11770 results for "cancer rna-seq"

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• Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue

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

  Study EGAS00001008283

• Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue

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

  Study EGAS00001008279

• Bulk_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue

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

  Study EGAS00001008278

• Single cells of colorectal cancer organoids

  Dataset contains 854 single cell sequenced colorectal cancer organoids.

  Dataset EGAD00001005422

• FFPE Normal Panel V3 Cancer Panel

  FFPE normal panel generation for use with V3 cancer panel 0618521

  Dataset EGAD00001001122

• 108 samples liver cancer and normal controls (54 pairs), whole exome sequencing

  liver cancer paired with normal controls, viral and non-viral origin

  Dataset EGAD00001006005

• Single Cell RNAseq of PBMC from renal cancer patients

  Single Cell RNAseq of PBMC from renal cancer patients

  Dataset EGAD00001006175

• Genomic and Genetic Characterization of Prostate Tumors Treated with Neoadjuvant Intense Androgen Deprivation Therapy

  The purpose of this study was to develop better ways of detecting prostate cancer before and after pre-operative treatment, and to test the feasibility of multi parametric magnetic resonance imaging (mpMRI) for the localization and detection of focal prostate cancer both before and after pre-operative treatment with ADT and enzalutamide. In this study, patients with intermediate and high risk prostate cancer received six months of neoadjuvant intense androgen deprivation therapy prior to radical prostatectomy. Biopsies were acquired prior to treatment. Tissue from biopsy and radical prostatectomy were subjected to sequencing and analysis for determination of features associated with response or resistance to treatment.

  Study phs001938

• Integrative Analysis of Lung Adenocarcinoma in EAGLE (Version 2)

  We performed a comprehensive analysis of intratumor heterogeneity of somatic mutations in cancer driver genes, copy number aberrations and DNA methylation in 292 tumor samples from 84 lung adenocarcinoma (LUAD) patients from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. SNVs of 37 established lung cancer driver genes were profiled by deep target sequencing in 180 tumor samples and 55 blood samples and 1 buccal sample from 56 subjects. Somatic copy number alterations were profiled using SNP arrays in 268 tumor samples from 80 subjects. DNA methylation levels were profiled with methylation arrays in 205 tumor samples and 74 normal tissue samples from 68 subjects.

  Study phs001169

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD43291_Novaseq__WG_

  Cancer is a genetic disease caused by an accumulation of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from lung tissue to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. We will deeply sample from individuals with smoking-related lung diseases (COPD, pulmonary fibrosis, lung cancer) and those without smoking history. This will allow us to determine how these processes are different between these groups of individuals, and gain insight into the earliest stages of tumor development.

  Study EGAS00001003502

• 2014_Lung_sq_WES

  Purpose Lung squamous cell carcinoma (SqCC) is the second most prevalent type of lung cancer. Currently, no targeted-therapeutics are approved for treatment of this cancer, largely due to lack of systematic understanding of the molecular parthenogenesis of the disease. To identify therapeutic targets and comparatively analyze them in lung SqCC, we probed somatic alterations of Korean lung SqCC. Patients and Methods We performed massively parallel whole-exome sequencing of 104 Korean lung SqCC patients’ samples with matched normal samples. In addition, copy number analysis and transcriptome analysis were conducted for a subset of these samples. Clinical association with cancer-specific somatic alterations was investigated.

