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• Microbiome

  16S-sequencing: All stool samples were processed according to the standards of the Flemish Gut Flora Project (Falony et al., 2016). All samples were processed together and sequenced in as a single batch (dual index run DI23R22) which included positive controls (PC, identical stool sample), negative controls (PCR-mix) and ‘blanks’ or negative controls of the extraction (no sample). In addition, a Runella strain (RS) was included to check for potential cross-contamination, as this strain is not present in human samples. The V4 region of the 16S rRNA gene was amplified with the primer pair 515F and 806R (GTGYCAGCMGCCGCGGTAA and GGACTACNVGGGTWTCTAAT, resp.), modified to contain a barcode sequence between each primer and the Illumina adaptor sequences to produce dual- barcoded libraries (Tito et al., 2019). Sequencing was performed on the Illumina MiSeq. Sequences were processed using the LotuS (Hildebrand et al., 2014) and DADA2 pipeline (Callahan et al., 2016) using RDP 16 as the reference taxonomy.

  Dataset EGAD50000002027

• L1 Retrotransposon sequencing in Cocaine Use Disorder - Study 1

  Cocaine Use Disorder (CUD) is a global public health problem, with no effective pharmacotherapies. While CUD is marked by high heritability, discovery of variants associated with risk for CUD has proven difficult. We used Restriction Enzyme Based Enriched L1 sequencing (REBELseq) to amplify L1 retrotransposons in gDNA isolated from medial prefrontal cortex NeuN+ neuronal nuclei from 25 CUD cases and 26 controls. Amplified libraries were sequenced on the Illumina HiSeq 4000 platform, and sequencing data was analyzed with the REBELseq bioinformatics pipeline.

  Study phs001966

• Small‑scale mutations are infrequent as mechanisms of resistance in post‑PARP inhibitor tumour samples in high grade serous ovarian cancer

  Targeted DNA sequencing of high-grade serous ovarian cancer (HGSC) tumour and normal samples from 26 patients. Following target hybrid capture of 63 genes involved in DNA repair and response to treatment with an Agilent SureSelect XT panel, sequencing libraries were generated using the SureSelect XT Low Input Target Enrichment System (Agilent) as per the manufacturer's protocol. Libraries were sequenced on an Illumina NextSeq 500 at the Peter MacCallum Cancer Centre (Melbourne, Australia).

  Study EGAS50000000146

• Duplex sequencing of 26 genes

  Buccal samples and paired esophageal epithelium were obtained using the three sizes of swabs and endoscopic biopsy, respectively. Forty samples from 10 subjects were analyzed via duplex sequencing. This dataset contains bam files that were mapped to the GRCh37 reference genome.

  Dataset EGAD50000000998

• WGS

  Whole Genome Sequencing

  Dataset EGAD00001001120

• Somatic mutations in twin breast cancers (2019-04-03)

  The aim of this study is to investigate the somatic mutations in twins with BRCA1/2 negative breast cancer with no strong family history. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004890

• Heart Failure Network: Diuretic Optimization Strategies Evaluation in Acute Heart Failure (HFN DOSE-BioLINCC)

  ObjectivesThe DOSE study sought to evaluate the most effective dosing (high vs. low) and administration (continuous infusion vs. intermittent boluses) combination of the diuretic Furosemide in the treatment of patients with acute decompensated heart failure.BackgroundAcute decompensated heart failure is the most common cause of hospital admissions among patients older than 65 years of age and is responsible for more than 1 million hospitalizations annually in the United States. Intravenous loop diuretics are an essential component of current treatment and are administered to approximately 90% of patients who are hospitalized with heart failure. Despite decades of clinical experience with these agents, prospective data to guide the use of loop diuretics are sparse, and current guidelines are based primarily on expert opinion. As a result, clinical practice varies widely with regard to both the mode of administration and the dosing.SubjectsA total of 308 patients were enrolled between March 2008 and November 2009 at 26 clinical sites in the United States and Canada. DesignThe DOSE study was a prospective, randomized, double-blind, controlled trial with a 2-by-2 factorial design. Patients were randomly assigned to either a low-dose strategy (total intravenous furosemide dose equal to their total daily oral loop diuretic dose in furosemide equivalents) or a high-dose strategy (total daily intravenous furosemide dose 2.5 times their total daily oral loop diuretic dose in furosemide equivalents) and to administration of furosemide either by intravenous bolus every 12 hours or by continuous intravenous infusion.The study treatment, with group assignments concealed, was continued for up to 72 hours. At 48 hours, the treating physician had the option of adjusting the diuretic strategy on the basis of the clinical response. An assessment of biomarkers, including creatinine, cystatin C, and N-terminal pro-brain natriuretic peptide, was performed at a central core laboratory at baseline, 72 hours, and 60 days. Patients were followed for clinical events to day 60. The coprimary end points were patients' global assessment of symptoms, quantified as the area under the curve (AUC) of the score on a visual-analogue scale over the course of 72 hours, and the change in the serum creatinine level from baseline to 72 hours.ConclusionsAmong patients with acute decompensated heart failure, there were no significant differences in patients' global assessment of symptoms or in the change in renal function when diuretic therapy was administered by bolus as compared with continuous infusion or at a high dose as compared with a low dose. (Felker et. al., 2011, PMID: 21366472)

