16787 results for "sec+and+unspecified+malignant+neoplasm"

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• Chip_seq_oesophageal_adenocarcinoma_

  There is complex interplay between underlying genetic sequence and epigenetic factors, however this interplay is still illusive. Massively reconstructed cancer genomes can be used in order to better understand this relationship. Six oesophageal adenocarcinoma organoids will be sequenced using long read sequencing technologies and will be profiled for a range of epigenetic marks. Combination of genetic and epigenetic data will allow the thorough characterisation of reference cancer genomes and will provide novel insights into mechanisms of gene regulation. Description: Chip-seq Sequencing of 5 patient derived organoid cell models. Each model was derived from a piece of patient tumour taken following surgical rescetion of the tumour. All model derivations took place with the CGaP facility in Sanger.

  Study EGAS00001007180

• Transcriptomic analysis of cell-of-origin CNS neuroblastoma, FOXR2 activated

  The transcription factor FOXR2 is the universal driver of childhood central nervous system neuroblastoma, FOXR2 activated (NB-FOXR2). NB-FOXR2 tumors arise exclusively in the brain hemispheres, and despite morphological similarities to other pediatric brain tumors, they are a molecularly distinct entity based on DNA methylation profiling. The cell-of-origin is unknown. Here, we profiled a cohort of rare NB-FOXR2 tumors by bulk and single-cell transcriptomics. Through systematic comparative analyses, we delineate tumor transcriptional states and candidate cell-of-origin. More broadly, we demonstrate systematic molecular profiling of childhood cancers to orient oncogenic targeting for in vivo modeling, a critical resource for the study of rare tumors and development of therapeutics.

  Study EGAS00001007247

• Single-cell RNA-seq of peripheral blood mononuclear cells in classic Hodgkin lymphoma

  Classic Hodgkin lymphoma (cHL) is a largely MHC class I-negative tumor with recurrent 9p24.1/ PD-L1/ PD-L2 copy gains and the highest reported response rates to PD-1 blockade. We utilized scRNA sequencing to characterize the peripheral immune response to PD-1 blockade and more broadly define non-CD8+ dependent mechanisms of immune evasion in cHL. Peripheral blood mononuclear cells were obtained from 20 patients with relapsed/refractory (R/R) cHL treated with PD-1 blockade (nivolumab) on the CheckMate 205 clinical trial (paired samples from cycle 1 day 1 [C1D1] and cycle 4 day 1 [C4D1]), 11 patients with newly diagnosed, previously untreated cHL and 13 healthy donors.

  Study EGAS00001007569

• Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor infiltrating T cells.

  Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying functional and dysfunctional states of human tumor infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify tissue-specific and general gene-regulatory landscapes in the wide breadth of CD8+ TIL functional states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor entity-matching samples and prioritize key elements by super enhancer analysis. Our analysis reveals a human core chromatin trajectory to TIL dysfunction and identifies key enhancers, transcriptional regulators, and deregulated target genes involved in this process. Finally, we validate enhancer regulation at loci encoding PD1, TCF1, and TIM3 by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study advances the understanding of molecular regulation of TIL (dys-)function and provides a framework for modulating immunotherapeutic relevant TIL genes via their enhancers.

  Dataset EGAD00001008662

• Duplexseq of the interstrand crosslinks_WGS

  One of the most dangerous forms of DNA damage are interstrand crosslinks (ICLs), which covalently crosslink the two strands of the DNA double helix. The repair of these lesions is crucial for cellular survival due to their ability to block transcription and DNA replication. Initially, the major pathway that has been described in ICL repair involves a network of 22 genes that are mutated in a severe human genetic disease known as Fanconi Anemia (FA). Using synthetic lethality screens in the near-haploid human HAP1 cell line, we recently identified two potentially novel regulators of ICL repair, C1orf112 and THAP12. Loss of C1orf112 and THAP12 causes hypersensitivity to ICL-inducing DNA damaging agents, such as Mitomycin C (MMC). Additionally, C1orf112-depleted cells show elevated levels of micronuclei and accumulation of DNA damage in S-phase. To better understand how C1orf112 and THAP12 mediate the repair of ICLs, we want to perform mutational signature analysis, using the BotSeq method. Therefore, WT, C1orf112 and THAP12 knockout cells were cultured in vehicle or MMC treated conditions for 10 days and the genomic DNA was isolated. FANCA and FANCD2 knockout cells are taken along as controls in this experimental setting. . This dataset contains all the data available for this study on 2023-04-20.

