16468 results for "sec+and+unspecified+malignant+neoplasm"

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• COVID_19_UK_CIC_Spatial

  Understanding the immune response to SARS-CoV-2 is critical to our ability to control the coronavirus pandemic. Spatial transcriptomics will be performed on COVID-19 post-mortem tissues in collaboration with the UK - Coronavirus Immunology Consortium (UK-CIC). UK-CIC encompasses a concerted effort by the UK's world-leading immunology community to deliver a co-ordinated and agile national research programme to increase our understanding of how the immune system interacts with SARS-CoV-2. UK-CIC is led by Professor Paul Moss (University of Birmingham) and brings together 20 UK immunology centres of excellence, with support from the British Society for Immunology.

  Study EGAS00001005817

• Human Developmental Biology Resource (HDBR) abnormal fetal samples

  The HDBR (www.hdbr.org) is a human embryonic and fetal tissue bank supplying registered researchers with access to these valuable research materials up to 22 weeks post-conception (PMC4640175). All of the samples collected are analysed for chromosomal abnormalities, and all samples with an abnormal phenotype are either analysed by SNP array, or exome sequenced. This dataset is generated from those abnormal samples that have been analysed by exome sequencing. To request access to this dataset, or if any researcher is interested in obtaining tissue from any of the samples HDBR collect, please email enquiries@hdbr.org.

  Study EGAS00001006300

• Measurement of SARS-CoV-2 variants fraction in infected alveolar cells

  With the continuous emergence of highly transmissible SARS-CoV-2 variants, the comparison of their infectivity has become a critical issue for public health. However, a direct assessment of the viral characteristic has been challenging due to the lack of appropriate experimental models and efficient methods. Here, we conducted full-length transcriptome sequencing of single human alveolar cells infected by multiple SARS-CoV-2 variants, including GR (B.1.1.119), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.1). Using unique mutations of each VOC, we calculated the fraction of VOCs in infected cells.

  Study EGAS00001006730

• An atlas of the developing human fetal spine

  The primitive streak emerges during the 14th day of human development and establishes dorsoventral and antero-posterior (craniocaudal) body axes. Segmentation along the craniocaudal axis is governed by Hox genes; four clusters of transcription factors whose 3’ to 5’ expression correlates with position along the axis. The precise utilisation of Hox genes in different cell types remains incompletely characterised in humans. In this study, we applied single-cell and spatial transcriptomics to contiguous regions of the human fetal spine between the 5th and 13th post-conception weeks. We built a detailed developmental atlas to examine the segmental expression of Hox genes across different cell types, observing that the Hox code was displayed by all anatomically fixed cell types along the craniocaudal axis. By contrast, mature derivatives of neural crest cells retained the anatomical Hox code of their origin within the crest, a pattern reproduced across neural crest derivatives in other human fetal organs. These findings indicate that scars of Hox gene expression persist in crest cells which may serve as barcodes of neural crest migration.

  Dataset EGAD00001009801

• Single cell transcriptional evolution of myeloid leukaemia of Down syndrome – scRNA

  Abstract: Children with Down syndrome have a 150-fold increased risk of developing myeloid leukaemia (ML-DS). Unusually for a childhood leukaemia, ML-DS arises from a preleukaemic state, termed transient abnormal myelopoiesis (TAM), and via a conserved sequence of mutations. Here, we examined the relationship between the genetic and transcriptional evolution of ML-DS from a rich collection of primary patient samples through single cell mRNA sequencing, complemented by phylogenetic analyses in progressive disease. We distilled the transcriptional consequence of each genetic step in the evolution of ML-DS, showing that TAM-defining GATA1 mutations account for most of the ML-DS transcriptome, including those of progressive disease. This transcriptional backbone may thus represent a common vulnerability in ML-DS. We extracted the transcriptional difference between TAM and ML-DS which, unexpectedly, reflected features shared across childhood leukaemia. Our approach delineates the transcriptional evolution of ML-DS and provides an analytical blueprint for distilling consequences of mutations directly from patient samples.

