Search Results - EGA European Genome-Phenome Archive

HipSci - Bardet-Biedl Syndrome - RNA Sequencing - January 2016

Dataset EGAD00001001954

HipSci - Bardet-Biedl Syndrome - RNA Sequencing - April 2015

Dataset EGAD00001001952

scRNA-seq and scTCR-seq from 7 MF patients

Dataset containing scRNA and scTCR sequencing of 7 patients with cutaneous T cell lymphoma. Sequencing was performed on Illumina NextSeq 550, HiSeq 4000 and NovaSeq 6000. The sequencing was always paired.

Dataset EGAD50000000332

Spontaneously differentiatiated iPSCs to EBs

SUM-seq data (single-cell chromatin accessibility and gene expression) for spontaneously differentiatiated iPSCs. This data is the representative data in the Nature Protocols publication.

Study EGAS50000001094

BLUEPRINT September 2016, ATAC-seq for tonsil, on Genome GRCh38

ATAC-seq data for 7 sample(s) from tonsil, on Genome GRCh38. 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002708

Transcription factor binding in human monocyte differentiation

This dataset consists of ChIP-seq data data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to mRNA transfection for PU.1, IRF4, and EGR2. In total, it the data set includes 18 samples.

Dataset EGAD00001006602

scRNA-seq dataset for AD and Pso patients

This dataset contains scRNA-seq fastq files to the paper entitled "Single-cell profiles reveal distinctive immune response in atopic dermatitis in contrast to psoriasis". The details of experiment setup was described in the paper.

Dataset EGAD00001010106

NKI-AvL OpACIN DNA-seq of stage III melanoma patients

The dataset “NKI-AvL OpACIN DNA-seq of stage III melanoma patients" includes 2 x 18 normal and 2 x 18 tumor FASTQ files from paired-end whole exome sequencing on Illumina HiSeq2500 for 18 stage III melanoma patients.

Dataset EGAD00001004217

siRNA knockdown of Allelic Imbalance target TFs followed by mRNA-seq

siRNA knockdown of 43 Allelic Imbalance target TFs followed by mRNA-seq done in triplicates in three (GP5D, LoVo, COLO320DM) different cell colorectal adenocarcinoma cell lines.

Dataset EGAD00001004098

COVID-19 Postmortem Lung snRNA-seq

A deeper understanding of the pathological mechanisms of SARS-CoV-2 infection is required to combat COVID-19. Through this dataset, we analyze postmortem lung cells from patients that are infected/uninfected with SARS-CoV-2 with snRNA-seq.

Dataset EGAD00001006584

BLUEPRINT September 2016, ATAC-seq Chronic Lymphocytic Leukemia from venous blood, on Genome GRCh38

ATAC-seq data for 106 sample(s) Chronic Lymphocytic Leukemia from venous blood, on Genome GRCh38. 111 run(s), 109 experiment(s), 109 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002916

BLUEPRINT September 2016, ATAC-seq Mantle Cell Lymphoma from venous blood, on Genome GRCh38

ATAC-seq data for 5 sample(s) Mantle Cell Lymphoma from venous blood, on Genome GRCh38. 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002918

Inferring tumor genomes from peripheral blood i.e. CTCs and plasma-DNA using deep sequencing and targeted enrichment

In this study we tested whether complex tumor genomes can be inferred from the peripheral blood (plasma DNA /CTCs) of 32 patients with stage IV colorectal carcinoma (CRC). To establish the percentage of mutated plasma DNA fragments we used 8 patient samples with different plasma DNA size distributions and KRAS mutations in their corresponding primary tumors and employed ultra-deep pyrosequencing with 3 different sequencing reaction sizes (i.e., 119 bp, 168 bp, and 323 bp). Furthermore, we used massive parallel sequencing of a panel of 68 CRC-associated genes to establish the mutation spectrum of cancer driver genes in the primary tumors, metastases, and CTCs of two colorectal cancer patients. To investigate, whether mutations found in only one CTC (“private CTC mutations”) are true mutations occurring with allele frequencies below the resolution limits of current detection methods, or whether they are amplification or sequencing artifacts, we performed ultra-deep sequencing of the primary tumors, metastases, plasma DNAs and normal tissues.

