8213 results for "canc*"

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• Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Glioblastoma multiforme (GBM) is a lethal brain tumour in adults and children. However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases. To explore the genetic events underlying this distinction, we sequenced the exomes of 48 paediatric GBM samples. Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48). Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V) involved in key regulatory post-translational modifications. Mutations in ATRX (alpha-thalassaemia/mental retardation syndrome X-linked) and DAXX (death-domain associated protein), encoding two subunits of a chromatin remodelling complex required for H3.3 incorporation at pericentric heterochromatin and telomeres, were identified in 31% of samples overall, and in 100% of tumours harbouring a G34R or G34V H3.3 mutation. Somatic TP53 mutations were identified in 54% of all cases, and in 86% of samples with H3F3A and/or ATRX mutations. Screening of a large cohort of gliomas of various grades and histologies (n=784) showed H3F3A mutations to be specific to GBM and highly prevalent in children and young adults. Furthermore, the presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles. This is, to our knowledge, the first report to highlight recurrent mutations in a regulatory histone in humans, and our data suggest that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis.

  Study EGAS00001000226

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

  With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using the Roche/454 technology coupled with Nimblegen sequence capture. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely BWA-SW and SSAHA2, coupled with the variant calling algorithm Atlas-SNP2 yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations.

  Study EGAS00001000268

• Inferring tumor genomes from peripheral blood i.e. CTCs and plasma-DNA using deep sequencing and targeted enrichment

  In this study we tested whether complex tumor genomes can be inferred from the peripheral blood (plasma DNA /CTCs) of 32 patients with stage IV colorectal carcinoma (CRC). To establish the percentage of mutated plasma DNA fragments we used 8 patient samples with different plasma DNA size distributions and KRAS mutations in their corresponding primary tumors and employed ultra-deep pyrosequencing with 3 different sequencing reaction sizes (i.e., 119 bp, 168 bp, and 323 bp). Furthermore, we used massive parallel sequencing of a panel of 68 CRC-associated genes to establish the mutation spectrum of cancer driver genes in the primary tumors, metastases, and CTCs of two colorectal cancer patients. To investigate, whether mutations found in only one CTC (“private CTC mutations”) are true mutations occurring with allele frequencies below the resolution limits of current detection methods, or whether they are amplification or sequencing artifacts, we performed ultra-deep sequencing of the primary tumors, metastases, plasma DNAs and normal tissues.

  Study EGAS00001000337

• Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single nucleotide variants and tumoral heterogeneity by massively parallel sequencing

  Tumor-derived DNA can be found in the plasma of cancer patients. We explored the use of shotgun massively parallel sequencing of plasma DNA obtained from cancer patients to scan a cancer genome noninvasively. We achieved the profiling of copy number aberrations and point mutations, in a genomewide manner using this approach. By measuring the genomewide aggregated allelic loss and point mutations, we determined the fractional tumor-derived DNA concentrations in plasma and correlated these values with tumor size and surgical treatment. We have also demonstrated the application of this approach to monitoring a complex oncologic scenario, in a patient with two synchronous cancers. In particular, through the use of multi-regional sequencing of tumoral tissues and shotgun sequencing of plasma DNA, we have shown that plasma DNA sequencing is a valuable approach for studying tumoral heterogeneity. Shotgun plasma DNA sequencing is thus a powerful tool for cancer monitoring and research.

