7147 results for "canc*"

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• 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

• RNA sequencing of in vitro generated suppressive myeloid cells using parental and Sialidase expressing A549 cancer cell lines

  Study EGAS00001007618

• Dataset for early breast cancer samples

  This dataset contains WGS data for 27 tumor, control and patient derived culture samples of patients with breast cancer. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X using TruSeq Nano DNA Kit. The sequencing was always paired

  Dataset EGAD50000000860

• EuroTARGET is a European study on mRCC, collecting clinical data, germline DNA, and tumor samples.

  For patients with metastatic renal cell cancer (mRCC), treatment choice is mainly based on clinical parameters. With many treatments available and the limited response to treatment and associated toxicities, there is much interest in identifying better biomarkers for personalized treatment. EuroTARGET aims to identify and characterize host- and tumor-related biomarkers for prediction of response to tyrosine kinase inhibitor therapy in mRCC. Here, we describe the EuroTARGET mRCC patient cohort.

  Study EGAS50000000798

• Brain Cancer Center Committee

  Dac EGAC50000000456

• Copy number profiling of circulating cell-free DNA from high grade serous ovarian cancer patients

  Study EGAS00001004670

• The Cancer Dependency Map (DepMap)

  The Cancer Dependency Map (DepMap) aims to accelerate precision cancer medicine by creating a comprehensive map of tumor vulnerabilities. The DepMap project genomically profiles a wide range of cancer models and characterizes them for their sensitivity to genetic and compound perturbations. The data is computationally analyzed to create a systematic overview of the genetic dependencies and compound sensitivities of cancer types and the predictive biomarkers that point to patient populations most likely to benefit from targeting of these vulnerabilities. The DepMap public portal has become a comprehensive resource to identify cancer vulnerabilities by providing datasets at scale, cutting-edge computational tools, and sophisticated visualization tools that together have accelerated the discovery of novel targets and biomarkers. Please visit Depmap.org to access the public portal.

  Study phs003444

• Genomic Landscape of Colorectal Cancer in a Multi-Ancestry Cohort

  Elucidating the tumor mutational landscape of colorectal cancer (CRC) in admixed and ancestrally diverse populations is essential to enable precision medicine advancements that benefit individuals of all backgrounds. This study draws from the Latino Colorectal Cancer Consortium (LC3) and other prior initiatives to characterize and examine the somatic mutational patterns of colorectal tumors in Hispanic/Latino/Latina patients (henceforth referred to as Latino) as compared to other racial and ethnic populations. It includes paired tumor-normal whole-exome sequencing from 718 patients with primary CRC (128 Latino and 469 non-Latino individuals) to investigate the associations between somatic mutational features and both self-reported ethnicity and genetic ancestry. Somatic mutations and inherited variants were called, and global genetic ancestry proportions (African, Asian, European, Native American) were estimated from inherited variants using ADMIXTURE based on reference samples from the 1000 Genomes Project (1KGP) and the Population Architecture using Genomics and Epidemiology (PAGE) Study. Associations between genetic ancestry and gene-level mutational status, microsatellite instability status, and tumor mutational burden were estimated using logistic regression, after adjusting for age at diagnosis, sex, tumor location, and stage.

  Study phs003464

• International Cancer Proteogenome Consortium (ICPC): Proteogenomics of Oral Squamous Cell Carcinoma in Taiwan

  Oral cavity squamous cell carcinoma (OSCC) is the major subtype (~90%) of oral cancer, which is leading cancer with high mortality worldwide. The environmental risk factors associated with OSCC are quite different in Taiwan as compared to other populations. In most non-Taiwanese populations, OSCC is often associated with tobacco chewing, cigarette smoking, alcohol drinking, or human papillomavirus (HPV) infection. In Taiwan, in contrast, the OSCC occurs mainly in males aged 30 years or older who have habitual betel nut chewing, cigarette smoking, and alcohol drinking. To uncover molecular mechanisms and identify new therapeutic strategies of oral squamous cell carcinoma, this study recruited 112 treatment-naïve OSCC patients and generated multi-omics data, including WES, RNA-Seq, TMT-labeled proteomes, and phosphoproteomes from paired normal/tumor tissues. We have investigated our multi-omics data, covering molecular characterizations such as mutation signatures, impacts of mutations on RNA/protein/phosphoprotein, RNA-protein correlation, somatic copy number alteration, and the relationship with RNA & protein, proteome, and phosphoproteome analysis (T vs NAT), novel peptides (somatic variants, neoantigens, CT antigens, T cell receptors, etc.), as well as molecular subtyping (& pathway analysis). Notably, we have discovered a higher frequency of APOBEC3B deletion polymorphism in the Taiwanese population, and APOBEC3A is a potential prognostic biomarker. Our proteogenomic data enable us to further stratify patients into four groups based on APOBE3A expression level, which is found inversely correlated with EGFR expression. Therefore, the patients with high EGFR and low APOBEC3A expression may benefit from anti-EGFR therapy, while those with low EGFR and high APOBEC3A expression may benefit from immunotherapy. To clarify if there is an interaction between genetic polymorphisms and betel nut chewing habit in Taiwanese OSCC, we plan to concurrently evaluate the effect of habitual betel nut chewing on the gene mutation pattern, the dysregulated protein/phosphoproteins as novel biomarkers and/or therapeutic targets, and the molecular subtyping of patients for effective treatments. 