  Dataset EGAD00001010298

• Ultrasensitive Profiling of UV Mutations in Facial Tumors in TSC

  In this study we searched for mutations in the TSC2 and TP53 genes in sample sets from individuals with Tuberous Sclerosis Complex (TSC) and from subjects without TSC. The study was focused on the analysis of TSC facial angiofibroma.

  Study phs002914

• An Omics View of Asthma through Monozygotic Twins

  The etiology of asthma involves both genetic and non-genetic factors. We performed whole transcriptome sequencing on monozygotic twins discordant or concordant for asthma (with concordant healthy twins as controls), and identified multiple potential transcriptomic profiles associated with the asthma phenotype.

  Study phs000886

• Single Cell ATAC-Seq of MELAS

  This dataset includes combined single Assay for Transposase-Accessible Chromatin, using sequencing (ATAC-seq), and mitochondrial DNA sequencing of peripheral blood mononuclear cells from three individuals with m.3243A>G associated MELAS (Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes).

  Study phs002217

• Characterization of Clonal Evolution in Microsatellite Unstable Metastatic Cancers through Multi-Regional Tumor Sequencing

  Whole exome sequencing was performed on blood and multiple tumor samples from six patients with known microsatellite unstable tumors. Subclones within each tumor site were identified and within each subclone, differing microsatellite instability was characterized.

  Study phs001925

• Eosinophil Activation and Function in Parasitic Infections and Other Conditions with Increased Tissue or Peripheral Blood Eosinophilia in Humans

  Whole-genome sequencing of tumors and matched normal samples from 11 patients with PDGFR-rearranged hypereosinophilic syndrome reveals simple genomic alterations in this disease without recurrent somatic changes besides the known rearrangement.

  Study phs003180

• University of Sydney Thyroid Cancer Data Access Committee

  This Data Access Committee (DAC) manages access to genomic data generated by the Thyroid Cancer Research Group at the University of Sydney and Royal North Shore Hospital. The DAC will evaluate data access requests to ensure they align with participant consent and the conditions approved by the Northern Sydney Local Health District Human Research Ethics Committee. Requests will be reviewed for scientific validity, alignment with the original consent, and compliance with institutional and regulatory data governance policies.

  Dac EGAC50000000661

• Single-cell gene expression profiling of human iPSCs-derived cortical organoids

  To investigate the relationships between cerebral cortical organoid morphological characteristics and cellular composition, we morphologically classifi ed human iPSC-derived cortical organoids and analyzed the cellular makeup of each morphological type by single-cell gene expression profi ling.

  Study JGAS000726

• Whole exome sequencing of uterine cervical cancer

  We conducted whole-exome sequencing of cervical tissue samples to evaluate HLA loss of heterozygosity (LOH) and B2M gene mutations, which are key mechanisms of immune evasion that allow cancer cells to escape T-cell recognition and antigen presentation.

  Study JGAS000824

• Whole exome sequence and transcliptomic analysis of tumor tissues with hepatocellular carcinoma and metastatic liver cancer

  We used our pipeline to select neoepitopes with high immunogenicity from the tumor tissues of 46 patients with hepatocellular carcinoma or metastasis of colorectal carcinoma by whole exome sequence and transcriptomic analysis with tumor tissue.

  Study JGAS000507

• Building a Database of Genomic Structural Variants in Japanese population

  Purified genomic DNA was purchased from Japanese Collection of Research Bioresources (Japanese B cell DNA bank), National Institutes of Biomedical Innovation, Health and Nutrition in Japan. We sequenced those genomic DNAs using PacBio Sequel II and analyzed genomic structural variations.

  Study JGAS000596

• Building a Database of Genomic Structural Variants in Japanese population

  Purified genomic DNA was purchased from Japanese Collection of Research Bioresources (Japanese B cell DNA bank), National Institutes of Biomedical Innovation, Health and Nutrition in Japan. We sequenced those genomic DNAs using PacBio Sequel II and analyzed genomic structural variations.

