7296 results for "canc*"

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• Feasibility_of_targeted_capture_sequencing_in_FFPE_cancer_specimens_2

  Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Study EGAS00001000402

• Clonal_architecture_of_pre_malignant_and_malignant_tumours

  Single cells have been isolated from normal and pre-invasive lung cancer lesions from one patient. These have been grown into colonies that will then be whole genome sequenced. This will reveal the mutational burden in normal and premalignant tissues, and the heterogeneity between different cells.

  Study EGAS00001001676

• Angiosarcoma_targeted_pulldown_cancer_gene_panel

  Extension of angiosarcoma whole genome sequencing study

  Study EGAS00001000589

• Profiling the genomic landscape and evolutionary history of polyploid giant cancer cells in undifferentiated pleomorphic sarcomas

  Polyploid giant cancer cells (PGCCs), characterised by multi-nucleation and atypical nuclear morphology, are a common feature of undifferentiated pleomorphic sarcomas. While PGCCs may be a critical substrate for cancer evolution, their formation pathways and the genomic consequences of PGCCs remain relatively under explored. In this study, we characterise PGCCs in undifferentiated pleomorphic sarcomas, as well as their histological mimics, and use topographic single-cell DNA sequencing (scDNA-seq) to investigate their genomic landscape. We selected PGCCs based on their nuclear morphology, including mono-nucleated or multi-nucleated bizarre, misshapen nuclei and analysed them at single-cell resolution. Our findings highlight PGCCs as a highly heterogeneous and evolutionarily dynamic component of undifferentiated pleomorphic sarcomas.

  Study EGAS50000001445

• Genomic analysis reveals novel secondary drivers and progression pathways in skin basal cell carcinoma

  Basal cell carcinoma of the skin (BCC) is the most common malignant neoplasm in humans. BCC is primarily driven by the aberrant activation of the Sonic Hedgehog (Hh) pathway. However, its extensive phenotypical variation remains to be explained. The genetic profiling of 293 BCCs revealed the highest mutation rate observed in cancer (65 Mutations/Mb), with strong prevalence of UV-light signature mutations. 85% of BCCs harbored mutations in Hh pathway genes: mutually exclusive PTCH1 (73%) and SMO (20%) (P=6.6x10-8), SUFU (8%), and in TP53 (61%). 85% of BCCs also harbored secondary driver mutations in other genes implicated in BCC tumorigenesis. Recurrent secondary driver mutations were observed in MYCN (30%), PPP6C (15%), STK19 (10%), LATS1 (8%), ERBB2 (4%), PIK3CA (2%), RAC1 (1%) and N/K/H-RAS (2%). Loss of function (LoF) and deleterious missense mutations were observed in PTPN14 (23%), RB1 (8%) and FBXW7 (5%). In line with the mutational profiles detected by RNAseq, we observed activation of the Hh pathway as well as upregulation of target genes of the Hippo-YAP pathway and activation of MYCN target genes. The functional analysis of the novel tumorigenic driver mutations in MYCN, PTPN14 and LATS1 demonstrates their relevance in BCC tumorigenesis and provides an expanded molecular understanding of BCC.

  Study EGAS00001001540

• Whole genome sequencing and whole exome sequencing of DIPG tumors and matched normal tissue

  Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling.

  Study EGAS00001000575

• WES Analysis of precancerous lesions in Lynch Syndrome

  The project focuses on identifying the genetic alterations involved in the early stages of tumor development in individuals with Lynch Syndrome. Using Whole Exome Sequencing (WES), the study aims to characterize somatic mutations and molecular pathways that drive the transformation from normal tissue to precancerous lesions. This research contributes to a better understanding of tumorigenesis in hereditary colorectal cancer syndromes.

  Study EGAS50000001546

• Whole_Exome_PC9_and_A375

  Drug resistant population of PC9(human non-small cell lung cancer) or A375 (human melanoma) cell lines were used for this study. By exome sequencing, we will analyse mutations of cells in drug tolerent state and after drug holiday.

  Study EGAS00001002493

• BCAC TIIC Data

  Data on spatially-resolved tissue infiltrating immune cells (TIICs) from 17,265 breast cancer patients of European descent, from studies participating in the Breast Cancer Association Consortium, together with linked clinical data.

