7367 results for "canc*"

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• The genomic landscape of large and small tumors in early-onset prostate cancer patients

  This study characterizes the genomic landscape of prostate cancer (PCA) cells in patients below or at the age of 50 years. Tumors of such early onset patients already show a broad spectrum of sizes. To test if the size differences are indicative of special cancer subgroups, we sequenced the genome of the tumor cells and matched control samples from blood.

  Study EGAS00001000383

• A Cancer Cell-Line Titration Series for Evaluating Somatic Classification

  Accurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies. Cell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300x. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1,500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease. Our cell-line titration series dataset, along with the associated verification results, is effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development.

  Study EGAS00001001016

• ICGC PanCancer Analysis of Whole Genomes

  The Pancancer Analysis of Whole Genomes (PCAWG) study is an international collaboration to identify common patterns of mutation in more than 2,800 cancer whole genomes from the International Cancer Genome Consortium. Building upon previous work which examined cancer coding regions (Cancer Genome Atlas Research Network, The Cancer Genome Atlas Pan-Cancer analysis project, Nat. Genet. 2013 45:1113), this project is exploring the nature and consequences of somatic and germline variations in both coding and non-coding regions, with specific emphasis on cis-regulatory sites, non-coding RNAs, and large-scale structural alterations.

  Study EGAS00001001692

• Single cell sequencing of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

  The quantity of tumor infiltrating lymphocytes (TILs) in breast cancer (BC) is a robust prognostic factor for improved patient survival particularly in triple negative and HER2-overexpressing BC subtypes. Whilst T cells are the predominant TIL population, the relationship between quantitative and qualitative differences in T cell subpopulations and patient prognosis remains unknown. We performed single-cell RNA sequencing (scRNA-seq) of 6311 T cells isolated from human BCs, and show for the first time that significant heterogeneity exists in the infiltrating T cell population. We demonstrated that high TIL BCs contained significant numbers of CD8+ T cells with features of tissue-resident memory T (TRM) cell differentiation and that these CD8+ TRM cells expressed high levels of immune checkpoint molecules and effector proteins. A CD8+ TRM gene signature developed from the scRNA-seq data was significantly associated with improved patient survival in early-stage triple negative breast cancer (TNBC) and provided better prognostication compared with CD8 expression alone. Our data suggests that CD8+ TRM contribute to BC immunosurveillance and are the key targets of modulation through immune checkpoint inhibition. Further understanding of the development, maintenance and regulation of TRM cells will be crucial for successful immunotherapeutic development in BC.

  Study EGAS00001002845

• AUBTRG - Whole Exome Sequencing of Diffuse Glioma Samples

  Study EGAS00001003035

• Transcriptome Sequencing Data of High Grade Serous Ovarian Cancer

  Study EGAS00001004714

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

  Study EGAS00001004800

• Integrated Genomic and Transcriptomic Analysis Reveals Unique Characteristics of Hepatic Metastases and Pro-metastatic Role of Complement C1q in Pancreatic Ductal Adenocarcinoma

  Study EGAS00001004821

• DEREGULATION OF PRE-mRNA SPLICING IN MISMATCH REPAIR DEFICIENT COLORECTAL CANCER

  Study EGAS00001004863

• EAC Genomic data

  Study EGAS00001004887