Search Results - EGA European Genome-Phenome Archive

EFFORT occupationally exposed human stool metagenomes (148 samples)

Metagenomes of stool samples from 54 pig farmers, 24 broiler farmers and 70 slaughter line workers. Note: Access to the data will only be granted for antibiotic resistance studies in accordance with the EFFORT consents issued by the participants.

Dataset EGAD00001005444

DAC Portal documentation

DAC Portal Welcome to the DAC Portal documentation! If you are involved in governance or legal aspects, technical or operational aspects, or serving as a data steward, this page will be helpful for you. By exploring these materials, you can define your own Data Access Committee (DAC) and policies, understand the minimal requirements for a DAC and a policy object, and comprehend how the EGA data access requests are managed. DAC Portal Index Setting up your account DACs and Policies Pending Request table Manage Data Requests History page Audit your DACs, policies, and datasets Deprecation User Preferences DAC API - A programmatic approach Setting up your account Register yourself as an EGA user. The Helpdesk team will validate your account (this could take up to 48 hours). After validation, you will receive an email with a link to verify your email - Make sure you click on the link to verify your account! If you don’t receive the email, please check your spam folder. Once your account is active you can login to the DAC Portal. We recommend you to check out the Take The Tour! DACs and Policies Create a DAC Click on Create a DAC Add the title and description to your DAC. Once ready, click on the ‘Create’ button. You will have to wait until the Helpdesk Team validates the creation of your DAC. Once approved by Helpdesk, your DAC will be assigned with a persistent identifier (EGAC). Edit a DAC Once your DAC is registered and approved, you can edit it and add contacts. Remember, you can add as many contacts as needed. And, you can also remove/add contacts anytime. To add a contact, you must write the username or email of a registered EGA user in the Members field. Once you have typed the whole username or email, a drop-down menu will appear where you can select the contact. Select a contact from the drop-down menu. Make sure you write the full username or email of the contact so it appears as an option. Make sure that you select one main contact. Set up the role you want to grant to the new contact of the DAC. We recommend you to check out the FAQ to learn more about the different roles! After adding all the necessary contacts and assigning roles, click on Update. This will send an email notification to the new DAC member, letting them know about the invitation to managing the DAC. Once they log into the DAC Portal, they will be able to either accept or turn down the invitation. Create a policy First, please note that all information registered in a policy metadata object will be publicly available on the EGA website. For each released dataset, all users will be able to read the policy under the “Data Access” tab. Select Create a Policy from the Policies tab. Select the DAC that you want your policy to depend on. Add the title and terms and conditions for accessing and using your data. If you already have an external website for data access requests, you can add the URL directly here (see example here). You can find a template of a Data Access Agreement (DAA) document in our Policy documentation page. The DAA template is provided for guidance only and should be adapted to suit your own purpose depending on the security policies, terms for publication or embargoes, and restrictions on data use or sharing. You can also add Data Use Ontologies (DUO) to your policy. These DUO codes are used to semantically tag the terms and conditions of using the data linked to the policy (example). For more information, you can refer to the Data Uso Ontology documentation. Once completed, make sure to click the Create button in order to register your policy. A persistent identifier (EGAP) will be assigned automatically. Edit a policy Please, note that you will not be able to edit the policy if it shows in orange. Meaning that you are a member of the DAC linked to that policy. Members don’t have edit rights. Only admins can edit objects. You can check your registered policies on My policies, available at the menu in the top-right corner. Select your policy. It will then display the information of that policy, allowing you to edit the information. Once you are done with the modifications, click Update. Pending Requests Table Table Settings Upon selecting a specific DAC, you will be presented with a customisable table showcasing all pending data access requests. This table allows you to tailor the displayed information according to your preferences by selecting desired columns. Available Columns (Displayed with the Eye Icon): Date: The date when the data access request was submitted. Full Name: Name and surname of the user submitting the request. Email: Email address associated with the user's request. Username: The username linked to the EGA account of the user submitting the request. Organisation: Affiliated organisation of the user submitting the request. Dataset: EGA accession ID for the requested EGA dataset. Dataset Title: Title of the requested dataset. DAC Comment: Space provided for internal comments related to the request. Expiration: Option to specify an expiration date for granted permissions. Check more information on the pending request table here! Table Filters By default, all data access requests are displayed. However, you have the option to apply filters to refine your view. Follow these steps to apply filters: Click on the More button. This action will reveal the different columns available for applying filters. As you select columns, the checked fields will be displayed at the top of the request table. Choose the specific values within the selected columns that you want to filter for. Click the Search button to apply the selected filters. Do you find yourself frequently applying the same filters? You can save multiple combinations of filters for easy access at any time! Here's how: Click the Save button. Provide a descriptive name for the filter combination. Click Save to confirm. To load saved filters, simply select the saved filter from the dropdown menu to apply it automatically. Check more information on filters here! Advanced Search For users requiring more granular control over their data access requests, the DAC Portal offers an Advanced Search feature using JIRA Query Language (JQL). With JQL, you can craft precise and complex queries to filter and retrieve specific data access requests based on various criteria such as date, user details, dataset attributes, and more. Using JQL's flexibility, you can create custom queries to meet your specific needs, allowing for advanced filtering options beyond the standard filters provided. You can find the Advanced Search feature following these steps: Click the … button Select Advanced To view the allowed fields for filtering and explore all available options, simply click on the info icon. Once you have written the filtering values, click the Search button to apply. Check more information on filters here! Manage Data Requests Upon logging into the DAC Portal, you'll notice a sand clock icon next to the DAC ID, indicating the number of pending requests. Click on the DAC to review these requests. Accept requests Click on the right side of the toggle button to grant access to the user. You can manage other requests before proceeding to the next step. After managing the requests, click on the Apply button. A confirmation box will appear summarising the options to be applied. Click on Yes, Confirm to proceed with granting permissions. Deny requests Click on the left side of the toggle button to deny access to the user. Provide a reason for the denial. Note that the user will receive an email with this reason. Click on the Done button. You can manage other requests before proceeding to the next step. After managing the requests, click on the Apply button. A confirmation