  Study phs003524

• A Perioperative Study of Safusidenib in Patients with IDH1-Mutated Glioma

  10 participants with a radiological or pathological diagnosis of WHO Grade 2 lower-grade glioma (LGG) were recruited at a single center starting in December, 2022. Eligibility criteria permitted participants who had undergone prior surgery for WHO Grade 2 LGG, but excluded those with a history of prior radiation or chemotherapy.In Part A of the study, participants underwent an initial craniotomy with tumor biopsy and a lumbar puncture for cerebrospinal fluid (CSF) collection at study entry. Following sample collection, participants received safusidenib at the recommended phase 2 doses of 250 mg twice daily (b.i.d.) for a period of 22–36 days. This was followed by a second craniotomy for maximal safe tumor resection and a repeat lumbar puncture within 5 hours of the final pre-resection dose of safusidenib. Tumor, blood, and CSF samples were collected at both surgical time points for comprehensive translational research.Molecular analyses were performed on samples collected at both time points. These included pharmacokinetics (PK), targeted metabolomics, whole-genome sequencing (WGS) of tumor tissue, single-nucleus RNA sequencing (snRNA-seq), and DNA methylation profiling on all patients. Targeted metabolomics was conducted on samples from 9 participants, while spatial transcriptomics and spatial metabolomics were performed on tumor tissue from 3 participants each. Histone methylation profiling was conducted on samples from 8 participants.

  Study phs003976

• scRNAseq dataset of circulating T cells in FL patient before and after Lenalidomide treatment

  scRNAseq dataset of circulating T cells from 3 FL patients (P011, P014 and P020) included in the GALEN clinical trial. There is two time points for each patient : One before treatment (D0) and one at day 7 of Lenalidomide treatment (D7).

  Dataset EGAD50000001529

• Cord blood progenitor CITE-seq dataset

  Sequencing results of single-cell transcriptome and antibody libraries from two biological experiments of cord blood progenitor cells. Four samples from different time points were processed using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Gene expression and antibody-derived libraries were sequenced separately.

  Dataset EGAD50000000405

• Delineate genomic and epigenomic changes in esophageal squamous cell carcinoma following radiotherapy

  We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  Dataset EGAD00001003799

• Genomic and Phenotypic Profile of Sickle Cell Disease in Human Population in Cameroon

  Sickle cell disease (SCD) is caused by a biallelic single nucleotide substitution in the beta-globin gene (HBB), resulting in an amino acid substitution, Glu7Val, formerly known as Glu6Val. An estimated 300,000 babies with SCD are born worldwide each year, with nearly 75% of these births being in sub-Saharan Africa. In Africa, at least 30-50% of children with untreated SCD die before the age of 5 years. Therefore, accelerating the path for novel therapies for SCD through genomics research on fetal hemoglobin (HbF) is critical. Variants in the currently known HbF‐modulating genes/loci, i.e., BCL11A, HBS1L-MYB, and XmnI-HBG2, explain only 10-20% of the variation of HbF levels in African individuals with SCD, compared with nearly 50% of the variation in HbF levels among Europeans. Expanding genomic research in populations of African ancestry could uncover the missing heritability of HbF-promoting loci. This study used the Human Heredity and Health (H3Africa) consortium SNP genotyping array developed from whole genome enriched for common variants in sub-Saharan Africans to investigate genomic variations associated with HbF levels in individuals with sickle cell anemia of the HbSS genotype from Cameroon. Two of the previously described loci, BCL11A and HBS1L-MYB were replicated, while a novel locus on chromosome 13 mapping to FLT1 was uncovered. The study therefore opens up a novel avenue for exploring SCD gene therapy.