  Study EGAS50000001477

• Integrative analysis of whole genome sequencing, RNA sequencing and methylome array of 20 carcinosarcomas.

  Carcinosarcomas of the female genital tract, or GCS, are uncommon but clinically highly aggressive neoplasms with biphasic histology of carcinomatous (C) and sarcomatous (S) elements. These tumors represent a unique model to study the genetic and phenotypic diversity of cancer cells and the link between cellular plasticity and resistance to therapy. The aim of ICGC GCS program is to genomically characterize C and S components of 20 tumors, from endometrium or ovary, through an integrative analysis of whole genome sequencing, RNA sequencing and methylome array.

  Study EGAS00001002271

• MPNST - 10X single nucleus DNAseq

  Understanding the spatial and temporal dynamics of tumour evolution is crucial for determining the drivers of cancer progression. Here, we comprehensively profile a primary malignant peripheral nerve sheath tumour (MPNST) and its recurrence with a multi-omic and spatial approach at single-cell resolution. Leveraging the extensive heterogeneity in copy number aberrations (CNAs) as a native barcoding system, we fully resolve the evolutionary tree of this tumour revealing multi-furcations suggestive of ongoing chromosomal instability. We show gene dosage effects contribute to phenotypic diversity and are predominantly linear with the exception of FOS in a specific subclone. Using laser capture microdissection, we performed spatial lineage tracing in a human tumour, elucidating the relationship between local expansions and interactions between tumour cells and the microenvironment.

  Study EGAS50000001790

• The spatial organization of intratumor heterogeneity andevolutionary trajectories of metastases in hepatocellular carcinoma

  Hepatocellular carcinoma (HCC) has one of the poorest survival amongst cancers. Using multi-regional sampling of nine resected HCC with different etiologies, we find that phylogenetic relationships of these sectors show diverse levels of genetic sharing spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear Isolation-By-Distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumor diversification respectively. Interestingly, metastatic tumors had much higher variability than their primary tumors, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumor heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy.

  Study EGAS00001001603

• Whole-genome sequencing analysis of low-grade astrocytomas within the ICGC PedBrain Tumor Project

  In order to investigate the full range of genetic alterations contributing to the tumourigenesis of low-grade astrocytoma, we have conducted a next-generation sequencing-based analysis on a large series of matched tumor-normal pairs. This study, conducted by the International Cancer Genome Consortium PedBrain Tumor Project (ICGC PedBrain, http://www.pedbraintumor.org/), has revealed multiple new insights into the biological basis of this tumor entity.

  Study EGAS00001000381

• Single cell RNA sequencing and Whole Genome Sequencing on different cells from the same sample for a triple negative patient derived xenograft and ovarian cancer cell lines.

  Measuring gene expression of genomically defined tumour clones at single cell resolution would associate functional consequences to somatic alterations, as a prelude to elucidating pathways driving cell population growth, resistance and relapse. In the absence of scalable methods to simultaneously assay DNA and RNA from the same single cell, independent sampling of cell populations for parallel measurement of single cell DNA and single cell RNA must be computationally mapped for genome-transcriptome association. Here we present clonealign, a robust statistical framework to assign gene expression states to cancer clones using single-cell RNA-seq and DNA-seq independently sampled from an heterogeneous cancer cell population. We apply clonealign to triple-negative breast cancer patient derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either DNA-Seq or RNA-Seq alone.

  Study EGAS00001003387

• MDSMPN_Rearrangement_Screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from 11 Myelodysplastic Myeloproliferative neoplasms (MDSMPN) and subjected to total of two lanes of 50 bp, paired end sequencing on the llumina HiSeq. 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 EGAS00001000034

• Long-read Nanopore and Ion Torrent sequencing data for BRCA1/2 variant detection

  This dataset contains long-read sequencing data generated using Oxford Nanopore Technologies for the analysis of BRCA1 and BRCA2 variants in individuals referred for hereditary breast cancer genetic testing. The study includes samples previously analyzed using Ion Torrent sequencing, enabling comparison between short-read and long-read sequencing approaches.