  Dataset EGAD00001015452

• Whole blood RNA sequencing of individuals from Nepal

  This study utilized blood samples collected in Lalitpur, Nepal as part of the Strategic Typhoid Alliance across Africa and Asia (STRATAA) study. The dataset comprises whole blood RNAseq of 376 febrile individuals from Nepal. Blood was collected in PAXgene tubes and sent to Monash University (Melbourne, Australia) where RNA was extracted using the PAXgene Blood RNA kit before being sent to the Wellcome Sanger Institute (Hinxton, UK) for sequencing. Library prep used NEBNext Ultra II RNA custom kits on an Agilent Bravo WS automation platform with poly(A) pulldown. After PCR, plates were purified using Agencourt AMPure XP SPRI beads and libraries were quantified using Biotium Accuclear Ultra high sensitivity dsDNA Quantitative kits. Pooled libraries were normalised to 2.8 nM. Samples were globin depleted using KAPA RNA HyperPrep with RiboErase. Libraries were then subjected to 2x100bp paired-end sequencing on Illumina NovaSeq. Each library was sequenced to an average of 80 million reads. The STRATAA study was approved by the Nepal Health Research Council (NHRC, ref 283 306/2015) and OxTREC (Oxford Tropical Research Ethics Committee, ref 39-15). All participants provided informed consent for human genetic tests.

  Dataset EGAD00001011131

• Autozygosity pilot - Born in Bradford (2014-11-20)

  The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples.Data Access is controlled by the Wellcome Trust Sanger Institute DAC and the Born In Bradford Executive Group. This dataset contains all the data available for this study on 2014-11-20.

  Dataset EGAD00001001079

• A prospective multicenter study of plasma ctDNA versus archival tumor tissue to guide FGFR-targeted therapy in metastatic urothelial cancer - Targeted

  Targeted sequencing data related to the publication titled "A prospective multicenter study of plasma ctDNA versus archival tumor tissue to guide FGFR-targeted therapy in metastatic urothelial cancer." FGFR alterations, seen in up to 25% of metastatic urothelial carcinoma, can be exploited with targeted therapy. Here, we perform targeted sequencing of cell-free DNA, archival FFPE, and white blood cell DNA to compare ctDNA versus tissue for FGFR biomarker status and monitor temporal changes to FGFR over the disease course, specifically after progressing on targeted therapy.

  Study EGAS50000001450

• Paired ONT and downsampled Illumina cfDNA dataset

  Dac EGAC00001002860

• Tumor-Normal matched colon adenomas and carcinomas

  Dac EGAC00001003248

• Microenvironment in lymphoma pathogenesis and therapy - DAC

  Dac EGAC00001003228

• Leucocyte eQTLs in autoimmune disease and health

  Dac EGAC00001000338

• Multiple esclerosis and mixed microbial infections DAC

  Dac EGAC00001000892

• 16S rRNA gene amplification and maternal factors DAC

  Dac EGAC00001000931

• Pathology and tumor biology

  Dac EGAC00001001923

• Sarcoma biology and genomics data access commitee

  Dac EGAC00001002609

• Sarcoma biology and genomics data access committee

  Dac EGAC00001002610

• Pheochromocytoma and paraganglioma single nuclei RNA-seq

  Dac EGAC00001002657

• Computational Cancer Genomics and Tumor Evolution Group

  Dac EGAC00001002722

• MSAT and JMS Data Access Committee

  Dac EGAC00001002734

• Human islet sQTL and eQTL DAC

  Dac EGAC00001002796

• Annie Huang and the Hospital for Sick Children

  Dac EGAC01000000015

• Genomics and Oncogenesis of Pediatric Brain Tumors

  Dac EGAC00001003123

• DAC - Institute for Pharmacology and Toxicology

  Dac EGAC00001003385

• RNASeq Javelin head and neck 100

  Study EGAS00001007497

• DAC Bone and soft tissue tumor pathology

  Dac EGAC50000000228

• The Mood and Methylation Study (MMS)