  Study EGAS00001002844

• The EGA joins EUCAIM, the European project powering AI and imaging in cancer research

  EUCAIM (EUropean Federation for CAncer IMages) is the cornerstone of the European Cancer Imaging Initiative, one of the flagships of the Europe’s Beating Cancer Plan (EBCP). The European Genome-Phenome Archive (EGA), as member of the EUCAIM consortium, attended the kick-off meeting organized this week in Brussels for the launch of the Initiative. The EGA will contribute to the project with the experience gained in the deployment of our federated network, the Federated EGA (FEGA), and the experience gained as partners of EuCanImage (AI4HI initiative) contributing to the definition of common data models, ontologies and data standards. The ultimate goal of the project is to unlock the power of imaging and Artificial Intelligence for the benefit of cancer patients, clinicians and researchers. The consortium will deploy a pan-European digital federated infrastructure hosting cancer-related images, and associated pathology, molecular and laboratory data from Real-World. This endeavour will provide a comprehensive dashboard for imaging data discovery, federated search, metadata harvesting, annotation and distributed data processing. EUCAIM joins 76 partners, gathering the experience and previous effort made by the different repositories of the AI4HI initiative, European Research Infrastructures and national/regional repositories. Find out more information about the EUCAIM launch here

  Blog the-ega-joins-eucaim

• Limited Association between HRR Gene Alterations and HRD in Molecular Tumor Board Cancer Samples: Who should be tested for HRD?

  Alterations in Homologous Recombination Repair (HRR) Pathway genes have been found to be associated with HR-Deficiency (HRD), which is an approved biomarker for PARP Inhibitor (PARPi) treatment. The aim of a Molecular Tumor Board (MTB) is to identify molecular alterations in cancer patients with advanced tumors that may suggest off-label treatment options. So far, few studies have analyzed the presence of HRR gene mutations and their association with HRD outside of clinical studies. Currently, no data on HRD testing in the setting of a MTB have been published. For the present study, a cohort of 237 patients encompassing 24 different tumor entities was collected from the MTB of the Comprehensive Cancer Center Erlangen-EMN. We show that an elevated Genomic Instability Score (GIS ≥ 42) can occur in samples with and without mutations in HRR-related genes. Overall, 38.1% of cancer samples with BRCA1/2 mutations, 10.9% of tumors with alterations in HRR genes other than BRCA1/2, and 4.3% of cancer samples without HRR gene mutations harbored an elevated GIS. Notably, our data show that various inactivating BRCA1/2 mutations are not associated with an elevated GIS. Taken together, panCancer assessment of HRD in addition to BRCA1/2 and other HRR gene mutational analysis is recommended to guide decisions regarding PARPi treatment. Further studies are needed to establish thresholds for GIS in non-ovarian cancer entities. Finally, HRD can be observed in 4.3% of BRCA1/2 and other HRR gene wildtype cancer samples, and may emerge as an independent biomarker for PARPi in the future.

  Study EGAS00001008063

• Integrated Genomic, Epigenetic, and Expression Analyses of Ovarian Cancer Cell Lines

  Epithelial ovarian carcinoma of all subtypes has one of the worst outcomes of any human cancer. To improve our understanding of underlying biology and therapeutic possibilities in this disease, we performed whole genome sequencing, methylation, and expression analyses of a comprehensive set of 47 ovarian cancer cell lines representing different histologic tumor subtypes. Given the challenges of genomic analyses in tumors without matched normal samples, we developed novel approaches for detection of somatic alterations and used these to identify sequence, copy number, and rearrangement changes and integrated these with genome-wide epigenetic and expression alterations. Ovarian cancer cell lines had molecular changes in genes involved in cell cycle, PI3K, RAS, BRCA, chromatin regulating, and p53 pathways, and displayed global mutation and methylation changes similar to primary ovarian carcinoma. We identified alterations not previously implicated in ovarian cancer including amplification or overexpression of ASXL1 and H3F3B, deletion or underexpression of CDC73 and members of the TGF beta receptor pathway, including TGFBR2, SMAD3 and SMAD4, in-frame rearrangements of YAP1-MAML2 and IKZF2-ERBB4, and fusions involving MET, NF1, FBXW7 and CCND1. Integrating cell line alterations with dose-response data using three targeted therapies revealed novel molecular dependencies, including increased sensitivity of tumors with PIK3CA and PPP2R1A alterations to PI3K inhibitor GNE-493, those with MYC amplifications to PARP inhibitor BMN673, and SMAD4 alterations to MEK inhibitor MEK162. Genome-wide analyses revealed intrachromosomal rearrangements as an improved measure of sensitivity to PARP inhibition compared to the homologous recombination defect (HRD) score. This study provides a comprehensive resource of molecular information for ovarian cancer cell line models and a pharmacogenomic platform for developing rational cancer therapeutic strategies.