Study EGAS00001000337

Systematic immune cell dysregulation and molecular subtypes revealed by single cell RNA-seq of subjects with type 1 diabetes

Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting beta-cells. A comprehensive immune cell phenotype evaluation in T1DM has not been performed thus far at the single. In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (Stage 3) cases and 31 matched controls.Our study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes and has the potential to guide non-invasive test development and patient stratification.

Study EGAS50000000231

Nasopharyngeal RNASeq Comparing SARS-CoV-2+ Patients and SARS-CoV-2 Negative Control Subjects

The goal of this analysis was to compare RNAs enriched in the upper respiratory tract of SARS-CoV-2 patients and SARS-CoV-2 negative controls. RNA-sequencing of RNA isolated from the viral transport medium associated with nasopharyngeal swab samples from SARS-CoV-2+ patients and SARS-COV-2 negative controls.

Study phs002433

Genomic characterization of a patient with AGS and CdLS transcriptomic comparison of his monocytes against healthy and disease control samples

In this study, we describe an extreme genetic phenotype of two simultaneous genetic lesions, leading to broad alterations in immunophenotype and transcriptome. Whole Exome Sequencing and RNA-Sequencing of CD14+ monocytes was performed on the case patient, and RNA-sequencing was also performed on disease (Systemic Lupus Erythematosus) and healthy controls.

Study EGAS00001007829

An Organoid Biobank of Rare Human Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping

We performed whole genome sequencing and RNA-sequencing of neuroendocrine neoplasm. The aim of this study was to provide genetic landscape of neuroendocrine neoplasm, to construct available animal models, and to engineer neuroendocrine neoplasm from normal colon epithelium. The reference genomes used are GRCh37 for whole genome sequencing and GRCh38 for RNA-sequencing.

Study JGAS000237

Gene expression in brain (Schizophrenia) study

The study included post-mortem brain tissue samples from 68 schizophrenia patients and 44 age and sex matched control subjects. Whole transcriptome poly-A selected paired-end RNA sequencing was performed on tissue from prefrontal cortex and orbitofrontal cortex. RNA expression differences were detected between case and control individuals, focusing both on single genes and pathways.

Study EGAS00001004199

NIH RECOVER-Pediatric: Understanding the Long-Term Impact of COVID on Children and Families