  Study JGAS000505

• Whole-exome sequencing of uterine carcinosarcoma in a young woman with HBOC (tumor-normal pair)

  This study deposits controlled-access human genomic data (tumor-normal whole-exome sequencing) from a patient with uterine carcinosarcoma and hereditary breast and ovarian cancer (HBOC) syndrome, to support reproducibility of reported genomic findings.

  Study JGAS000883

• Whole Genome Methylation in CLL

  We have extensively characterized the DNA methylome of chronic lymphocytic leukemia (CLL) with mutated and unmutated IGHV as well as several mature B cell subpopulations using whole-genome bisulfite sequencing and high-density microarrays.

  Study EGAS00001000272

• Liquid biopsy to identify taxane resistance in castration-resistant prostate cancer patients

  Taxanes are life-prolonging treatments for patients with advanced prostate cancer. However, treatment resistance and lethal disease invariably develops. We here used liquid biopsies to identify and characterize resistance to cabazitaxel using a targeted sequencing panel (PCF-SELECT).

  Study EGAS50000001292

• DNAmet

  DNAmet analysis of olfactory mucosa (OM) cells derived from cognitively healthy and individuals with AD exposed to traffic-related ultrafine particles (UFPs) for 72h in submerged cultures. The UFPs used for exposures were: A0 and A20. Exposures were compared to the corresponding blank samples.

  Study EGAS50000001051

• miRNA seq

  miRNA Sequencing of olfactory mucosa (OM) cells derived from cognitively healthy and individuals with AD exposed to traffic-related ultrafine particles (UFPs) for 72h in submerged cultures. The UFPs used for exposures were: A0 and A20. Exposures were compared to the corresponding blank samples.

  Study EGAS50000001050

• Cohort B tumor exome sequencing

  Cohort B includes IDH-wild type, EGFR amplified, surgically derived glioblastoma tissue samples from male and female individuals. Tumor DNA was isolated from FFPE tissue. Both tumor and germline DNA are present for each sample in the overall dataset.

  Study EGAS50000000955

• Chromatin accessibility of clear cell renal cell carcinoma

  To investigate chromatin accessibility in ccRCC, we performed ATAC-seq in 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001325

• RNAseq of preneoplasia lung adenocarcinoma

  RNA sequencing of 168 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=38), adenocarcinoma in situ (AIS, N=22), minimally invasive adenocarcinoma (MIA, N=19) and invasive lung adenocarcinoma (ADC, N=38) and adjacent lung tissues (Normal, N=62).

  Study EGAS50000000271

• Single-cell RNA seq-derived signatures define response patterns to atezolizumab + bevacizumab in advanced hepatocellular carcinoma

  FASTq files and normalised gene expression counts from bulk RNA-sequencing of pre-treatment tumour (n=39) and adjacent non-tumour tissue samples (n=13) from advanced hepatocellular carcinoma (HCC) patients treated with atezolizumab plus bevacizumab.

  Study EGAS50000000838

• Low-coverage whole-sequencing of metastasised colorectal cancer samples treated with bevazicumab

  Low-coverage whole-genome sequencing (LC-WGS) was performed on tumor tissue, normal tissue and plasma samples collected from mCRC patients from the AC-ANGIOPREDICT Phase II trial (NCT01822444) and the University Medical Center Mannheim (UMM).

  Study EGAS50000000131

• Lifelines NEXT

  The Lifelines-NEXT is a cohort of newborns followed up from birth up to the age of 1 year and later. The cohort includes approximately 1,500 newborns and their mothers from the 3 provinces of the Northern Netherlands.

  Study EGAS50000000133

• Colorectal cancer functional annotation - MPRA

  We performed a Massively Parallel Reporter Assay (MPRA) in colorectal cancer (CRC) cell lines HT29 and SW403 and normal colon cell line HCEC-1CT. We specifically targeted the regions around the CRC GWAS loci to identify which variants alter transcription.

  Study EGAS50000000406

• Non-KMT2Ar infant Acute Lymphoblastic Leukemia Sequencing

  Integrated genomic analysis of non-KMT2A rearranged infant ALL reveals clinically relevant alterations and common disease origins with childhood ALL. Whole genome and whole transcriptome sequencing from 21 infant ALL patients with no matched normal DNA sequencing.