  Study EGAS00001000370

• 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

• 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

• 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

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

  Study EGAS00001005033

• Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

  Study EGAS00001004975

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

  Study EGAS00001005045

• Molecular analysis of inflammatory myofibroblastic tumor (WGS and WES)

  Study EGAS00001005081

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

  Study EGAS00001005111

• Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

  Study EGAS00001005115

• Identification of novel colorectal cancer predisposition genes

  Study EGAS00001005118

• An integrated multi-omic cellular atlas of human breast cancers

  Study EGAS00001005173

• Secondary Resistance to Anti-EGFR Therapy by Transcriptional Reprogramming in Patient-Derived Colorectal Cancer Models (hipo_B012)

  Study EGAS00001005320

• Evolutionary trajectories and clonal migration underlying tumor progression and lymph node metastasis in resectable lung cancer

  Study EGAS00001005242

• Mutations in ALK signaling pathways conferring resistance to ALK inhibitor treatment lead to collateral vulnerabilities in neuroblastoma cells

  Study EGAS00001005791

• Identification of early disease progression in ALK-rearranged lung cancer using circulating tumor DNA analysis (hipo_K34R)

  Study EGAS00001005327

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

  Study EGAS00001005313

• Novel de novo pathogenic variant in the GNAI1 as a cause of severe disorders of intellectual development with autistic features

  Study EGAS00001005355

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

  Study EGAS00001005358

• Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

  Study EGAS00001005472

• A renal cell carcinoma tumorgraft platform to advance precision medicine

  Study EGAS00001005516

• Pearl study

  Study EGAS00001005523

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

  Study EGAS00001005546

• Mutation and Microsatellite Burden Predict Response to PD-1 Inhibition in Children with Germline DNA Replication Repair Deficiency: An Observational Registry Study

  Study EGAS00001005579

• Berlin Neuroblastoma Dataset Update 2021

  Study EGAS00001005604

• Genomic Signatures Define Three Subtypes of EGFR-Mutant Stage II-III NSCLC With Distinct Adjuvant Therapy Outcomes

  Study EGAS00001005632

• DNA methylation and Panel sequencing for pancreatic neuroendocrine carcinomas (PanNECs) and pancreatic neuroendocrine tumors (PanNETs)

  Study EGAS00001005731

• IN UTERO ORIGIN OF MYELOFIBROSIS PRESENTING IN ADULT MONOZYGOTIC TWINS AFTER A PROLONGED DISEASE LATENCY

  Study EGAS00001005744

• Paired healthy & tumor organoid Biobank _B15PON

  Study EGAS00001005865

• Initial cohort of 500 solid tumors screened for Basket of Baskets

  Study EGAS00001005893

• Molecular analysis in bowel malignancies in cancer survivors vs. primary malignancies

  Study EGAS00001005940

• Patient-derived organoids_Vumc

  Study EGAS00001005947

• Overexpression of the miR-17-92 cluster in colorectal adenoma organoids induces a carcinoma-like genotype

  Study EGAS00001005949

• Oesophageal adenocarcinoma whole exome and RNA-seq raw sequencing data

  Study EGAS00001005957

• Targeted analysis of cell-free circulating tumor DNA is suitable for early relapse and actionable target detection in patients with neuroblastoma

  Study EGAS00001006027

• Tumour evolvability metrics predict recurrence in advanced localised prostate cancer (normal data)

  Study EGAS00001006098

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

  Study EGAS00001006148

• Enhancer profiling to identify identifies epigenetic markers of endocrine resistance in metastatic castration resistant prostate cancer patients

  Study EGAS00001006161

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

  Study EGAS00001006228

• Biomarker Data from KATHERINE: A Phase III Study of Adjuvant Trastuzumab Emtansine versus Trastuzumab in Patients with Residual Invasive Disease after Neoadjuvant Therapy for HER2-Positive Breast Cancer

  Study EGAS00001006229

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

  Study EGAS00001006247

• Molecular characterization of a renal cell carcinoma PDX cohort

  Study EGAS00001006249

• Shallow nanopore RNA sequencing enables transcriptome profiling for precision cancer medicine (Hipo_021)

  Study EGAS00001006317

• ATM germline variants in a young adult with chronic lymphocytic leukemia: 8 years of genomic evolution

  Study EGAS00001006268

• Characterization of alternative promoter usage in advanced prostate cancer

  Study EGAS00001006275

• Evolutionary histories of breast cancer and related clones

  Study EGAS00001006282

• Molecular determinants of outcomes in relapsed mantle cell lymphoma treated with ibrutinib or temsirolimus in the MCL3001 (RAY) trial

  Study EGAS00001006342

• Soft tissue sarcoma sequencing data

  Study EGAS00001006356

• RNAseq analysis on metastatic Colorectal Cancer xenografts samples

  Study EGAS00001006492

• Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation.