box will appear summarising the options to be applied. Click on Yes, Confirm to proceed with denying permissions. Tips! Apply a filter to view all requests to be managed at once. Use the toggle in the row with column names to grant or deny permissions for multiple requests simultaneously. You can grant and deny permissions in the same action, simplifying the process. The confirmation box will provide a summary of all actions, including grants, denials, DAC comments, and expiration dates. History Page The History page serves as a dedicated space to view information regarding all requests managed by all DAC members. Here, you can review active permissions and revoke them as needed. Go to the History page by clicking on the "HISTORY" button from a DAC page in the DAC Portal. Here are the different row types you may find: Current permissions: row in green with a toggle button to revoke permissions on the right. Approved requests: row in green, with no toggle button. Request denied: row in red with “request denied” on the right. Permission revoked: row in red with “permission revoked” on the right. Distinctions to Note! Between Request Denied and Permission Revoked: Request Denied: Refers to requests that were rejected from the outset, indicating that access to the dataset was never granted. Permission Revoked: Indicates that permissions were previously granted but have since been revoked. Users with permissions revoked have previously accessed the dataset. Between Approved Request and Current Permissions: Approved Request: Represents an entry when a data access request has been approved in the past. Current Permissions: Denotes ongoing permissions where a user has present access to the dataset. An approved request may now appear as Permission Revoked in the present. By observing these different rows, users can gain insight into the complete history of a user's interactions and permissions regarding a dataset over time. To revoke access to a specific user for a dataset, follow these steps: Go to History page Look for the row with the specific permissions. You can use the filters! Click on the toggle button to revoke access. Add a denial reason. Bear in mind that the requester will receive the denial reason! Click on the Apply button. Check more information on the Hisotry page here! Audit your metadata objects In the DAC Portal, you can efficiently manage and audit various metadata objects pertinent to your role as a Data Controller. Upon accessing the DAC Portal, you will encounter three primary tabs on the homepage: DAC: Contains information about Data Access Committees (DACs). Policies: Provides insights into linked policies. Datasets: Displays datasets and relevant details. Within each tab, you'll find a comprehensive list of the objects you manage, these being grouped by type (DAC, Policies, Datasets), as well as by your role (member/admin). Whilst the lists give you a quick look, to check how things are connected, we've added a table at the bottom DACs and policies. DACs Let’s check which policies are linked to a specific DAC: Go to "My DACs." Select a DAC. Click on "EDIT" to see more details. You are now on this page: Scroll down to see the linked policies. Click on “List of linked policies of this DAC” and you will see a list of all policies linked to your selected DAC. Policies Do you want to view a list of datasets connected to a particular policy? Follow the same steps mentioned earlier, but head to the policy tab this time. In the policy tab, you'll find a list of all your policies. Here, you may notice two different icons next to the policy ID (EGAP): DAC Icon (): This represents the DAC. Hover your mouse over the icon to see the DAC ID. Dataset icon (): This indicates datasets falling under that policy. The number next to the icon tells you how many datasets are linked to the policy. For example, if you see "2" next to the icon, it means there are two datasets linked to that policy. If you want to check the linked datasets and their relevant information, simply click on a specific policy. You'll then find the "List of linked datasets of this policy" at the bottom of the page. Datasets Finally, in the dataset tab, by default you will see a list of all the datasets you can manage with all your DACs and policies. Yet, we've included two handy ways to organise them: DAC vs. policy: You can group by datasets, either by DAC or policy. Released vs. unreleased: You can sort out datasets based on their release status. Feel free to experiment with both options! For instance, if you want to see which DACs have unreleased datasets, simply select DAC and unreleased, and you'll get the details you need! Deprecation Do you have a bunch of metadata objects like DACs and policies that you don’t need anymore? This section shows you how to get rid of them! But what does "deprecation" mean for EGA? It's basically changing the status of a metadata object to "deprecated," which means we won't be using it in the future. In simple terms, it's like saying these objects are no longer useful. However, because we believe in making metadata FAIR, once an object has a persistent identifier, we can't just delete it. So, instead of deleting, we deprecate it. Here's a helpful tip! If you want to make a metadata object disappear from the DAC Portal, deprecate it. You won’t see it in the portal anymore! Let’s say you want to deprecate a DAC. Let’s do it! Go to "My DACs." Select a DAC. Click "EDIT" to see more details. You are now in this page: Click on the Deprecate button It will then appear a message. There are two options here: Your DAC is not linked to any policy, hence it’s ready to be deprecated. Click on “Yes. Confirm” to deprecate your DAC object! Your DAC is linked to at least one policy, and you need to either: Deprecate the linked policy first, or Link the policy to a different DAC Now, let’s say you don’t want to get rid of the policy altogether, but you want to change the DAC it’s linked to. Here's how: Go to the policy tab. Find the policy you want to change (for example, EGAP50000000019). Choose a new DAC to link it to. Click on Update. See the Edit Policy section for more details. After ensuring that the DAC we want to deprecate isn’t linked to any policy, return to the "My DACs" section and follow the steps outlined previously. This will lead you to a confirmation message. You can only deprecate DACs and Policies. To deprecate a dataset, please contact our Helpdesk team. Check more information on how deprecation works here! User Preferences We have implemented email notifications in the DAC Portal. Here’s the complete list: DACs: Pending requests Approved by Helpdesk Rejected by Helpdesk DAC Invitation Requesters: Data access request approved Data access request denied Permissions revoked Upcoming expiration date As a DAC member, you will be able to decide whether you want to receive the DAC notifications or not. For that, go to the top-right corner menu, select User Preference. You will be able to decide whether you want to receive notifications for: Approved by Helpdesk Rejected by Helpdesk DAC Invitation For pending requests, you will be able to select how often do you want to receive the notification: Daily Weekly Fortnightly As a DAC member, you are responsible for managing data access requests. Consequently, you will receive notifications for pending requests. If you prefer not to manage these requests, please arrange to be removed as a contact for your DAC. Here's a tip! Do you have a pending request that you don’t want to receive a notification? Add a DAC comment! The EGA understands that a request resolution can take some time, for this reason, if you add a comment (make sure you save it by clicking the APPLY button!) we will filter those requests at the time of sending the notification! DAC API - A programmatic approach In addition to the new DAC Portal, we are excited to announce the release of the DAC API. This enables users to programmatically manage permissions. If you are interested in learning more about the technical specifications, you can click the button below. Check out the DAC API specification!