  Study EGAS00001002998

• Genetics and therapeutic responses to TIL therapy of pancreatic cancer PDX models

  Pancreatic cancer is the 7th leading cause of cancer-related deaths worldwide. Checkpoint immunotherapy has not yet showed encouraging results in pancreatic cancer possibly owing to a poor immunogenicity and/or an immune suppressive microenvironment. The aim of this study was to develop patient-derived xenografts (PDX) models and to assess if autologous tumor-infiltrating lymphocytes (TILs) would have anti-tumoral activity in pancreatic cancer. Tumor biopsies from 29 patients were subcutaneously transplanted into NOG mice. Tumor growths were confirmed in 11 out of 29 transplantations. The PDX tumors histologically resembled their original biopsies, but since stromal cells in the PDX model tumors were from mouse, their gene expression differed from the original biopsies. Immune checkpoint ligands other than PD-L1 were expressed in pancreatic cancers but PD-L1 was rarely expressed. One of the three tumors that did express PD-L1 was an adenosquamous cancer and another had a mismatch repair deficiency. TILs were expanded from six tumors and were injected into NOG or human interleukin-2 transgenic-NOG (hIL2-NOG) mice carrying PDX tumors. Regression of tumors could be verified in hIL2-NOG mice in 3 of the 6 PDX models treated with autologous TILs, including the adenosquamous PDX model. In conclusion, PDX models of pancreatic cancer can be used to learn more about tumor characteristics and biomarkers, and to evaluate responses to ACT and combination therapies. The major benefit of the model is that modifications of T cells can be tested in an autologous humanized mouse model to gain preclinical data to support the initiation of a clinical trial.

  Study EGAS00001005596

• Evaluation of somatic mutations in urine samples as a non-invasive method for the detection and molecular classification of endometrial cancer

  Purpose: Current diagnostic methods for endometrial cancer lack specificity, leading to many women undergoing invasive procedures. The aim of this study was to evaluate somatic mutations in urine to accurately discriminate endometrial cancer patients from controls. Experimental Design: Overall, 72 samples were analyzed using next-generation sequencing with molecular identifiers targeting 47 genes. We evaluated urine supernatant samples from women with endometrial cancer (n=19) and age-matched controls (n=20). Cell pellets from urine and plasma samples from seven cases were sequenced; further, we also evaluated paired tumor samples from all cases. Finally, immunohistochemical markers for molecular profiling were evaluated in all tumor samples. Results: Overall, we were able to identify mutations in DNA from urine supernatant samples in 100% of endometrial cancers. In contrast, only one control (5%) showed variants at a variant allele frequency (VAF)≥2% in the urine supernatant samples. The molecular classification obtained by using tumor samples and urine samples showed good agreement. Analyses in paired samples revealed a higher number of mutations and VAFs in urine supernatants than in urine cell pellets and blood samples. Conclusions: Evaluation of somatic mutations using urine samples may offer a user-friendly and reliable tool for endometrial cancer detection and molecular classification. The diagnostic performance for endometrial cancer detection was very high, and cases could be molecularly classified using these noninvasive and self-collected samples. Additional multi-center evaluations using larger sample sizes are needed to validate the results and understand the potential of urine samples for the early detection and prognosis of endometrial cancer.

