aggressive. We sought to characterize prostate cancer intracranial metastases in order to improve our understanding of their pathogenesis and to promote the search for new treatment strategies. We evaluated the clinical and molecular characteristics of 36 patients with metastatic prostate cancer to either the dura or brain parenchyma. We performed whole genome sequencing (WGS) on samples from 21 patients. The WGS samples include 10 intracranial prostate cancer metastases, as well as WGS of primary prostate tumors from men who later developed metastatic disease (n=6) and non-brain prostate cancer metastases (n=26).

  Study phs003357

• Targeted_analysis_of_chondrosarcoma_cancer_genes

  Targeted analysis of chondrosarcoma cancer genes

  Study EGAS00001001765

• Identification of Cancer Predisposition Genes in Breast Cancer Families

  Breast cancer has a significant genetic component. The strongest epidemiologic risk factor is family history of the disease. Familial studies have identified a number of genes contributing to increased risk. Of these, the highly penetrant BRCA1 and BRCA2 genes account for the majority of families in whom disease-causal mutations have been identified. However, mutations in other genes have been associated with predisposition to breast or breast and ovarian cancer including (CHEK2, ATM, PALB2, RAD51C, RAD51D). Together these genes account for less than 20% of excess familial breast cancer risk and do not explain ~50% of high-risk families referred for genetic testing. This significant gap in our understanding of the genetic basis of breast cancer poses a significant barrier to our ability to identify women at increased risk, who would benefit greatly from appropriate clinical management. To identify additional breast cancer predisposition genes whole exome sequencing of familial high-risk breast cancer patients was undertaken. DNA samples from 50 pairs of breast cancer patients from high-risk breast cancer families with no pathogenic mutations in the BRCA1 or BRCA2 breast cancer predisposition genes were subjected to whole exome sequencing. The goal was to select candidate predisposition genes for further validation studies based on sharing of putative protein inactivating mutations among both members of each family and/or the frequency of inactivating mutations among the 50 families.

  Study phs000480

• Genomic Characterization of African-American Prostate Cancer

  African-American men have the highest incidence and mortality rate from prostate cancer. This study represents a whole exome sequencing study of prostate cancer samples from African-American men. We performed exome sequencing and analysis of prostate tumors and matched normal tissues to identify somatic mutations and insertion/deletions across this cohort. All sequencing was performed at the Broad Institute. This study has the potential to identify novel recurrently mutated genes in prostate cancer and improve our understanding of prostate cancer in African-Americans.

  Study phs000945

• Human pan-cancer plasma cfRNA study - raw data

  This study contains mRNA capture sequencing data from plasma of 266 different human donors. The first, pan-cancer, cohort covers 25 high-grade to metastatic cancer types (8 cancer patients per type) and a control group (8 healthy donors). The validation cohort comprises additional plasma samples from ovarian, prostate and uterine cancer patients (12 per type) as well as additional samples from controls (22 new and 8 repeated). Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.

  Study EGAS00001006755