  The Mood Methylation Study (MMS) is an observational study designed to understand epigenetic mechanisms underlying major depression symptoms (MDD) using a co-twin control design. Twins enrolled in the MMS were monozygotic (MZ) twin pairs discordant on lifetime history of MDD. All twins were members of the Washington State Twin Registry (WSTR), a community-based twin registry consisting of over 10,000 twin pairs. Lifetime and current MDD diagnoses were determined using the Structured Clinical Interview for DSM-IV Research Version (SCID-4-RV). DNA methylation in blood monocytes was measured using the Infinium HumanMethylationEPIC BeadChip. Monocyte gene expression was quantified by paired end RNA-seq (50 PE). Zygosity of the twin pairs included in the MMS was self-reported and confirmed using the polymorphic SNPs included in the DNA methylation array.

  Study phs002858

• Hereditary Cancer Predisposition Syndromes and Uveal Melanoma

  Uveal melanoma (UM) is a subtype of melanoma characterized by the strong contribution of genetic rather than environmental factors in the pathogenesis of the disease, making it an ideal model disease to study the genetic basis of cancer. The long-term goal of our laboratory is to determine the genes and mechanisms responsible for hereditary cancer predisposition associated with UM. BAP1 has been identified as a candidate gene with definitive association with predisposition to UM. However, pathogenic variants in BAP1 are detected in only a small subset of UM patients even those with strong personal and family history of cancer suggesting the existence of other candidate genes. The goal of this project is to identify novel candidate genes contributing to hereditary predisposition to UM in patients with no detectable germline pathogenic variant in BAP1.

  Study phs001943

• Transcriptomics of Liver and PBMCs in Alcohol-Associated Liver Disease

  This study was designed to characterize the transcriptome of alcohol-associated hepatitis using RNA sequencing (RNA-seq) technology for both liver tissue biopsies and peripheral blood mononuclear cells (PBMCs) extracted from blood samples, in order to identify expressed genes that are markers of the disease. To distinguish genes that differentiate alcohol-associated hepatitis from other inflammatory liver diseases, we compared the RNA-seq data generated from participants with alcohol-associated hepatitis, alcohol-associated cirrhosis, chronic hepatitis C infection, non-alcohol-associated fatty liver disease, and healthy controls. We utilized computational approaches to demonstrate that gene expression data generated from either liver tissue or blood samples can be used to identify a small set of gene biomarkers to distinguish between these liver diseases. The raw RNA-seq data will be available through dbGaP.

  Study phs003112

• Hereditary Gastric Cancer Syndromes: An Integrated Genomic and Clinicopathologic Study of the Predisposition to Gastric Cancer

  Gastric cancers are cancers of the stomach. Hereditary cancers are passed from parent to child. Researchers want to gather data about hereditary gastric cancers. Bulk RNA sequencing (RNA-seq) of signet ring cells (SRCs) and adjacent non-SRC epithelium (NEP) was performed on laser-capture microdissected (LCM) regions of interest found in risk-reducing total gastrectomy specimens from hereditary diffuse gastric cancer (HDGC) patients (Clinicaltrials.gov ID: NCT03030404). Twenty patients (6 male, 14 female) with confirmed HDGC were identified. Analysis of differentially expressed genes (DEGs) demonstrated upregulation of certain individual epithelial–mesenchymal transition (EMT) and proliferation genes. SRC regions had significant enrichment in pathways involved in T cell signaling. CIBERSORTx predicted significant increases in the presence of regulatory T cells (Tregs) specific to SRC regions.