  Study EGAS50000000405

• Indonesian Genome Diversity Project 3

  Low coverage whole genome sequences were collected to study the population history in Eastern Indonesia, in particular Wallacea and Papua region. We have sequenced the genomes of 254 individuals from 12 Wallacean and 3 Papuan populations spanning this geographical region.

  Study EGAS50000000447

• High-depth whole genome sequencing of clonal colorectal cancer PDX-derived organoids and xenografts

  High-depth WGS was performed on two clonal organoids, one ancestor and one endpoint of a single lineage in a mutation accumulation experiment, and of the same clonal organoid that has been engrafted and grown in xenografts during the accumulation period. Paired sequencing was performed on a Novaseq X Plus with 150bp reads aiming at 500Gbp - 150x. 6 fastq files have been deposited for the 3 samples

  Dataset EGAD50000002528

• WGS data of pediatric T-ALL acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one T-ALL patient (ALLT-317). Relapsed (BM ALLT-317L and Tonsil ALLT-3107L) sample files are in dataset set2 of this submission. Sequencing library was made using PCR free-based WGS library preparation (PCR-), using TruSeq DNA PCRfree library preparation kit v1 (PE150). Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000002013

• scRNA and V(D)J sequencing of WM under ibrutinib

  Single-cell RNA sequencing (5′ gene expression) and single-cell V(D)J sequencing (B-cell receptor and T-cell receptor) were performed on bone marrow mononuclear cells from patients with Waldenström macroglobulinemia treated with ibrutinib monotherapy. Sequential bone marrow aspirate samples were collected at baseline and after treatment. A total of 222 BAM files are included in this dataset.

  Dataset EGAD50000002279

• mRNA profiling of CAFs and cancer cells in response to TGF-β and BMP signaling

  TGF-β and BMP signalings are important signaling pathways in the tumor microenvironment during cancer progression. This RNA-sequencing (62 fastq pairs) analysis explored how cancer-associated fibroblasts (CAFs) from human (19TT) and mice (Balbc A/B) respond to TGF-β, BMP2, or Gremlin antibody, as well as how cancer cells (66cl4) respond to Gremlin antibodies.

  Dataset EGAD50000001351

• Transcriptomic and chromatin accessibility profiling in T cells for the MTOR genetics paper.

  This submission contains raw ATAC and RNA sequencing data from human primary CD4+ and CD8+ T cells, either stimulated or unstimulated with anti-CD3/CD28 Dynabeads, from three healthy donors. It includes 24 paired-end FASTQ files consisting of 12 poly(A)-enriched RNA-seq samples and 12 ATAC-seq samples sequenced on the Illumina NextSeq 500 platform.

  Dataset EGAD50000001307

• Whole Exome Sequencing of paired gDNAs and PPGL tumor DNA from patients with cyanotic congenital heart disease

  Fastq files from Whole Exome Sequencing of 12 paired germline DNA (from blood/saliva) and 14 PPGL tumor DNA (from formalin-fixed paraffin-embedded (FFPE) blocks from surgery) from patients with cyanotic congenital heart disease (CCHD) and pheochromocytoma and paraganglioma (PPGL). Sequencing was performed using the Illumina HiSeq4000.

  Dataset EGAD50000001201

• Single-cell RNA-sequencing of CSF cells and PBMCs from individuals with neurological disorders

  We undertook single-cell RNA sequencing to establish gene expression and lymphocyte receptor sequences of CSF and peripheral blood leukocytes derived from patients with a variety of inflammatory, infectious and non-inflammatory neurological disorders. The aim of the study was the investigation of functional changes of the cells involved in neuroinflammatory responses.

  Dataset EGAD50000001173

• Anti-MPO BCR sequences described in 'Anti-myeloperoxidase IgM B cells in anti-neutrophil cytoplasmic antibody-associated vasculitis'

  FASTA files from quality-checked Sanger Sequencing results from BCR-specific PCR products. B cells from 4 different MPO+ AAV patients were single cell sorted and processed to sequence the specific BCR, resulting in 51, 175, 12 and 3 heavy chain BCR sequences for AAV1, 2, 3, and 5 respectively. Sequence names indicate patient ID and isotype (IgG, IgM or IgA).