  Study EGAS00001007396

• PanCuRx Translational Research Initiative

  The goal of the PanCuRx TRI is to seek solutions to the high fatality rate of pancreatic adenocarcinoma (PDAC), the most common type of pancreatic cancer, by generating new knowledge about the genetics and biology of the disease, mechanisms of how tumours grow and tailored treatment options. PDAC is the fourth leading cause of cancer death in Canada and is expected to become the second-leading cause of cancer death within the next decade. The current five-year survival rate of eight per cent is the lowest of all epithelial cancers. There are major clinical challenges to treating the disease, including the fact that PDAC spreads to other parts of the body early so surgical removal of the tumour benefits few patients, that PDAC has proven relatively resistant to systemic therapies such as chemotherapy and that there has been limited benefit from the use of newer molecular targeted agents. The PanCuRx team has created the world’s first resource of tumour-purified PDAC whole genomes; more than 500 PDAC samples, with combined clinical annotation, have been successfully sequenced and analyzed at the Ontario Institute for Cancer research in Toronto. The resulting clinical genomic resource created from this data has led to multiple new findings that have established a framework to better understand PDAC biology and lays the foundation for new genomic approaches to better understanding the disease. The team also launched a clinical trial called COMPASS (Comprehensive Molecular Characterization of Advanced Ductal Pancreas Adenocarcinoma for Better Treatment Selection: A Prospective Study), which is recruiting patients with advanced PDAC (both locally advanced and metastatic) at The Princess Margaret Cancer Centre (PM) in Toronto. The study uses the molecular results from individual patient tumours to guide selection of better second line treatment on a case-by-case basis. The primary objective of the initial study was to assess the feasibility of collecting tumour materials from patients with advanced PDAC and delivering results within 56 days of biopsy. Having achieved this objective, the trial has expanded to other cancer centres across Canada. Pancreatic cancer is one of the most deadly forms of cancer and outcomes have not improved in four decades. The PanCuRx initiative is providing a better understanding of the disease and actively applying new knowledge to cancer patients through clinical trials. This knowledge will help to improve quality of life and prolong survival for pancreatic cancer patients worldwide.

  Study EGAS00001002543

• Duplex sequencing of selected breast cancer patients

  Investigation of post-zygotic and germline variants using whole exome and ultra-deep duplex sequencing in paired uninvolved margin and primaty tumor samples from 126 breast cancer patients with differing survival outcomes, with skin or blood samples as reference. Pairs of uninvolved margin and blood samples were also collected for 15 reduction mammoplasty patients without personal or familial history of cancer, serving as controls.

  Dataset EGAD50000000769

• WES of breast cancer patients and controls

  Investigation of post-zygotic and germline variants using whole exome and ultra-deep duplex sequencing in paired uninvolved margin and primary tumor samples from 126 breast cancer patients with differing survival outcomes, with skin or blood samples as reference. Pairs of uninvolved margin and blood samples were also collected for 15 reduction mammoplasty patients without personal or familial history of cancer, serving as controls.

  Dataset EGAD50000000770

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established three kinds of esophageal tumoroids derived from esophageal cancer patient. We performed whole exome sequencing to analyze genetic background of the tumoroids.

  Study JGAS000749

• Colorectal cancer genomics with primary and metastatic samples

  We performed whole genome sequencing of metastatic colorectal cancer from 16 patients. Normal adjacent tissue, primary tissue, and metastatic tissue were analyzed to uncover metastatic progression and difference between primary and distant metastatic lesions.

  Study EGAS00001006465

• Y_chromosome_mis_segregation_in_the_DLD_1_cell_line

  Study of the well-established DLD-1 colorectal cancer cell line, engineered with an inactivatable Y centromere that leads to mis-segregation. The goal is to gain insights into the mechanism of chromothripsis due to chromosome mis-segration.

  Study EGAS00001002551

• Breast_Cancer_Matched_Pair_Cell_Line_Whole_Genomes

  We propose to definitively characterise the somatic genetics of matched pair breast cancer cell lines through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000166

• Triple_Negative_Breast_Cancer_Whole_Genomes

  We propose to definitively characterise the somatic genetics of Triple negative 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 EGAS00001000092

• Transcriptome_Sequencing_of_Cancer_Cell_Lines

  In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Study EGAS00001000261