  Study phs003422

• Ribosome profiling shows variable sensitivity to detect open reading frames for conventional and different types of cryptic T cell antigens

  The aim of the study was to explore the sensitivity of ribosomal profiling to detect ORFs for cryptic antigens targeted by T cells in immune responses. Ribosomal profiling was performed for six EBV-LCLs. Detection of conventional and cryptic MiHA-encoding ORFs was compared. The data showed that open reading frames (ORFs) for conventional MiHAs as well as cryptic MiHAs in upstream ORFs were frequently detected with similar sensitivity. However, only a limited number of MiHAs in in reading frames alternative to protein-coding sequences and no ORFs derived from long non-coding RNAs were detected. In conclusion, Ribo-seq for identification of antigen-encoding ORFs is useful to screen for cryptic antigens in upstream ORFs as potential targets for immunotherapy.

  Study EGAS50000000322

• Adeno-associated virus in the liver: natural history and consequences in tumor development

  Adeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population (40-80%). AAV infection has long been considered as non-pathogenic1, however few years ago we reported for the first time recurrent clonal AAV2 insertion in the pathogenesis of human hepatocellular carcinoma (HCC) developed on normal liver. These clonal viral insertions target cancer driver genes, including CCNA2, CCNE1, TERT, TNFSF10 and MLL4, leading to their overexpression. The viral inserted sequences involved in almost all the cases the 3’ inverse tandem repeat (ITR) of AAV2, which is important for virus integration in host DNA and exhibits a promoter/enhancer activity. Here, we used RNA sequencing (RNA-seq) to investigate their functional impact on the tissue, such as fusion transcript generation events.

  Study EGAS00001003310

• Paired-end RNA-seq analysis of the TERT promoter mutant GBM cell lines

  This dataset contains 9 RNA-seq BAM files. RNA was derived from TERT promoter mutant GBM cell lines and sequenced on an Illumina HiSeq4000 sequencer with paired-end reads and an average read length of 50 base pairs. Reads were aligned with TopHat (v2.0.14) using a GENCODE V19 transcriptome-guided alignment.

  Dataset EGAD00001005435

• Methylome profiling of Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) and a patient derived cell-line model

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1 using the twist human methylome panel.

  Dataset EGAD50000000040

• Suspected Lynch syndrome dataset

  This dataset comprises a genomic and a phenotypic excel sheet displaying 137 cases classified as suspected Lynch syndrome. Included are genotypic data such as tumour mutational burden, tumour mutational signatures and germline/somatic variant calls for each colorectal, endometrial or sebaceous skin tumour screened. Genomic data is derived from targeted multigene panel sequencing including ~300 hereditary cancer genes.

  Dataset EGAD50000000031

• Primary ER-positive Breast Cancer Treated with Neoadjuvant Letrozole

  These are tumor biopsies and corresponding normal samples from patients with early stage ER+/HER2- breast cancer who had received the aromatase inhibitor letrozole for 10-21 days prior to surgery.

  Study phs000857

• PEDS-PLAN - Pediatric Precision Laboratory Advanced Neuroblastoma Therapy

  A multi-center clinical trial for newly diagnosed high-risk neuroblastoma patients. Molecular tumor boards selected one of six targeted agents based on tumor-normal whole exome sequencing and tumor RNA sequencing data.

  Study phs002303

• TOTHER3 dataset

  This dataset contains the FASTQ and BAM files for TOTHER3 study. Targeted DNA-Seq experiment were realized with 49 samples. Since this data was obtained with a panel of genes protected by Intellectual Property (IP), these files only contain information to validate the results published and, in consequence, sensible data had to be specifically removed.

  Dataset EGAD50000000562

• Disease recurrence after pathologic response

  In this study we aim to gain insight into the mechanisms of immune evasion after initial pathologic response to neoadjuvant immune checkpoint inhibition in macroscopic stage III melanoma by pooling data of the neoadjuvant OpACIN, OpACIN-neo and PRADO trials. Therefore we analyzed in-depth paired baseline and recurrent tumor samples through a.o. DNA sequencing analyses.