  Study phs002580

• Childhood Cancer Data Initiative (CCDI): CCDI Pediatric In Vivo Testing Program - Leukemia

  The goal of this study is to molecularly characterize a large panel of pediatric acute lymphoblastic leukemia (ALL) patient-derived xenografts (PDXs) previously established in immune-deficient mice. These PDXs are utilized as part of the NCI-funded Pediatric Preclinical In vivo Testing (PIVOT) program to identify novel agents and combinations. Biospecimen data include next-generation sequencing (RNAseq, whole exome sequencing, DNA copy number variation), whole-genome analysis of cytogenetic abnormalities, and DNA fingerprint for quality control.

  Study phs003164

• A comprehensive DNA methylation landscape of human and mouse cell lines derived from hematological malignancies

  Human cancer cell lines constitute useful models to study the primary disease and many relevant findings in tumor biology have been originated from them since the first immortalized cell line (HeLa) was obtained. The easy experimental intervention, the purity of the transformed cells and their versatility to undergo high-throughput screenings represent advantageous features of the established cancer cell lines. In recent years, major efforts have characterized in detail the multiomics make-up of hundreds of cancer cell lines and studied their association with sensitivity to anticancer drugs. Most of these studies have been genetic-centric and have not characterized in detail the epigenetic profiles underlying the characteristics of these cells or their impact on the efficacy of antitumoral compounds. In this regard, a past version of a DNA methylation microarray or a less accessible and more time-consuming such as reduced representation bisulfite sequencing have been used in those attempts to interrogate the epigenetic setting. Herein, we have obtained the DNA methylation profiles of 210 cell lines derived from hematological malignancies utilizing comprehensive DNA methylation microarrays that interrogates more than 850,000 and 285,000 CpG sites from human and mouse genomes, respectively. Importantly, we also provide a pharmacoepigenetic example of the potential use of this resource by showing how DNA methylation can predict response to nucleoside analogues.

  Study EGAS50000000627

• Non-small cell lung cancer sequencing

  Study EGAS00001005499

• Atezolizumab Plus Chemotherapy With or Without Bevacizumab in Advanced Biliary Tract Cancer: Clinical and Biomarker Data From the Randomized Phase II IMbrave151 Trial

  PURPOSE Biliary tract cancers (BTCs) harbor an immunosuppressed tumor microenvironment (TME) and respond poorly to PD-1/PD-L1 inhibitors. Bevacizumab (anti-VEGF) plus chemotherapy can promote anticancer immunity, augmenting response to PD-L1 inhibition. PATIENTS AND METHODS This randomized, double-blind, proof-of-concept Phase II study enrolled patients (n=162) with previously untreated advanced BTC (IMbrave151; NCT04677504). Patients were randomized 1:1 to receive 3-weekly cycles of atezolizumab (1200 mg) plus bevacizumab (15 mg/kg) or atezolizumab plus placebo until disease progression or unacceptable toxicity. All patients received cisplatin (25 mg/m2) plus gemcitabine (1000 mg/m2; CisGem) on Days 1 and 8 every 3 weeks for up to 8 cycles. Stratification of patients was by disease status, geographic region, and primary tumor location. The primary endpoint was progression-free survival (PFS). No formal hypothesis testing was performed. Exploratory correlative biomarker analysis was undertaken using transcriptome analysis (n=95) and mutation profiling (n=102) on baseline tumor samples. RESULTS Between February and September 2021, 162 patients were enrolled. Median PFS was 8.3 months in the bevacizumab arm and 7.9 months in the placebo

  Study EGAS50000000387

• Single-cell targeted DNA-sequencing and protein sequencing

  We performed single-cell targeted DNA sequencing (MissionBio) on 13 high hyperdiploid B-ALL patients at diagnosis to study the genetic heterogeneity. For a number of patients single-cell surface protein antibody sequencing was added (DAB-seq) to better characterize the different cell types. Furthermore, additional samples during treatment were collected and analysed for some patients. In this way we want to study the clonal heterogeneity of these B-ALL samples, based both on mutations and CNVs, and identify resistant clones that could be targeted after relapse.