Documentation access/data-access-committee/dac-portal

Multicenter Study of Hydroxyurea (MSH)

This study aimed to determine whether or not treatment with hydroxyurea titrated to maximum tolerated doses would reduce the frequency of vaso-occlusive (painful) crises by at least 50% in 299 men and women between 18 and 50 years old with a diagnosis of sickle cell anemia by gel electrophoresis conducted by a Core Laboratory. A secondary objective investigated correlations of fetal hemoglobin (HbF) levels and other patient or treatment characteristics with the occurrence of vaso-occlusive (painful) crises, and the effect of treatment on the quality of life.This controlled trial made hydroxyurea the first drug of proven benefit in preventing vaso-occlusive pain crisis and acute chest syndrome caused by sickle cell disease, with additional findings including reduced mortality in adult patients taking hydroxyurea for frequent painful sickle cell episodes after 9 of years follow-up. No significant side-effects of hydroxyurea therapy were noted.Instructions for requesting individual-level data are available on BioData Catalyst at https://biodatacatalyst.nhlbi.nih.gov/resources/data/. Apply for data access in dbGaP. Upon approval, users may begin accessing requested data in BioData Catalyst. For questions about availability, you may contact the BioData Catalyst team at https://biodatacatalyst.nhlbi.nih.gov/contact.

Study phs002348

GCAT | Genomes for life

The GCAT project is a prospective cohort study that was designed to recruit the general population of Catalonia, the north-east region of Spain. This study is a long-term genomic, environmental and lifestyle cohort project that aims to evaluate and track multiple pathologies as well as biologically related traits. By the end of 2017, the GCAT Study had recruited a total of 20 000 participants aged 40–65 years. Participants who agreed to take part in the study completed a self-administered computer-driven questionnaire, and underwent blood pressure, cardiac frequency and anthropometry measurements. For each participant, blood plasma, blood serum and white blood cells are collected at baseline. The GCAT Study has access to the electronic health records of the Catalan Public Healthcare System. Participants are followed biannually for/during, at least, 20 years after recruitment. Therefore, the GCAT Study offers a unique opportunity to integrate diverse data to allow the identification of novel relations among different biomarkers and conditions. Results may lead to the development of new genetic, genomic, epigenomic and proteomic diagnoses and screening tests, as well as new public health recommendations. The only currently available population-based prospective cohort study in Spain to the date, including more than 4899 genotyped participants and 800 whole genome sequences is now stored in the EGA archive under accession id EGAS00001003018.

Blog gcat-genomes-for-life

Resuscitation Outcomes Consortium Pragmatic Trial of Airway Management in out-of-Hospital Cardiac Arrest (ROC PART-BioLINCC)

Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To determine the effect of an initial airway management strategy using laryngeal tube (LT) insertion, compared with endotracheal intubation (ETI), on survival among adults with out-of-hospital cardiac arrest (OHCA).Background: Out-of-hospital cardiopulmonary arrest (OHCA) affects more than 350,000 adults in the United States each year, with only a low percentage of patients surviving to hospital discharge. Emergency medical services (EMS) paramedics commonly perform ETI or insertion of supraglottic airways (SGAs), such as the LT, on patients with OHCA to facilitate oxygenation and protect the lungs from aspiration of vomitus. Because SGA insertion is rapid, simple, and requires less training compared to ETI, many EMS agencies have incorporated this as the primary method of ventilation during OHCA resuscitation. However, the optimal method for OHCA advanced airway management is unknown.Participants: A total of 3004 patients were included; 1505 assigned to initial LT and 1499 assigned to initial ETI.Design: PART was a multicenter cluster-crossover randomized trial. The trial included 27 EMS agencies associated with US sites of the Resuscitation Outcomes Consortium (ROC). The EMS agencies were grouped into 13 randomization clusters. Each cluster selected a crossover interval of 3 or 5 months. Within each cluster, treatment assignments for consecutive intervals were computer-randomized in blocks of 2 to ensure balanced exposure to both airway groups. Crossovers between study groups could occur more than once. Treatment assignments were initial LT insertion or initial ETI. Neuromuscular blocking agents or video laryngoscopy was permitted for initial intubation efforts. The trial did not limit the number of initial LT insertion or ETI attempts. If the initial insertion efforts were unsuccessful, EMS personnel performed rescue airway management using any available airway technique. EMS personnel followed local protocols for confirmation of airway placement and management of OHCA, including field termination of resuscitation efforts. Patients receiving bag-valve mask (BVM) ventilation only were retained in their assigned treatment group per intention-to-treat principles. The trial did not prescribe clinical care at the receiving hospitals, including use of EMS airway, targeted temperature management, percutaneous coronary intervention, or the timing of withdrawal of life-sustaining therapy.The primary outcome was 72-hour survival. Secondary outcomes included return of spontaneous circulation, survival to hospital discharge, and favorable neurological status at hospital discharge (Modified Rankin Scale score ≤3). Conclusions: Among adults with OHCA, a strategy of initial LT insertion was associated with significantly greater 72-hour survival compared with a strategy of initial ETI. These findings suggest that LT insertion may be considered as an initial airway management strategy in patients with OHCA, but limitations of the pragmatic design, practice setting, and ETI performance characteristics suggest that further research is warranted.

Study phs003902

Immuno-nephrology Data Access Committee Amsterdam UMC

In this experiment we investigated kidney immunology in two autoimmune kidney diseases (ANCA-associated glomerulonephritis and Lupus Nephritis). Single cell transcriptome analysis of CD45+ immune cells from freshly retrieved kidney biopsies of 5 AGN patiënts, 1 disease-control with lupus nephritis (class II), and 1 "healthy" nephrectomy control was performed using 10X Genomics technology.

Dac EGAC50000000024

Neuroblastoma_MP-PCR_MultiplexPCR_TargetedSequencing_BAMs

This dataset contains raw sequencing data (BAM/BAI files) generated from human neuroblastoma patient samples. The data were produced using targeted high-throughput next-generation sequencing and are intended to support genomic analyses of tumor-associated alterations. All files are provided under controlled access in accordance with EGA data protection requirements.