  Study EGAS50000001783

• Whole-genome sequencing of high-retrotransposition rate tumours

  We performed whole-genome sequencing of 137 tumours and their matched-normal (adjacent tissue) samples to identify tumours with high rates of somatic retrotransposition

  Study EGAS50000000414

• MPNST - 10X single nucleus RNAseq

  Understanding the spatial and temporal dynamics of tumour evolution is crucial for determining the drivers of cancer progression. Here, we comprehensively profile a primary malignant peripheral nerve sheath tumour (MPNST) and its recurrence with a multi-omic and spatial approach at single-cell resolution. Leveraging the extensive heterogeneity in copy number aberrations (CNAs) as a native barcoding system, we fully resolve the evolutionary tree of this tumour revealing multi-furcations suggestive of ongoing chromosomal instability. We show gene dosage effects contribute to phenotypic diversity and are predominantly linear with the exception of FOS in a specific subclone. Using laser capture microdissection, we performed spatial lineage tracing in a human tumour, elucidating the relationship between local expansions and interactions between tumour cells and the microenvironment.

  Study EGAS50000001787

• Benchmarking_CRISPR_Whole_genome_Drop_out_Screen___B_S

  This study is a benchmarking exercise to explore potential source of variation between different CRISPR drop out libraries.

  Study EGAS00001002931

• The Genomic Landscape of Prostate Cancer Brain Metastases

  Study EGAS00001004557

• PREDICT

  PREDICT/Predicting individual response and resistance to VEGFR/mTOR pathway therapeutic intervention using biomarkers discovered through tumour functional genomics.

  Study EGAS00001000094

• Most HCCs in Taiwan show the mutational signature of aristolochic acid

  Plants in the genus Aristolochia contain the mutagen aristolochic acid (AA) and have been widely used in traditional medicines and for weight loss. AA binds covalently to genomic DNA and induces a highly distinctive mutational signature. While AA involvement in urinary-tract cancers in Taiwan is known, the possible role of AA in hepatocellular carcinomas (HCCs) in Taiwan has not been examined. Here, we whole-exome sequenced 98 unselected HCCs from Taiwan and analyzed the mutational signatures for evidence of AA mutagenesis. Remarkably, more than 78% of HCCs showed strong evidence of AA mutagenesis, often associated with high mutation burdens. Non-synonymous mutations in genes known to be HCC driver genes were detected. Importantly, we elucidated the potential of immunotherapy in this cohort of liver cancer patients.

  Study EGAS00001002301

• Recurrent intra-tumour heterogeneity is a hallmark of metastatic prostate cancer

  The evolution of cancers from low grade to metastatic disease is a major determinant of cancer mortality. Cancer evolution involves a complex interplay between cell intrinsic genetics and transcriptional alterations and the extrinsic microenvironment. To define the key mechanisms underpinning metastatic development, we focused on the most lethal form of prostate cancer, metastatic castration-resistant prostate cancer, and employed single-cell multi-omics and whole-genome sequencing to deeply profile 34 metastatic lesions from 9 patients obtained from rapid autopsy. We found that intra-tumour heterogeneity is an indicator of key evolutionary processes, characterised by recurrent tumour populations acting as critical functional components of the tumour ecosystem, irrespective of clonal and microenvironmental backgrounds. Unexpectedly, microenvironments across metastatic sites played a limited role while clonal evolution primarily promoted transcriptional noise. Intra-patient functional convergence of tumour ecosystems was observed across metastatic sites, pointing towards system-level selection pressures that drive the heterogeneity landscape of mCRPC. Our findings reveal functional evolutionary convergence of metastatic disease into units of intra-tumour heterogeneity identifying critical determinants of metastatic progression for therapeutic targeting. Note: matched WGS for some tumour single-cell experiments, as well as germline WGS for patients CA0027, CA0034, CA0035, CA0043, and CA0076, can be found in EGAS00001006598.

  Study EGAS50000001312

• Acute_Lymphoblastic_Leukemia_Exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Acute Lymphoblastic Leukemia samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000201

• Mutant_clone_mapping_in_normal_oesophagus

  We will use targeted exome sequencing to examine normal appearing epithelium and whole exome and whole genome sequencing of microdissected clones identified by immunostaining Some of the samples will be of low DNA concentration and therefore may require extra rounds of amplification during library prep.

  Study EGAS00001001874