  Study EGAS50000000580

• Bone marrow breakout lesions act as key sites for tumor-immune cell diversification and exhaustion in multiple myeloma

  Multiple myeloma is a disease characterized by the expansion of cancerous plasma cells in the bone marrow. The bone marrow microenvironment plays a pivotal role in supporting myeloma growth and modulating tumor immunity. As the disease progresses, myeloma cells may become independent of the bone marrow environment, leading to extramedullary disease associated with poor prognosis. However, the early processes associated with bone marrow independence and its implications for disease and immune control remain poorly understood. Here, we employed comprehensive single-cell and spatial mapping to identify the disruption of the cortical bone and subsequent expansion of myeloma cells in breakout lesions as a key event in multiple myeloma pathogenesis and tumor immunity. Breakout lesions harbor an adapted niche and a unique immune microenvironment conferred by sustained immune-tumor interactions. In particular, tumor-reactive T cells with a highly exhausted phenotype, alongside unique NK cell and macrophage subtypes, specifically expanded in breakout lesions. Spatially-resolved genomic, transcriptomic and cellular analyses uncovered extensive intra-lesion heterogeneity, suggesting a divergent co-evolution of genomic variation and locally confined T cell responses in distinct subregions. Ultra-high plex imaging revealed that tumor-reactive T cells, together with other immune-regulatory cells and dendritic cells, co-expand and exhaust upon sustained tumor interactions in locally confined immune islands. In contrast, immune-regulatory macrophage and NK cell subsets operate spatially separated within myeloma cell deserts. Jointly, our analyses uncover bone marrow breakout lesions as a hotspot for tumor-immune cell interactions, diversification and exhaustion, representing a key event in myeloma pathogenesis with significant therapeutic implications.

  Study EGAS50000000304

• Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes

  Head and neck squamous cell carcinoma (HNSCC) tumors were sampled from 88 patients. Samples were implanted subcutaenously into the flank of NOD/SCID/IL2R-/- mice. Mice were then monitored weekly for tumor growth and the time of initial palpation was recorded. Mice were euthanized when tumors reached 15 mm in diameter or after 6 months. If no tumor formed by 6 months, the patient tumor was defined as Non-engrafter (N). RNA-seq was performed on all primary tumor samples and successfully engrafted patient-derived xenograft (PDX) samples.

  Study EGAS50000000714

• Molecular biomarkers in progression from refractory celiac disease to the lethal cancer variety enteropathy associated T cell lymphoma (EATL)

  Enteropathy associated T cell lymphoma (EATL) is frequently preceded by a state of refractoriness to the gluten-free diet, called “refractory celiac disease” or RCD. We aim to study which mutations and copy number aberrations are already manifest in RCD and to identify differences between RCD patients that do, and do not, develop EATL. We have applied whole exome sequencing to detect mutations and copy number aberration predictive for progression from RCD to EATL.

  Study EGAS00001006669

• Patient-derived models of primary breast cancer for preclinical development of novel neoadjuvant therapies

  Generation of the first large-scale cohort of mouse intraductal patient-derived xenograft (MIND-PDX) models of primary invasive breast cancer (IBC) and a collection of matched PDX-derived organoids (PDXO) representing all molecular subtypes of IBC, including estrogen receptor (ER-) positive breast cancer. Furthermore, we show that our IBC-MIND cohort can serve as a platform to test experimental neoadjuvant treatment options in different molecular subtypes of breast cancer.

  Study EGAS50000000398

• WES IDC samples

  PDX samples of breast cancer IDC mouse models created from patient tumor material of the NKI. Genomescan prepared the samples according to the procedure for Hybridization Capture using the Agilent SureSelectXT Human All Exon V7 kit. The prepared libraries were sequenced with Illumina sequencing technology. The samples are in fastq format and consist of the following PDX samples: IDC001, IDC125, IDC147, IDC200, IDC233, IDC244, IDC251, IDC272, IDC278, IDC281 and ILC120.