  Dataset EGAD50000000699

• RNAseq Data Cyr61-MAC and HUVEC

  Gene expression of MAC enriched by adhesion to Cyr61 in comparison to HUVEC. This dataset includes RNAseq Data from myeloid angiogenic cells (MAC) enriched from peripheral blood by adhesion to Cyr61 (4 samples prepared from different donors) and of human umbilical vein endothelial cells (HUVEC) (4 samples). Illumina NextSeq500 technology was used. FASTQ data are provided.

  Dataset EGAD50000000758

• Short-read single-cell RNA-sequencing of the human brain in neurodegenerative diseases

  Nuclei were isolated from postmortem human brain tissue, and single-nucleus barcoded cDNA libraries were generated using the 10X Genomics 3' v3.1 kit. Samples were sequenced on an Illumina NovaSeq 6000 to an average of 343 million reads per sample and 52,000 reads per cell.

  Dataset EGAD50000000178

• Processed Total RNA Counts for the RNA Profiling from Indian HFrEF Cohort Dataset

  This dataset contains processed RNA count data for the 49 Heart Failure samples profiled by RNAseq for the Indian HFrEF Cohort from the study Integrated Transcriptomic and Regulatory RNA Profiling Reflects Complex Pathophysiology and Uncovers a Conserved Gene Signature in End Stage Heart Failure RNA-Seq data.

  Dataset EGAD50000001193

• Processed miRNA Counts for the miRNA Profiling from Indian HFrEF Cohort Dataset

  This dataset contains processed miRNA count data for the 49 Heart Failure samples profiled by miRNAseq for the Indian HFrEF Cohort from the study Integrated Transcriptomic and Regulatory RNA Profiling Reflects Complex Pathophysiology and Uncovers a Conserved Gene Signature in End Stage Heart Failure RNA-Seq data.

  Dataset EGAD50000001195

• Identification of phenotype-modifier genes

  Patients were stratified at the extremes of the renal phenotype according to their estimated glomerular filtration rate annual decline and subjected to whole exome sequencing (WES) aiming to find candidate phenotype-modifier genes.

  Study EGAS50000000829

• EMBARCAM BC360 PROJECT

  This dataset is related to the EMBARCAM BC360 PROJECT. A total of 106 breast cancer samples, from Pregnancy-Associated Breast Cancer (PABC) (n=57) and non-PABC (n=49) patients, were analysed using the nCounter Breast Cancer 360 V2 panel on the NanoString platform. All samples were FFPE tumor samples from breast cancer patients, derived from GEICAM/2012-03, GEICAM/2017-07, and EpiGEICAM studies, sponsored by GEICAM.

  Dataset EGAD00010002709

• Mutational Profile in Newly Diagnosed Diffuse Large B-Cell Lymphoma: Insights from the GAINED Study

  The GAINED study (NCT01659099) is a randomized phase 3 trial comparing obinutuzumab (G) to rituximab (R) in combination with ACVBP or CHOP14 induction, followed by PET-guided consolidation. This post-hoc analysis focuses on primary mediastinal B-cell lymphoma (PMBL) patients, confirmed through expert pathological review and characterized using gene-expression profiling (GEP) and Next-Generation Sequencing (NGS).

  Dac EGAC50000000540

• Poland Opole Voivodeship WGS

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 10 samples (5 female, 5 male of Opole Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

  Dataset EGAD50000000124

• Poland Podlaskie Voivodeship WGS

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 12 samples (6 female, 6 male of Podlaskie Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

  Dataset EGAD50000000125

• Poland Lubusz Voivodeship WGS

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 19 samples (8 female, 11 male of Lubusz Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

  Dataset EGAD50000000127

• Poland Holy Cross Voivodeship - WGS

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 6 samples (6 female of Holy Cross Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

  Dataset EGAD50000000162