  Dataset EGAD50000001112

• WES of head and neck cancer patients refractory to anti-PD-1 therapy

  Whole exome sequencing (WES) was performed on baseline (before low-dose 5-aza treatment) blood and tumor paired samples from 12 participants with head and neck cancer who were refractory to anti-PD-1 therapy. DNA extractions were performed by the Broad Institute of MIT and Harvard using Qiagen AllPrep DNA/RNA kits (Cat. 80204). In total, 24 150-bp pair-end WES data were generated by Illumina.

  Dataset EGAD50000001011

• Targeted RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoietic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood. Samples were tested in a clinical diagnostic lab to identify relevant SNVs, indels and gene fusions.

  Dataset EGAD50000000980

• Clinical and demographics data from IMvigor210, IMvigor211, IMvigor130 and IMvigor010

  Clinical data include demographics (gender, race), specimen type (primary vs. metastatic), tract (upper vs. lower), liver metastasis status, PD-L1 IHC, tumor mutation burden, CD8 T cell infiltration status, neutrophil enrichment score, treatment arm, objective response rate, overall survival and progression free survival, and ctDNA status (IMvigor010 only) for 2803 patients across the four IMvigor trials.

  Dataset EGAD50000001101

• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression (non-hipo)

  This dataset contains 115 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001097

• IMPRESS_all

  Dataset containing tumor, normal and blood sample data, for various tissue and tumor types. Data is targeted methylation data, using smMIP probes to target informative CpG sites in the genome. Sample type can be inferred from the name, with 'W' being normal samples and 'TC' tumor samples. Dataset contains 259 samples in duplicate, with one half of the runs being cut by MSRE's, and the other not. For every sample paired fastq files are present.

  Dataset EGAD50000000882

• Targeted capture sequencing to identify MYC, BCL2, and BCL6 rearrangements in non-Hodgkin lymphoma

  Targeted capture sequencing of 364 samples representing a mix of Burkitt lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, and high-grade B-cell lymphomas with MYC and BCL2 or BCL6 rearrangements. Capture space covers 3.5 Mb of the human genome including regions around MYC, BCL2, BCL6, PAX5, and IGH/K/L.

  Dataset EGAD50000000489

• CITE-seq AdaptNK

  CITEseq was performed as outlined in Biolegend ‘TotalSeqTM-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol’ with minor modifications, using Biolegend oligo-conjugated antibodies and streptavidin TotalSeq reagents. Briefly, ADAPT-NK cells were stained with CD56-biotin mAb (Miltenyi, clone REA196), followed by TotalSeq antibodies and streptavidin-PE and Live/Dead Aqua (Invitrogen). Cells were subsequently sorted for viable CD56+ cells by flow cytometry.

  Dataset EGAD50000000329

• Endoresist panel sequencing

  Patients with endocrine-resistant breast cancer in Stockholm Sweden. DNA obtained from patients primary and relapse tumors, and tumor-free lymph nodes used as germline control. DNA was extracted from formalin-fixed paraffin-embedded tissue and sequenced by 370-gene panel-based sequencing with Kapa HyperPlus library preparation and Twist Bioscience hybrid capture. Custom bait sets (panels) from Twist Bioscience. Paired end 2x150 bp using NovaSeq X. The data is presented as fastq-files.

  Dataset EGAD50000000350

• InterPregGen-GWAS-UZB-1

  GWAS genotype data for maternal and fetal (baby) cases of preeclampsia and controls from Uzbekistan. This dataset is a component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium members in Tashkent, Uzbekistan at the Institute of Immunology, Uzbek Academy of Sciences and at the Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology

  Dataset EGAD00010001918

• Large deletion predisposes to familial melanoma

  Mutations in CDKN2A and CDK4 account for ~40% of multi-case melanoma families, with another ~10% attributable to BAP1 and genes associated with telomere maintenance. Thus, a substantial proportion of the genetic risk underlying familial melanoma remains unexplained.

  Study EGAS50000001496

• Genetic landscape of pediatric ependymoma

  We performed whole-genome sequencing of 42 paired tumor/normal EPD genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000254

• BGISEQ-500 Cancer Dataset - WGS tumour/normal pairs

  This study contains whole genome sequencing data for 3 matched tumour / normal pairs from Mesothelioma patients. The sequencing is 50bp paired-end generated using the BGISEQ-500 and is provided as 6 aligned and duplicate-marked BAM files.

  Study EGAS00001002298