  Dataset EGAD50000001148

• PanelSeq IDC samples

  PDX samples of breast cancer IDC mouse models created from patient tumor material of the NKI. Genomescan prepared the samples according to the procedure for Hybridization Capture using an Agilent SureSelect custom 0.5-2.9Mb kit. The prepared libraries were sequenced with Illumina sequencing technology. The samples are in fastq format and consist of the following PDX samples: IDC025, IDC026, IDC029, IDC031, IDC032, IDC038, IDC057, IDC062, IDC065, IDC069, IDC072, IDC090B, IDC092, IDC097, IDC099, IDC107, IDC113, IDC117, IDC143, IDC152, IDC159A, IDC159B, IDC180, IDC186, IDC192, IDC197, IDC198, IDC207, IDC209, IDC216, IDC218, IDC222, IDC229, IDC232, IDC274, IDC282, IDC290, IDC299, IDC307, IDC338, IDC344, IDC346, ILC006, ILC012, ILC083 and ILC248.

  Dataset EGAD50000001149

• Count Me In (CMI): The Metastatic Breast Cancer (MBC) Project (CMI-MBCproject)

  Count Me In - The Metastatic Breast Cancer Project: A Patient-Driven Research Initiative to Accelerate Metastatic Breast Cancer Research The Metastatic Breast Cancer Project is a research study that directly engages patients with metastatic breast cancer via social media and advocacy groups and empowers them to accelerate cancer research by sharing their samples and clinical information. Our goal is to create a publicly available dataset of genomic, molecular, clinical, and patient-reported data to enable research. Patients in the US or Canada may register online. Registered patients are sent an online consent form that asks for permission to obtain and analyze their medical records, tumor tissue, saliva, and blood samples. Once enrolled, patients are sent a saliva kit and asked to mail back a saliva sample, which is used to extract germline DNA. Study staff contact participants' medical providers and obtain medical records and a portion of their stored tumor biopsies. Patients may be asked to mail in a blood sample, which is used to extract cell free DNA (cfDNA). Whole exome sequencing (WES) is performed on tumor DNA, germline DNA, and cfDNA; transcriptome sequencing is performed on tumor RNA. Clinically annotated genomic data are used to study specific patient cohorts (including outliers) and to identify mechanisms of response and resistance to therapies. All de-identified data, including genomic, clinical, and patient-reported data, are shared via public databases on a pre-publication and recurring basis as it is generated. The latest data release in cBioPortal is available here. Study updates are shared with participants regularly.

  Study phs001709

• Exome Recapture and Sequencing of Prospectively Characterized Clinical Specimens From Cancer Patients

  The study cohort comprises samples from patients whose tumors have been prospectively characterized as part of their care at Memorial Sloan Kettering Cancer Center. This includes a variety of distinct tumor type and molecular subtypes.

  Study phs001783

• Atezolizumab and Bevacizumab in Treating Patients With Rare Solid Tumors

  This phase Ib/II single-arm study evaluated atezolizumab + bevacizumab for patients with treatment-refractory metastatic HPV+ anal cancer. The primary endpoint was best overall response, and secondary endpoints included progression-free survival, overall survival, and safety/tolerability. Paired tissue biopsies were collected in patients before treatment and at the time of first restaging and analyzed for whole-exome sequencing, RNAseq (Bulk), and multiplex immunofluorescence. The overall response rate among 20 patients was 10%. WES and RNAseq data are provided here.

  Study phs003845

• Childhood Cancer Data Initiative (CCDI): Pediatric In Vivo Testing Program - Neuroblastoma

  The goal of NCI's Pediatric In Vivo Testing Consortium (PIVOT) is to advance the development of effective treatments for pediatric cancers through preclinical in vivo testing of novel therapeutic agents. To design impactful experiments that can be rapidly translated to the clinic, PIVOT investigators require comprehensive genomic characterization of the patient-derived xenograft (PDX) models used across the consortium. This robust experimental design enhances collaboration with industry partners by providing proof-of-concept data for drugs in development. As part of this effort, neuroblastoma PDX models are being molecularly characterized to identify promising therapeutic candidates. The molecular profiling includes whole exome sequencing (WES), RNA-seq, MethylEPIC array, CytoSNP array, and DNA fingerprinting for quality control. Additionally, demographic and clinical data (e.g., diagnosis, disease site, disease status) are shared. These characterized PDX models, matched with patient tumors, guide model selection for preclinical drug testing.

  Study phs003163