The NIH Researching COVID to Enhance Recovery (RECOVER) initiative comprises a set of three combined retrospective and prospective, longitudinal and observational meta-cohort studies with nested case-control studies designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection (PASC or Post-COVID syndrome) in a diverse study population representative of the general COVID-19 population in the US. Enrolled patients, with and without known SARS-CoV-2 infection, will be observed for clinical signs and symptoms of PASC and will be assessed for risk and resiliency factors and potential mediating factors associated with the severity and progression of PASC. The objective of the RECOVER initiative is to enhance knowledge of recovery from SARS-CoV-2 infections in order to support development of novel diagnostic and therapeutic interventions. Overarching scientific objectives are as follows:Characterize the incidence and prevalence of sequelae of SARS-CoV-2 infection.Characterize the spectrum of clinical symptoms, subclinical organ dysfunction, natural history, and distinct phenotypes identified as sequelae of SARS-CoV-2 infection. Define the biological mechanisms underlying pathogenesis of the sequelae of SARS-CoV-2 infection. The RECOVER observational studies comprise three cohorts across the lifespan (adult, pediatric, and tissue pathology (autopsy)). The data collection and data analysis plans for each cohort have been harmonized to use common data elements where feasible. Brief descriptions of each cohort are provided in the following paragraphs: 1) NIH RECOVER: A Multi-site Observational Study of Post-Acute Sequelae of SARS-CoV-2 Infection in Adults (see phs003463)The RECOVER adult cohort study is a combined retrospective and prospective, longitudinal, observational meta-cohort of individuals who will enter the cohort with and without SARS-CoV-2 infection and at varying stages before and after infection. Individuals with and without SARS-CoV-2 infection, and with or without PASC symptoms, will be followed to identify risk factors and occurrence of PASC. This study will be conducted in the United States and subjects will be recruited through inpatient, outpatient, and community-based settings. Study data including age, demographics, social determinants of health, medical history, vaccination history, details of acute SARS-CoV-2 infection, overall health and physical function, and PASC symptom screen will be reported by subjects or collected from the electronic health record using a case report form at specified intervals. Biologic specimens will be collected at specified intervals, with some tests performed in local clinical laboratories and others performed by centralized research centers or banked in the Biospecimen Repository. Advanced clinical examinations and radiologic examinations will be performed at local study sites with cross-site standardization. 2) A Multi-Center Observational Study: The RECOVER Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study (this study)The RECOVER pediatric study is a combined retrospective and prospective, longitudinal, observational meta-cohort of individuals ages newborn-25 years who will enter the cohort with and without SARS-CoV-2 infection at varying stages before and after infection. Individuals with and without SARS-CoV-2 infection and with or without PASC symptoms will be followed to identify risk factors and occurrence of PASC. This study recruit participants inpatient, outpatient, and community-based settings in the United States. Study data including age, demographics, social determinants of health, medical history, vaccination history, details of acute SARS-CoV-2 infection, overall health and physical function, and PASC symptoms will be reported by participants or collected from the electronic health record using a case report form at specified intervals. Biologic specimens will be collected at specified intervals, with some tests performed in local clinical laboratories and others performed by centralized research centers or banked in the Biospecimen Repository. Advanced clinical and radiologic examinations will be performed at local study sites with cross-site standardization. 3) NIH RECOVER: A Multi-site Pathology Study of Post-Acute Sequelae of SARS-CoV-2 Infection The RECOVER tissue pathology study is a cross-sectional study designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection in a diverse population representative of the general COVID-19 population in the US. The autopsy study will characterize the pathology of PASC in (i) non-hospitalized patients who die 30 days or later from symptom onset of COVID-19, and (ii) hospitalized patients who die 30 days or later after discharge from a hospitalization for COVID-19. The study will include decedents who had previously fully recovered from SARS-CoV-2 infection (i.e., >30 days from onset in non-hospitalized, or >30 days from discharge in hospitalized patients), and decedents who meet clinical criteria of PASC as defined by the recent World Health Organization publication (see Section 5.4 below). The autopsy study will also explore the pathology of acute SARS-CoV-2 infection in a smaller subset of patients who died 15-30 days from symptom onset. This protocol defines the common set of clinical data elements, autopsy procedures for tissue collection, core measures, pathology protocols, shared pathology tissues, data elements, and methodology. Each investigator site is expected to perform autopsies on the decedents to address the pathophysiology of the potential long-term effects of SARS-CoV-2 infection on human health. The Consortium analysis plan aims to address research questions by incorporating: 1) tissue obtained from autopsies performed at each Phase II participant's site; and 2) tissue available from other pathology investigators/autopsy sites within the Consortium.

Study phs003461

NIH RECOVER: A Multi-Site Observational Study of Post-Acute Sequelae of SARS-CoV-2 Infection in Adults