Dataset EGAD50000002260

Comparison of the treated celiac disease microbiome to that of controls

Coeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterised by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and environmental factors. While recent data show that alterations in gut microbiome composition could play an important role, many current studies are constrained by small sample sizes and limited resolution. To address these limitations, we analysed faecal gut microbiota from two Dutch cohorts, CeDNN (128 treated CeD patients (tCeD), 106 controls) and the Lifelines Dutch Microbiome Project (24 self-reported tCeD, 654 controls), using shotgun metagenomic sequencing. Self-reported IBS (570 cases, 1710 controls) and IBD (93 cases, 465 controls) were used as comparative conditions of the gastrointestinal tract. Interindividual variation within the case and control groups was calculated at whole microbiome and strain level. Finally, species-specific gene repertoires were analysed in tCeD patients and controls. Within-individual microbiome diversity was decreased in patients with self-reported IBS and IBD but not in tCeD patients. Each condition displayed a unique microbial pattern and, in addition to confirming previously reported microbiome associations, we identify an increase in the levels of Clostridium sp. CAG:253, Roseburia hominis, and Eggerthella lenta, amongst others. We further show that the observed changes can partially be explained by gluten-free diet adherence. We also observe increased interindividual variation of gut microbiome composition among tCeD patients and a higher bacterial mutation frequency in tCeD that contributes to higher interindividual variation at strain level. In addition, the immotile European subspecies of Eubacterium rectale, which has a distinct carbohydrate metabolism potential, was nearly absent in tCeD patients. Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiome’s role in intestinal health and disease. Note that some of the data in this study belong to the Lifelines cohort. Access to this dataset can be requested via the page of the EGA data access committee EGAC00001001996. The phenotype data can be requested, for a fee, by filling the application form at https://www.lifelines.nl/researcher/how-to-apply/apply-here.

Study EGAS50000000959

A Platform Study of Combination Immunotherapy for the Neoadjuvant and Adjuvant Treatment of Patients with Surgically Resectable Adenocarcinoma of the Pancreas

This is a single-institutional, randomized, open label platform clinical trial testing various immunotherapy combinations. Patients with newly diagnosed and surgically resectable pancreatic ductal adenocarcinoma (PDA) and scheduled to undergo the Whipple procedure at Johns Hopkins Hospital were eligible to participate in this study. Criteria for determining resectability strictly followed National Comprehensive Cancer Network (NCCN) guidelines. The study consisted of 6 parts: parts 1-5 constituted the Prime Phase (see below), and part 6 was the Extended Treatment Phase. Part 1: Participants received one cycle of immunotherapy two weeks prior to undergoing the Whipple procedure. Part 2: Subjects underwent the Whipple procedure. Part 3: Subjects received a second cycle of immunotherapy 4-10 weeks following the Whipple procedure (2-4 weeks prior to adjuvant chemoradiation). Part 4: Subjects underwent chemoradiation. Part 5: Subjects received 4 additional 28-day cycles of immunotherapy beginning 1-2 months after completing chemoradiation for a total of six cycles (two before chemoradiation and 4 following chemoradiation). Eligible subjects were randomized to Arms A and B in a 1:1 ratio, stratified up-front by age (≤65, >65). Arm A participants received Cy/GVAX. Arm B participants received the combination of Cy/GVAX and nivolumab. GVAX Vaccine consists of equal numbers (2.5 x 108 each) of Panc 6.03 pcDNA1GM-CSF and Panc 10.05 pcDNA1GM-CSF combined into a single vaccination. Each vaccination consisted of six total intradermal injections. A single intravenous (IV) dose of 200 mg/m2 Cy (CytoxanR) was given one day prior to GVAX. Anti-PD-1 Therapeutic Antibody Nivolumab 480 mg every 4 weeks was administered as an intravenous infusion. The primary objective for Arms A and B was to compare IL17 expression (Th17) in vaccine-induced lymphoid aggregates between resected PDAs from patients treated with the combination of Cy/GVAX and anti-PD-1 blockade antibody vs. the treatment of Cy/GVAX alone. Secondary objectives were to assess the safety, overall survival (OS), and disease free survival (DFS) of patients treated with each of the study drug combinations, and to assess the effects of each of the immunotherapy study drug combinations on PD-L1/PD-1 associated pathways, vaccine-induced immune regulatory signatures, and peripheral and intratumoral antigen specific T cell responses. The exploratory objective was to explore the effects of therapy on tumor and peripheral blood and tumor infiltrating immune cells, and to explore potential molecular determinants of response, progression and disease stability. To these ends, tumor infiltrating immune cells (TIICs) were obtained from surgically resected tumors following the neoadjuvant treatment of the study immunotherapy. TIICs were sorted into CD3+CD4+ T cells, CD3+CD8+ T cells, CD3-CD19+ B cells, and CD3-CD19-CD11b+ myeloid cells by flow cytometry. The sorted immune cell subtype pellets were sent to the commercial vendor (Eurofins) for RNA extraction and sequencing. SMART-seq v4 Ultra Low Input mRNA Sample Prep Kit was used for library preparation with 100bp paired end reads. FASTQ files, that were returned from the vendor, are deposited here.