  Study EGAS00001006364

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

  Study EGAS00001006411

• WGS of PMBCL

  Study EGAS00001006452

• Complex patterns of genomic heterogeneity identified in 42 tumor samples and ctDNA of a pulmonary atypical carcinoid patient

  Study EGAS00001006530

• Sequencing Data of HGSC patient-derived cell lines and organoids

  Study EGAS00001006557

• bulk RNA-Seq of colorectal cancer patient samples

  Study EGAS00001006666

• Genomic profiling of subcutaneous patient derived xenograft models of solid childhood cancer

  Study EGAS00001006710

• Human primary and metastatic colorectal cancer (CRC) samples

  Study EGAS00001006746

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

  Study EGAS00001006820

• TK-EPN862 - Patient-dervied xenograft model of Posterior Fossa A Ependymoma - WGS

  Study EGAS00001006843

• Mechanism of action and resistance to Trastuzumab Deruxtecan in patients with metastatic breast cancer: the DAISY trial

  Study EGAS00001006905

• Genetic landscape of ENKTCL

  Study EGAS00001006906

• Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

  Study EGAS00001007291

• Whole Exome and RNA sequencing of synchronous female bilateral breast cancers

  Study EGAS00001006910

• Genomic Analysis of a Metastatic Fusion-negative Embryonal Rhabdomyosarcoma

  Study EGAS00001006946

• Treated and control Patient Derived Xenografts of colorectal cancer (CRC) samples

  Study EGAS00001006973

• A capture-based next-generation sequencing panel for the molecular characterization of chronic lymphocytic leukemia

  Study EGAS00001006975

• Whole genome, RNA-seq and single-cell Multiome profile of multiple myeloma

  Study EGAS00001007014

• RNAseq analysis on primary sites Colorectal Cancer xenografts (PRX) samples

  Study EGAS00001007051

• LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients

  Study EGAS00001007072

• Point-of-care monitoring of head and neck cancer treatment response and recurrence development using nanopore-based ctDNA consensus sequencing

  Study EGAS00001007090

• Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells

  Study EGAS00001007091

• Human colorectal cancer single-cell RNA sequencing

  The aim was to investigate changes in transcriptomics following irradiation. This was studied in colorectal cancer-patient derived organoids. Analysis was performed with scRNA-seq.

  Study EGAS50000001348

• Genomic Landscape of Follicular Lymphoma Across a Wide Spectrum of Clinical Behaviors

  Study EGAS00001007105

• Persister cell phenotypes contribute to poor patient outcomes after neoadjuvant chemotherapy in PDAC (Hipo_015)

  Study EGAS00001007143

• HGSOC organoid sequencing study

  Study EGAS00001007189

• Integrated genetic analysis of primary CNS lymphoma

  Study EGAS00001007222

• Early ctDNA molecular response captures therapeutic response in the first stage of CCTG BR.36 ctDNA-directed, multi-center phase II study of molecular response adaptive immunotherapy in non-small cell lung cancer

  Study EGAS00001007298

• Breast cancer sequencing data

  Study EGAS00001007336

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

  Study EGAS00001007372

• Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

  Study EGAS00001007402

• Patient-derived organoids identify tailored therapeutic options and determinants of plasticity in sarcomatoid urothelial bladder cancer

  Study EGAS00001007430

• Finding structural variation and functional consequences from primary acute myeloid leukemia cells with complex karyotype (CK-AML) at the single-cell level