The NIH Researching COVID to Enhance Recovery (RECOVER) initiative comprises a set of three combined retrospective and prospective, longitudinal, observational meta-cohort studies with nested case-control studies designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection (PASC or Post-COVID syndrome) in a diverse study population representative of the general COVID-19 population in the US. Enrolled patients with and without known SARS-CoV-2 infection will be observed for clinical signs and symptoms of PASC and will be assessed for risk and resiliency factors and potential mediating factors associated with the severity and progression of PASC. The objective of the RECOVER initiative is to enhance knowledge of recovery from SARS-CoV-2 infections in order to support development of novel diagnostic and therapeutic interventions. Overarching scientific objectives are as follows: Characterize the incidence and prevalence of sequelae of SARS-CoV-2 infection. Characterize the spectrum of clinical symptoms, subclinical organ dysfunction, natural history, and distinct phenotypes identified as sequelae of SARS-CoV-2 infection.Define the biological mechanisms underlying pathogenesis of the sequelae of SARS-CoV-2 infection. The RECOVER observational studies comprise three cohorts across the lifespan (adult, pediatric, and tissue pathology (autopsy)). The data collection and data analysis plans for each cohort have been harmonized to use common data elements where feasible. Brief descriptions of each cohort are provided in the following paragraphs:1) NIH RECOVER: A Multi-site Observational Study of Post-Acute Sequelae of SARS-CoV-2 Infection in Adults (this study)The RECOVER adult cohort study is a combined retrospective and prospective, longitudinal, observational meta-cohort of individuals who will enter the cohort with and without SARS-CoV-2 infection and at varying stages before and after infection. Individuals with and without SARS-CoV-2 infection and with or without PASC symptoms will be followed to identify risk factors and occurrence of PASC. This study will be conducted in the United States and subjects will be recruited through inpatient, outpatient, and community-based settings. Study data including age, demographics, social determinants of health, medical history, vaccination history, details of acute SARS-CoV-2 infection, overall health and physical function, and PASC symptom screen will be reported by subjects or collected from the electronic health record using a case report form at specified intervals. Biologic specimens will be collected at specified intervals, with some tests performed in local clinical laboratories and others performed by centralized research centers or banked in the Biospecimen Repository. Advanced clinical examinations and radiologic examinations will be performed at local study sites with cross-site standardization. A summary of information available by request in the RECOVER Adult Cohort (this study) can be reviewed via the "Adult Cohort Dataset Release Notes" and the "REDCap Codebook for the Adult Cohort" documents.2) The RECOVER Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study: A Multi-Center Observational Study (data not yet released)The RECOVER pediatric study is a combined retrospective and prospective, longitudinal, observational meta-cohort of individuals ages newborn-25 years who will enter the cohort with and without SARS-CoV-2 infection at varying stages before and after infection. Individuals with and without SARS-CoV-2 infection and with or without PASC symptoms will be followed to identify risk factors and occurrence of PASC. This study recruit participants inpatient, outpatient, and community-based settings in the United States. Study data including age, demographics, social determinants of health, medical history, vaccination history, details of acute SARS-CoV-2 infection, overall health and physical function, and PASC symptoms will be reported by participants or collected from the electronic health record using a case report form at specified intervals. Biologic specimens will be collected at specified intervals, with some tests performed in local clinical laboratories and others performed by centralized research centers or banked in the Biospecimen Repository. Advanced clinical and radiologic examinations will be performed at local study sites with cross-site standardization.3) NIH RECOVER: A Multi-site Pathology Study of Post-Acute Sequelae of SARS-CoV-2 Infection (data not yet released)The RECOVER tissue pathology study is a cross-sectional study designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection in a diverse population representative of the general COVID-19 population in the US. The autopsy study will characterize the pathology of PASC in (i) non-hospitalized patients who die 30 days or later from symptom onset of COVID-19, and (ii) hospitalized patients who die 30 days or later after discharge from a hospitalization for COVID-19. The study will include decedents who had previously fully recovered from SARS-CoV-2 infection (i.e., >30 days from onset in non-hospitalized, or >30 days from discharge in hospitalized patients), and decedents who meet clinical criteria of PASC as defined by the recent World Health Organization publication (see Section 5.4 below). The autopsy study will also explore the pathology of acute SARS-CoV-2 infection in a smaller subset of patients who died 15-30 days from symptom onset. This protocol defines the common set of clinical data elements, autopsy procedures for tissue collection, core measures, pathology protocols, shared pathology tissues, data elements, and methodology. Each investigator site is expected to perform autopsies on the decedents to address the pathophysiology of the potential long-term effects of SARS-CoV-2 infection on human health. The Consortium analysis plan aims to address research questions by incorporating: 1) tissue obtained from autopsies performed at each Phase II participant's site; and 2) tissue available from other pathology investigators/autopsy sites within the Consortium.

Study phs003463

Ewing's sarcoma sequencing data

This study shares DNA and RNA sequencing data for patients with Ewing's sarcoma

Study EGAS00001005689

Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort

Pathogenic germline variants in the protection of telomeres 1 gene (POT1) have been associated with predisposition to a range of tumor types, including melanoma, glioma, leukemia and cardioangiosarcoma. We sequenced all coding exons of the POT1 gene in 2,929 European-descent melanoma cases and 3,298 controls, identifying 43 protein-changing genetic variants. We performed functional studies on each of these variants and explored their possible contribution to disease risk.