Study phs003002

The Finland-United States Investigation of NIDDM Genetics (FUSION) Study - Islet Expression and Regulation by RNAseq and ATACseq

This study evaluates gene expression and its regulation in human pancreatic islets, a tissue relevant in the study of genetic risk factors contributing to diabetes. We obtained pancreatic tissue sections and purified pancreatic islets from deceased donors and processed these biological samples to generate various data types. We generated spatial transcriptomic data from pancreatic tissue samples using the 10X Genomics VISIUM technology with sequencing on the Illumina NovaSeq platform. We also generated multiple data types from the purified pancreatic islets using genome-wide SNP chips, bulk RNA-Seq, microRNA (miRNA)-Seq, whole genome sequence, DNA methylation (methyl)-Seq, cap analysis of gene expression (CAGE)-Seq, single cell RNA-seq, and single nuclei ATAC-seq approaches. These data include ATAC-seq of two islet subjects, RNA-seq of 31 additional subjects, genome-wide chip genotypes, and imputed genotypes of the 33 subjects released with phs001188.v1. For genotyping, 500-1000 islet equivalents (IEQ) were cultured as in Gershengorn (Science, 2004, PMID: 15564314); genomic DNA isolated from islet cultures. For RNA analyses, 2500-5000 IEQ from each islet source were used for bulk or single-cell RNA isolation. Messenger RNA was isolated with trizol extraction and 12-plex libraries were generated using the Illumina TruSeq directional mRNA-seq library protocol. Bulk RNA sequencing was performed on HiSeq2000/HiSeq2500/Hiseq4000/NovaSeq6000 sequencers using paired-end reads at the NIH Intramural Sequencing Center (NISC). miRNA libraries were prepared from total RNA from 68 samples, pooled and sequenced 50bp single-end reads on Illumina HiSeq2500. CAGE libraries were prepared from total RNA samples using the nAnT-iCAGE protocol at DNAFORM, Japan. CAGE libraries were sequenced at the NIH Intramural Sequencing Center (NISC) on the HiSeq2000 sequencer. Genotyping on the Illumina Omni2.5M array was performed at the NHGRI Genomics Core facility. Genotypes were imputed using the HRC.r1.1.2016 reference panel. To assess regions of open chromatin in islets, we performed bulk ATAC-seq on HiSeq2000 sequencers using paired-end reads at NISC. Single-nuclei ATAC-seq libraries were prepared using single-cell-combinatorial-indexing (sci-) ATAC-seq protocol and sequenced on Illumina NextSeq using paired-end reads. scRNA-seq libraries were generated using the 10X Genomics platform and sequenced on Illumina HiSeq3000 at the Genomics Technology Core of the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS). Greater than 90% of the loci associated with T2D through genome-wide association studies occur in non-coding regions, suggesting a strong regulatory component to disease susceptibility. Therefore, there is a critical need to understand the full spectrum of genetic variation and regulatory element usage in T2D-relevant tissues. To that end, this study contains multiple genomic and transcriptomic data sets from pancreas tissue sections and pancreatic islets, a resource that will contribute to our efforts to investigate the genetic risk factors for type 2 diabetes.

Study phs001188

The Dynamic Landscape of Open Chromatin During Human Cortical Neurogenesis

Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. To obtain a high resolution depiction of chromatin structure and gene expression in developing human fetal cortex, we dissected the post-conception week (PCW) 15-17 human neocortex into two major anatomical divisions to distinguish between proliferating neural progenitors and post mitotic neurons: (1) GZ: the neural progenitor-enriched region encompassing the ventricular zone (VZ), subventricular zone (SVZ), and intermediate zone (IZ) and (2) CP: the neuron-enriched region containing the subplate (SP), cortical plate (CP), and marginal zone (MZ). Tissues were obtained from three independent donors and three to four technical replicates from each tissue were processed for ATAC-seq to define the landscape of accessible chromatin and RNA-seq for genome-wide gene expression profiling.

Study phs001438

Pomalidomide for the Treatment of Bleeding in HHT (PATH-HHT)

Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To determine efficacy (reduction in severity of epistaxis), tolerability, and improvement in quality of life of pomalidomide compared to placebo after 24 weeks of treatment.Background: This study addresses the efficacy of pomalidomide in the treatment of epistaxis in patients with Hereditary Hemorrhagic Telangiectasia (HHT) who have anemia and/or require blood transfusion or iron infusion for treatment of bleeding-induced anemia and iron deficiency. HHT (also known as Osler-Weber-Rendu disease) is an inherited bleeding disorder. Over 95% of patients develop recurrent epistaxis, which may be severe and result in chronic anemia, need for iron infusions and blood transfusions, substantial psychiatric comorbidity (including depression and post-traumatic stress disorder) and reduction in health-related quality of life (HRQoL). HHT is clinically diagnosed using the Curacao criteria, which consists of 1) spontaneous and recurrent epistaxis, 2) telangiectasias at characteristic sites, 3) visceral arteriovenous malformations (AVMs) or telangiectasias, and 4) a first degree relative with HHT (inheritance is usually autosomal dominant). Patients with three criteria are considered to have definite HHT, and those with 2 criteria probable HHT. HHT affects approximately 1 in 3,800 individuals. Significant manifestations of HHT often do not appear until the third or fourth decades, sometimes later.Participants: 144 patients from 11 clinical centers were enrolled.Design: This is a multi-center, double blind, randomized placebo-controlled trial that investigated the efficacy and safety of pomalidomide in patients with HHT and chronic epistaxis leading to iron-deficiency anemia or requiring intravenous iron infusions or blood transfusion.Screening evaluation included the Epistaxis Severity Score (ESS) with three-month recall, which reflected the patient's history of epistaxis and bleeding over the prior three months, as well as detailed review of iron infusion and red cell transfusion over the preceding six months. Eligible patients were provided a diary to record the duration of each epistaxis event that occurred during the 4 weeks prior to the baseline visit, and then returned for the baseline randomization visit, at which time patients underwent genetic testing, if this had not been previously performed, and completed an ESS with 4-week recall and quality of life assessments. Patients were randomized 2:1, stratified by study site, to either pomalidomide 4 mg/day or matching placebo during each of six 28 day cycles (24 weeks). Patients were seen every four weeks during treatment, and at a 4-week post-treatment follow-up visit to measure the ESS (with 4-week recall), laboratory assessments including iron stores and need for iron infusion, CBC, and metabolic profile. Patients were assessed for adverse events (AE) throughout the study. Treatment dosage could be reduced, or temporarily or permanently discontinued following AE-specific guidelines related to fatigue, cytopenias or other toxicities.Quality of life assessments were completed at baseline, and the 12- and 24-week visits, and the 4-week post-treatment follow-up visit using validated NIH instruments of 1) Neuro-QOL satisfaction with social roles and activities, 2) PROMIS emotional distress – depression, and 3) PROMIS fatigue, and the HHT-specific quality of life instrument developed specifically for this study. The effect of pomalidomide on duration of epistaxis was assessed via diary between weeks 8-12, 20-24 and the 4-week post-treatment period.Conclusions: Among patients with HHT, pomalidomide treatment resulted in a significant, clinically relevant reduction in epistaxis severity. No unexpected safety signals were identified (Al-Samkari et al., 2024; PMID: 39292928)