  Study EGAS00001007436

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

  Study EGAS00001007445

• BCL3-rearrangements in B-cell lymphoid neoplasms occur in two breakpoint clusters associated with different diseases

  Study EGAS00001007465

• Integrative genomic analyses of European intrahepatic cholangiocarcinoma: new ROS1 fusion gene and PBX1 as prognostic marker

  Study EGAS00001007525

• Low-coverage whole-genome sequencing of cancer and healthy plasma circulating DNA

  Study EGAS00001007593

• Neoantigen Peptides derived from V(D)J-recombined Immunoglobulins Drive Outgrowth of Cytolytic CD8+ T-cells

  Study EGAS00001008229

• Transposable elements are co-opted as oncogenic regulatory elements by lineage-specific transcription factors in prostate cancer

  Study EGAS00001007188

• 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

• Circulating RNAs prior to endometrial cancer diagnosis

  We analyzed circulating RNA levels using small RNA sequencing, targeting RNA in the size range 17 to 47 nucleotides, in samples collected prior to endometrial cancer diagnosis compared to cancer-free controls. The analysis included 316 cases with samples collected 1-11 years prior to diagnosis , and 316 matched controls, both from the Janus Serum Bank Cohort in Norway.

  Study EGAS50000000267

• Effects of Metformin on Transcriptomic and Metabolomic Profiles in Breast Cancer Survivors Enrolled in the Randomized Placebo-Controlled MetBreCS Trial

  Metformin reduces the incidence of breast cancer in patients with obesity and type 2 diabetes. However, our knowledge of the effects of metformin on breast cancer recurrence is limited. Within the randomized double-blind placebo-controlled phase II trial MetBreCS, we examined changes in breast tissue from breast cancer survivors with BMI >25 kg/m2 after treatment with metformin. To identify metformin-regulated signaling pathways, we integrated the transcriptomic, metabolomic and steroid hormone profiles using bivariate and functional analyses. We identified MS4A1, HBA2, MT-RNR1 and MT-RNR2 expression to be differentially expressed in breast tissues from metformin-treated women. We also found metformin-associated down-regulation of EGFL6 and FDCSP in postmenopausal women. The integration of transcriptomic and metabolomic profiles revealed down-regulation of immune response genes associated with reduced levels of arginine and citrulline in the metformin-treated group. The integration of transcriptomic and steroid hormone profiles showed an enrichment of steroid hormone biosynthesis and metabolism pathways with highly negatively correlated CYP11A1 and CYP1B1 expression in breast tissue from postmenopausal metformin-treated women. Our results indicate that breast cancer survivors treated with metformin have specific changes in breast tissue gene expression that may prevent the development of new tumors. Within the randomized double-blind placebo-controlled phase II trial MetBreCS, we examined changes in breast tissue from breast cancer survivors with BMI >25 kg/m2 after treatment with metformin using bulk RNAseq (total mRNA sequencing), that is deposited in Federated EGA. The steroid hormones, and metabolomics and the insulin sensitivity serum biomarker data underlying this article may be shared upon reasonable request to the PI of the MetBreCS study (Dr. Bernardo Bonanni), following approval by the Data and Safety Monitoring Board at IEO, Milan.

  Study EGAS50000000874

• A Combined Omics and Tissue Biobank for Paediatric Cancers

  The Swedish Childhood Tumour Biobank (BTB) is a nonprofit national infrastructure for samples and genomic data collection from pediatric patients diagnosed with central nervous system and other solid tumours in Sweden. Fresh frozen tumour tissue and patient’s matched blood are collected from affected patients and genomic data is continuously generated and made available for approved medical research projects. We expect that the accessibility of biological samples and/or data to the research community will contribute to further advances in the understanding of tumour biology, which in turn will impact many aspects of clinical care of children with cancer, by refining diagnosis and/or identifying oncogenic drivers and therapeutic targets.

  Study EGAS50000000209