  Study phs003748

• Detection of cancers three years prior to diagnosis using plasma cell-free DNA

  A major goal of early cancer detection is to identify subclinical disease when the tumor burden is low, so that treatments are more effective. But how early can cancers be detected prior to clinical signs or symptoms? This question can be answered only through the evaluation of participants whose clinical course has not been altered by the study itself. We here describe such an evaluation, performed on prospectively collected plasma samples from the Atherosclerosis Risk in Communities (ARIC) study, including 26 participants diagnosed with cancer and 26 matched controls. At the index time point, eight of these 52 participants scored positively with a multicancer early detection (MCED) blood test. All eight of these participants were diagnosed with cancer within 4 months after blood collection. In six of these 8 participants, we were able to assess an earlier plasma sample collected 3.1 to 3.5 years prior to clinical diagnosis. In four of these six participants, the same mutations detected by the MCED test could be identified, but at 8.6 to 79-fold lower levels. These results demonstrate that it is possible to detect circulating tumor DNA (ctDNA) more than three years prior to clinical diagnosis, and provide benchmark sensitivities required for the success of ctDNA-based tests for this purpose.

  Study EGAS00001008068

• Chromatin accessibility in human monocyte differentiation

  This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting TET2, IRF4 and EGR2. In total, it includes 26 samples.

  Dataset EGAD00001006601

• About

  About What's the EGA? The European Genome-phenome Archive (EGA) is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona, we aim to advance biomedical research and promote personalised medicine worldwide by enabling discovery of and access to human genomic and health research data. The EGA contains data collected from individuals whose consent agreements authorise data release for specific research use to bona fide researchers. We ensure strict security measures to control access to the data and maintain patient confidentiality. With expertise in data management and technical infrastructure, we promote FAIR data reuse and enable researchers to share their data securely. By leveraging public funding and our strategic partnerships, the EGA provides a free service for permanent data storage, data discovery, and secure data access. In addition, we foster a federated network to provide transnational access to human research data in compliance with legal frameworks. For additional information about the EGA, please contact: Helen Parkinson and Mallory Freeberg EMBL European Bioinformatics Institute Arcadi Navarro, Roderic Guigó, and Jordi Rambla Center for Genomic Regulation History The European Genome-phenome Archive was launched in 2008 at the European Bioinformatics Institute (EMBL-EBI), an outstation of the European Molecular Biology Laboratory (EMBL), to address an identified need for archiving and sharing the results of genome-wide association studies from the Wellcome Trust Case Control Consortium. With the signing of a memorandum of understanding in 2013 and a formal agreement in 2016, the EGA became a joint project of EMBL-EBI and the Centre for Genomic Regulation (CRG). The two institutes work together to support the EGA services, including supporting submissions, website, strategic leadership, and data infrastructure developments. In 2022, the Federated EGA was officially launched with the signature of the first five countries: Finland, Germany, Norway, Spain, and Sweden. With more than 20 additional nodes worldwide preparing to join, the Federated EGA aims to become the largest human omics data sharing initiative towards understanding human health and disease. EGA overview If you're a researcher you may need to deposit, manage, or access genomic data in a secure and regulated way. The European Genome-phenome Archive (EGA) is a platform that facilitates these processes, ensuring that sensitive data is stored and shared in accordance with legal and ethical regulations. Submission process To start a submission, you need to become an EGA submitter. For that, you’ll need to sign a Data Processing Agreement (DPA) with us, that defines the terms and conditions under which your data will be processed and shared within the EGA system. The access to each study is controlled by its Data Access Committee (DAC). The DAC is responsible for managing data access requests and ensuring that the release of data is in accordance with the General Data Protection Regulation (GDPR). Please, note that once your data is released, all public metadata related to your study and dataset(s) will be searchable on the EGA website. However, the files are only accessible under controlled access, which means that a DAC has to agree to a previous data access request. Request process It is possible to submit an access request to data stored at the EGA. The DAC assigned to the study will assess the request and, if approved, grant access to the data. Requesters must provide sufficient justification for your request and comply with the intended data usage in order to get access to it. Each dataset is covered by a Data Access Agreement (DAA) that defines the terms and conditions of use for the specified dataset/s. The DAA is created and provided by the DAC, and must be signed by the individual requesting access to the given dataset/s. Download process Once the request for access is approved, the data and metadata can be downloaded. The EGA offers various download options to fit the needs: it is possible to preview files without downloading them, download specific files of interest, or even download terabytes of data. Overall, the EGA provides a secure and regulated environment for depositing, managing, and accessing human data. Regardless of the role - submitter, DAC member, or requester - the EGA provides assistance for each while ensuring that sensitive data is managed in an ethical and responsible manner. More information on how EGA handles data is available in the EGA dataflow.

  Documentation about/ega

• Human four week embryo head as reference for generating an enhancer compendium for neuronal and neural crest development using neural tube organoids.