Study phs003948

EpiMatch_DNA_Methylation_Resource

Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 403 healthy individuals. Additional raw data (IDAT files) and associated phenotype information are available for all individuals included in this study (n=570) directly from CIBMTR. Data are available under controlled access release upon reasonable request and execution of a data use agreement. Requests should be submitted to CIBMTR at info-request@mcw.edu and include the study reference IB17-04

Dataset EGAD00010002283

Childhood Cancer Data Initiative (CCDI): Molecular Characterization Initiative

The National Cancer Institute's (NCI) Childhood Cancer Data Initiative (CCDI) focuses on the critical need to collect, analyze, and share data to address the burden of cancer in children, adolescents, and young adults (AYAs). The Molecular Characterization Initiative (MCI) will further the CCDI's goals by providing access to better diagnostic tests for pediatric and AYA patients. The molecular characterizations of solid tumors, soft tissue sarcomas, and rare diseases are performed in a CLIA-certified setting as results may be used to screen for and/or confirm clinical trial eligibility, direct treatment, or otherwise contribute to the conduct of the trial. The following molecular characterization assays were performed:Tumor/Normal Whole Exome sequencing Methylation arraysArcher fusion panel Deidentified clinical reportsNote: New data will be added periodically, please check the CCDI Hub Explore site for updates.

Study phs002790

Ensilication as a Cold‑Chain–Free Solution for High‑Fidelity DNA Preservation in tumor samples

Nucleic acid preservation requires continuous refrigeration at -20 °C to -80 °C, creating infrastructure barriers limiting genomic medicine access globally. While ambient-temperature preservation methods exist, their effects on DNA integrity and sequence fidelity remain incompletely characterized. The project aims to evaluate ensilication as a method for preserving DNA at ambient temperatures and to determine whether it can match or exceed the fidelity of conventional ultra‑low‑temperature storage. It seeks to assess the technology’s ability to maintain diagnostic accuracy, including detection of clinically actionable variants in tumor samples. Another goal is to compare sequencing‑related artifact rates between ensilicated and cryogenically stored DNA to quantify improvements in data quality. Ultimately, the project aims to establish ensilication as a cold‑chain‑independent solution that enables more accessible global genomic testing and biobanking.

Study EGAS50000001698

From matrimonial practices to genetic diversity in Southeast Asian populations: the signature of the matrilineal puzzle

This project aims at revisiting the "matrilineal puzzle" from a population genetics' point of view. The dataset consists of 719 individuals from 12 populations sampled in continental Southeast Asia and genotyped at 598764 loci. This dataset can only be accessed and used for non-commercial research purposes with a finality complying with the informed consent provided by donors. For accessing the data, please provide: 1. An explicit title for the project you wish to use the data for. 2. A detailed institutional affiliation of all recipients and users of the data. 3. A summary (500 words) of the research project, with emphasis on its scientific and societal finality, and predicted outputs. If access is granted by the DAC, data cannot be shared with a third party not initially involved in the project, without the third party officially applying for accessing the data.

Study EGAS00001003727

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

FEGA Sweden Helpdesk

FEGA Sweden is an archive for storing and sharing all kinds of data resulting from biomedical research projects. As a national node of the Federated European Genome-phenome Archive (FEGA), we enable researchers to store their data in Sweden in a way that meets the requirements of the General Data Protection Regulation (GDPR). Any data submitted to the archive is subject to controlled access, meaning access to the data only will be granted after a formal application procedure. Using FEGA Sweden for storing and sharing data is free of charge for academic users affiliated with a Swedish university. However, the university must have a signed Data Processing Agreement (DPA) with Uppsala University. The current list of universities with a signed DPA can be found here: https://fega.nbis.se/submission/complying-with-gdpr.html. FEGA Sweden is hosted by the National Bioinformatics Infrastructure Sweden (NBIS), which legally is part of Uppsala University. NBIS forms the bioinformatics platform at SciLifeLab and constitutes the Swedish node of the European organisation ELIXIR. Contact the FEGA Sweden Helpdesk at fega-sweden@nbis.se for further questions.

Dac EGAC50000000077

Lung Tissue Research Consortium (LTRC-BioLINCC)

Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions. Biospecimens: Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from LTRC include DNA, Plasma, Serum, Tissue - FFPE Cassettes, Tissue – RNALater Frozen, and Tissue - Snap Frozen. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: The LTRC was a biobank resource established by the NHLBI to collect and distribute lung tissue, blood samples, clinical data, and radiographic studies from participants with chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), other related idiopathic interstitial pneumonias (IIP) and interstitial pneumonias associated with connective tissue diseases who undergo medically-indicated lung resection. All tissue and blood specimens and clinical data were banked centrally and stored for distribution to external investigators who have approved study proposals to investigate the pathogenesis or management of lung diseases. The ultimate goal of this program was to enable research that illuminates the pathobiology of lung diseases and leads to novel interventional treatments for these conditions. Background: Chronic lung diseases are a main cause of death and disability in the United States. COPD affects over 14 million individuals in the United States and represents the third leading cause of mortality. Cigarette smoking is a major risk factor. However, only one of six individuals who smoke develops COPD. This could imply either an individual susceptibility or an additional immunologic or infectious injury to lung cells. Current treatments offer symptomatic relief, but do not prevent disease progression. Better understanding of disease pathogenesis, including the potential roles of lung parenchymal cell apoptosis, immunologic injury, and inflammation may lead to therapies that improve survival and quality of life. Interstitial pneumonias, including IPF and those associated with connective tissue disease, are less common than COPD, but for many of these diseases there are poor outcomes. For example, IPF has a 50% survival rate 2-3 years following diagnosis, and currently no treatment exists which prolongs survival. The prevalence of IPF is approximately 28 cases per 100,000. The underlying histology of IPF is usual interstitial pneumonia (UIP), which can also occur in connective tissue diseases. The incidences of other interstitial pneumonias such as non-specific interstitial pneumonia (NSIP) or acute interstitial pneumonia (AIP) are less frequent but also occur as an expression of interstitial lung disease in the connective tissue diseases. Moreover, there is significant crossover of these three interstitial pneumonias so that cases of IPF/UIP may also reveal fibrotic NSIP and be complicated by episodes of AIP. This implies common injuries but dissimilar histological responses. All of these processes are characterized by epithelial injury, uncontrolled fibroproliferation and the deposition of collagen, irrespective of the histology. It is clear that a better understanding of the genesis of the interstitial pneumonias is required before effective interventions can be developed. Participants: A total of 4,486 participants were enrolled, and lung tissue was obtained from 3,333 of these participants.Design: Written informed consent of each participant was required before any LTRC procedure was performed. Phenotypic data were then obtained that included recording of relevant medical information, a limited exposure history, radiological evaluation, and pulmonary physiological and lung function testing. Questionnaires were administered to determine the extent of symptoms, associated medical illnesses, smoking, environmental and occupational exposures, and quality of life. Laboratory testing included pulmonary function testing, a six-minute walk test, and chest x-ray CT. Blood specimens were collected both for defining the clinical phenotype of donors and to obtain serum, plasma, and DNA for later investigative purposes. At the time of surgery, lung tissues were collected and processed for long-term storage. The LTRC collected only the 'non-tumorous' portions of lung tissue from surgical procedures performed for primary or metastatic lung tumors and received those specimens only after the local pathologist had procured all tissue required for clinical care. Samples of appropriate size were cut and placed in formalin, RNAlater, glutaraldehyde, or liquid nitrogen within 30 minutes of excision (approximately 5% of cases exceeded this target time). Blood and tissue specimens were subsequently shipped to a central Tissue Repository for further processing and long-term storage. A Radiology Center provided quality control and quality assessment of CT data. A Data Coordinating Center managed study operations and maintained a repository of study data. Conclusions: LTRC established a biospecimen collection that is unique in its size, diseases included, standardization of methods, and extent of phenotypic data, serving as a valuable resource to facilitate research on the pathobiology of lung diseases.

Study phs003913

Sahel Data Access Committee

Genome-wide genotype array data of Fulani populations presented in Fortes-Lima et al. 2025. Citation: Population History and Admixture of the Fulani People from the Sahel. Cesar A. Fortes-Lima, Mame Y. Diallo, Václav Janoušek, Viktor Černý, and Carina M. Schlebusch. American Journal of Human Genetics 112(2), February 6, 2025. doi: https://doi.org/10.1016/j.ajhg.2024.12.015

Dac EGAC50000000290

GA4GH

Standards The EGA is a long-standing supporter of the Global Alliance for Genomics & Health (GA4GH) to enhance responsible sharing of human genetic data through the development of interoperable global standards for human data access. The EGA is one of the founding GA4GH Driver Projects and has contributed to the development and implementation of several GA4GH standards and APIs. Below is a list of the GA4GH standards and APIs that are currently available or planned for implementation at EGA. TechnicalStandards Purpose SpecificationVersion SupportedVersion Implementation Large Scale Genomics htsget A protocol for secure, efficient, and reliable access to sequencing read and variation data. V1.3.0 V1.0.0 Specification Documentation Endpoint Read File Formats (SAM/BAM/CRAM) Specifications for storing next-generation sequencing read data. V3.0.0 V3.0.0 Implementation Example of Usage Variation File Formats (VCF/BCF) The specifications for Variant Call Format Files (VCF) and its binary counterpart BCF. V4.0.0 V2.0.0 V4.0.0 V2.0.0 Implementation Example of Usage Crypt4GH v1.0 Enables direct byte-level compatible random access to encrypted genetic data stored in community standards (e.g. CRAM, VCF) V1.0 V1.0 Specification Documentation Endpoint refget API Enables access to reference sequences using an identifier derived from the sequence itself. V1.2.6 NA Specification RNAget API v1 Provides a means of retrieving data from several types of RNA experiments including (i) feature-level expression data from RNA-seq type measurements and (ii) coordinate-based signal/intensity data similar to a bigwig representation via a client/server model. V1.0.0 NA Documentation Discovery Beacon v2 Supports discovery of genomic variants, phenotypes, and individuals V1.0.1 V0.3 Web UI API Source Code Service Info API v1 The Service Info API is an endpoint for describing GA4GH service metadata, designed for extension and inclusion in other APIs. Service info is used to describe a single service, while Service Registry is used to describe multiple services. V1.0.0 NA Documentation Service Registry API v1 provides information about other GA4GH services, primarily for the purpose of organizing services into networks or groups and service discovery across organizational boundaries. V1.0.0 NA Documentation Data Use Researcher Identities Data Use Ontology (DUO) Allow users to semantically tag genomic datasets with usage restrictions, allowing them to become automatically discoverable based on a health, clinical, or biomedical researcher’s authorisation level or intended use. 2021-02-23 2021-02-23 Specification Documentation Endpoint Authentication & Authorization Infrastructure (AAI) The GA4GH AAI specification leverages OpenID Connect (OIDC) Servers for use in authenticating the identity of researchers desiring to access clinical and genomic resources from data holders adhering to GA4GH standards, and to enable data holders to obtain security-related attributes of those researchers. V1.2.0 V1.2.0 API URI: ega.ebi.ac.uk:8443 Documentation Repository Researcher IDs (passport, visa) Specify the collection of researchers that may access a dataset at any given time, and the credentials they must supply. V1.0.1 V1.0.1 Specification Documentation Endpoint Cloud Tool Registry Service API TRS is a standard API for exchanging tools and workflows to analyze, read, and manipulate genomic data. V2.0.1 NA Documentation Repostiory Data Repository Service API DRS API is a standard for building data repositories and adapting access tools to work with those repositories, works with other approved APIs from the GA4GH Cloud Work Stream to allow researchers to discover algorithms across different cloud environments and send them to datasets they wish to analyse. V1.0.3 NA Documentation Repostiory Workflow Execution Service API This API lets users run a single workflow (defined using CWL or WDL) on multiple different platforms, clouds, and environments, and be confident that it will work the same way. The API provides methods to request that a workflow be run, pass parameters to that workflow, get information about running workflows, and cancel a running workflow. V1.0.1 NA Documentation Repostiory Genomic Knowledge Standards Variation Representation v1 Provides a flexible framework of computational models, schemas, and algorithms to precisely and consistently exchange genetic variation data across communities. V1.3.0 EGA team is contributing to including it in in Beacon v2 Specification and Elixir Reference Implementation Documentation Repostiory Clin/ Pheno Data Capture Phenopackets Provides information models with different levels of complexity to enable high level clinical phenotype information as well as deep clinical phenotype information to be exchanged. V2.0.0 Included in Ongoing Submissions EGA team is contributing to including it in in Beacon v2 Specification and Elixir Reference Implementation Documentation Repostiory Driver Project The EGA, jointly coordinated by the EBI and the CRG, was announced, in 2017, to be one of the 15 Driver Projects for GA4GH. Driver Projects are international genomic data initiatives, focussed on real projects and challenges that will guide the development efforts in order to accelerate and enable completely responsible and standarised data sharing by 2022. All chosen Driver Projects make a cross-sectional effort by playing an important role across the different workstreams. Thomas Keane, Jordi Rambla, Mallory Freeberg, and Aina Jené have been named Driver Project Champions for the EGA. All Driver Project Champions will be leading this ambitious initiative for the following years.