Dataset EGAD00001009848

Genetic Associations in Idiopathic Talipes Equinovarus (Clubfoot) - GAIT

Isolated clubfoot or idiopathic talipes equinovarus (ITEV) is one of the five most common birth defects, affecting approximately 4,000 newborns each year in the US. While the orthopedic care of these children has improved, long-term problems persist and the health care costs are significant. Studies suggest that clubfoot is a complex disorder with segregation analyses and family studies indicating that genetic factors play an important etiologic role in the development of clubfoot. Only one environmental factor, maternal smoking during pregnancy, has been implicated. We postulate that a small number of genes account for a substantial fraction of clubfoot and that these genes can be identified in a defined population. The challenge now is to identify the genetic loci and, later, the effect of environmental exposures. To accomplish this task, it is important to have a well-defined population and the methodology to detect linkage with and without association. Towards these goals, we have identified and characterized multiplex clubfoot families, including two large clubfoot families, a resource which is among the largest ITEV populations in existence. We will perform a high-density SNP genome scan (GWAS) on our clubfoot dataset to identify chromosomal regions that may harbor clubfoot genes with subsequent interrogation of these regions and candidate genes. We are in a position with our unique clubfoot population and with the methodology in place to undertake this study. The study phases are: 1) continued ascertainment of multiplex and simplex families and 2) GWAS and characterization of identified chromosomal regions and candidate genes. The results of this study will provide data essential to the identification of the gene(s) contributing to the clubfoot phenotype. Identification of high-risk genotypes can lead to the development of prevention programs in selected populations and may suggest gene-based prevention strategies.

Study phs000314

McGill Epigenomics Mapping Centre

The McGill Epigenomics Mapping Centre (EMC) and Data Coordination Centre (EDCC) were established in 2012 at the McGill University and Genome Quebec Innovation Centre (Montreal, Canada) to support large-scale human epigenome mapping for a broad spectrum of cell types and diseases. Previous epigenetic studies have provided profiles of specific chromatin marks in relation to basic biological processes, and future studies of molecular mechanisms must build upon these proofs-of-concept by integrating sequence-based variation with multiple levels of epigenetic and transcriptional regulation across the genome of human tissues and animal disease models. This project leverages the high-throughput sequencing infrastructure and expertise in genomics and transcriptomics at the McGill Innovation Centre to carry out this research. Controlled access to the data by collaborators and the greater scientific community is gained via a portal, which takes advantage of Compute Canada high-performance computing cluster resources to manage the large volume of data associated from the generation of reference epigenome maps. McGill University is one of two Canadian mapping and data coordination centres, the other based at the Michael Smith Genome Sciences Centre in Vancouver, British Columbia. The generation of comprehensive epigenome maps at McGill University is part of a larger international effort that is coordinated by the International Human Epigenome Consortium (IHEC), whose overall long-term objective is to determine the extent to which the epigenome shapes human populations over generations and in response to the environment. This project is funded under the Canadian Epigenetics, Environment, and Health Research Consortium (CEEHRC) by the Canadian Institutes of Health Research and by Genome Quebec, with additional support from Genome Canada. The computing and networking infrastructure, and part of the software development, are provided by Compute Canada and CANARIE.

Study EGAS00001000995

GDAP___Genome_Diversity_in_Africa_Project

The Genomic Diversity in Africa Project (GDAP) started with the plan to develop a genomic resource from African populations, characterise genomic diversity and population history, and facilitate clinical studies in Africa. Currently, 25 individuals from 24 ethnolinguistic groups have been whole-genome sequenced at high depth totalling 585 individuals. An additional 41 individuals have been sequenced with 10X Genomics libraries. At this stage, the initial curation of this dataset has been finished and we are performing the analysis in coordination with our collaborators. The current state of the GDAP represents a very diverse panel of African populations that maximizes geographical and ethnic variation and represents a great starting point to achieve the aforementioned goals. However, southern sub-Saharan countries, Bantu speakers and hunter gatherer groups are currently underrepresented, despite being crucial to understand the evolutionary history of the continent. After extensive effort to collate studies documentation, we finally have the opportunity to sequence 600 new individuals from these groups, including countries as Gabon, Rwanda and Zambia, and address these deficiencies. We aim to proceed with the same strategy: to sequence at high depth 25 individuals with standard PCR free libraries, with 2 additional individuals with 10X Genomics Chromium libraries per ethnolinguistic group. The former allows a good representation of variants down to low frequency in any given population, and the latter allows accurate phasing and the analysis of structural variation. By including these new populations, we want to investigate three crucial questions in African history in addition to the initial objectives: the Bantu expansion, the evolutionary history of hunter gatherers and the transatlantic slave trade. Additionally, the expanded dataset will help us better discover the genetic variation present in Africa and characterize the African pangenome. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Study EGAS00001003602

15020 results for "cancer studies using rna-seq"

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