  This study has the aim of generating an enhancer code compendium of early human neuronal and neural crest development. For this purpose, we generated human neural tube organoids from single cells from two induced pluripotent stem cell lines. The organoids were subject to combined single cell multiomics at four time points of differentiation. To evaluate the biological relevance of the cell types and states obtained from the organoids, we compared with data obtained from 10XGenomics single cell multiomics on the head of a single four weeks post conception human embryo.

  Study EGAS50000001031

• SCI-MAP: Single Cell Microgel embedded iPS-cells to map molecular variability of cell differentiation using a systems biology approach.

  In the SCI-MAP project we will map cell states encountered across a previously established 49 day in vitro chondrogenic differentiation protocol. We do this to optimise the differentiation process for therapeutic and in vitro modelling ends. We collect epigenetic open chromatin and phenotypic transcriptome data to determine cell states and so performed single nucleus sequencing in two modalities: RNA- and ATAC-sequencing. Data was collected in a time series experiment at 7 points: Days 0, 3, 6, 8, 14, 21, and 49, starting with the first pilot data from day 21 (D21).

  Study EGAS50000001041

• B cell activation

  To investigate the gene programs involved in B cell activation and antibody switching, we profiled the gene expression at the single cell level as well as the antibody repertoire of human naive and memory B cells at resting and following three time points of activation. Through CRISPR perturbations, we defined IRF4 as a central regulator of both GC and plasma cell fates, acting independently of PRDM1 in GC commitment. Finally, leveraging machine learning classification methods trained solely on transcriptomic profiles, we accurately predicted sister cell relationships, revealing that plasma cell gene expression programs are heritable and tightly conserved within a clone.

  Study EGAS50000001468

• Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies

  To identify early driver mutations in ovarian cancer cells, we used dense whole genome sequencing of micrometastases and microscopic residual disease collected at three time points from a single patient during treatment for high-grade serous ovarian cancer (HGSOC). Laser capture microdissection of tumour islets was performed on samples prior to chemotherapy, after three cycles of chemotherapy and at recurrence. Long frament read whole genome sequencing was performed and mutations were identified. To our knowledge, this is the first longitudinal study that attempts to investigate spatial and temporal micro-heterogeneity in cancer.

  Study EGAS00001001909

• Genomic profiling of patient-derived xenograft models of myxoid liposarcoma either sensitive or resistant to trabectedin

  The dataset consists of two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. Both models underwent the same treatment schedule with trabectedin (tree time points and one treatment with doxorubicin). We performed genomic profiling using Agilent OneSeq assay.

  Dataset EGAD00001005099

• scRNA-Seq & scATAC-Seq Feature-counting Results Derived from 10X Cellrange-arc-count pipeline

  The feature-counting outputs from Cellrange-arc-count pipeline contain information at the single cell level, jointly for both scRNA-Seq and scATAT-Seq on 103 DLBCL samples and 3 normal controls (Please note that sc-40 only has scRNA-Seq data without scATAC-Seq). These files can be used as the input files for further downstream analysis software (e.g. Seurat Package). Moreover, a matrix of single-cell barcodes and associated cell biological types (used in the study) is also provided for users’ reference. This dataset is large and split into two parts to facilitate downloads. This dataset is large and split into two parts to facilitate downloads. The Linux command line of "tar -xvf xxxx_PART1.gz" should be used to extract the individual files. For additional information regarding the genomic data associated with the study, please also see the paper companion website at https://llmpp.ccr.cancer.gov/local/DLBCL_singlecell/

  Dataset EGAD50000002490

• Exome sequencing of 142 gastric cancer and matched normal from Japanese cohorts (UT)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 142 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Dataset EGAD00001004041

• Exome sequencing of 102 gastric cancer and matched normal from Japanese cohorts (YCU)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 102 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Dataset EGAD00001004042

• DNA and RNA sequencing data from Ovarian Carcinosarcoma patients from the Glasgow Cohort.

  In this study, we analysed DNA and RNA sequencing data from Ovarian Carcinosarcoma patients, from isolated carcinoma and sarcoma components and investigated DNA variants as well as gene expression. Genomic analyses from this data and further investigation from preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate anti-tumour immunity.

  Study EGAS00001006605

• Characterization of the molecular signature of human monocytes in aging and myelodysplastic syndrome

  Deep immunophenotypic profiling of peripheral blood immune cells from young and older control subjects as well as patients with MDS was initially performed, using mass cytometry to identify monocyte subpopulations. Abundance of monocyte subpopulations separated the samples from patients with MDS from elderly control subjects was identified. Therefore, targeted immunophenotyping of monocytes was also performed with flow cytometry and RNA sequencing from isolated CD14+ peripheral blood longitudinally in 26 subjects, six young healthy individuals, nine older healthy individuals and eleven patients with MDS.

  Study EGAS00001007676