Documentation about/projects-and-funders/ga4gh

SPECTA: NGS Screening Program for Efficient Clinical Trial Access

SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer.

Dataset EGAD00001000894

Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-Like Synoviocytes

We characterized the epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes (FLS) compared with osteoarthritis FLS. Multiple technologies were used, including ChIP-seq to assay H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3, ATAC-seq for chromatin accessibility, the transcriptome by RNA-seq and whole genomic bisulfite sequencing for DNA methylation. Integrative analysis was performed using a novel unbiased method to identify regions of the genome that have similar epigenetic marks. The regions that distinguished RA and osteoarthritis cells were primarily located in active enhancers and promoters. The regions and genes identified included immunological pathways. In addition, some unexpected pathways, most notably "Huntington's Disease Signaling", were discovered. The Huntington's Disease pathway was biologically validated for Huntingtin-interacting protein-1, which regulated invasive behavior of FLS. For a complete description, see R. Ai et al., Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes. Nat Commun 9, 1921 (2018). Sequencing data of study participants are available through dbGaP's Authorized Access portal, while analyses of the sequencing data may be obtained through NCBI's GEO portal under GSE112658.

Study phs001615

A Single-Cell and Spatial Atlas of Early Human Olfactory Development

The human nasal region is a complex anatomical structure comprising neural crest- and placode-derived lineages, yet its developmental dynamics in humans remain poorly understood due to limited access to fetal tissue and challenges in resolving its spatial and cellular complexity. We built a single-cell and spatial transcriptomic atlas of the human fetal nasal region from 10 fetuses spanning post-conceptional weeks 7 to 12. Using snRNA-seq, we identify 34 cell types in the fetal nasal region and reconstruct lineage trajectories in the olfactory epithelium (OE). Spatial analyses uncover regionalized OE organization, dorsoventral gradients of olfactory receptors (ORs) and high-resolution OR expression. Combining snRNAseq and MERFISH, we reveal early onset of OR gene expression, with most olfactory sensory neurons (OSNs) following the one neuron-one receptor rule already during the first trimester. This work provides the first integrated molecular and spatial framework of early human nasal region and it provides an unprecedented molecular blueprint of the human olfactory system development. In addition, this study offers a foundational resource for embryologists and developmental biologists investigating sensory neurogenesis, epithelial patterning, and congenital diseases.

Study EGAS50000001203

Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT-BioLINCC)

Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives The Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT) was designed to evaluate the hypothesis that amiodarone or a conservatively programmed shock-only, single-lead implantable cardioverter defibrillator (ICD) would decrease the risk of death from any cause in a broad population of patients with mild-to-moderate heart failure. Background Patients with congestive heart failure (CHF) can die suddenly and unpredictably from arrhythmia despite the use of proven medical therapies, such as beta-blockade. Two approaches have been developed to prevent sudden death among patients with CHF: therapy with amiodarone and therapy with an ICD. However, most of the mortality data on amiodarone and ICD therapy at the time of the study had been obtained in clinical trials performed after myocardial infarction in patients without CHF or those with ventricular arrhythmias. Thus, more data was needed to guide these therapies in patients who did not meet these criteria. Participants There were a total of 2521 participants. 847 were randomly assigned to placebo, 845 to amiodarone, and 829 to ICD therapy. Design Before randomization, participants underwent electrocardiography, a 6-minute walk test, 24-hour ambulatory electrocardiography, liver and thyroid function studies, and chest radiography. Participants were required, if clinically reasonable, to receive treatment with a beta-blocker and an angiotensin-converting-enzyme inhibitor, as well as an aldosterone antagonist, aspirin, and statins, when appropriate. Participants were randomly assigned in equal proportions to receive placebo, amiodarone, or a single-chamber ICD programmed to shock-only mode. Participants assigned to amiodarone or matching placebo began therapy as outpatients immediately after randomization. Placebo and amiodarone were administered as a loading dose of 800 mg/day for one week, 400 mg/day for three weeks, and then as a daily maintenance dosage according to weight and bradycardia status. Participants assigned to ICD therapy received their device a median of three days after randomization. The goal of ICD therapy was to treat only rapid, sustained ventricular tachycardia or ventricular fibrillation. Dual-chamber or biventricular devices, or antitachycardia or rate-response pacing therapies were not permitted. The ICD was uniformly programmed to have a detection rate of 187 beats per minute or more. Antibradycardia pacing was initiated only if the intrinsic rate decreased to less than 34 beats per minute. Median follow-up was 45.5 months. The primary end point was death from any cause. Secondary outcome measures included cardiac mortality, arrhythmic mortality, morbidity, quality of life, and incremental cost-effectiveness of the interventions. Each active treatment arm was compared to the placebo drug arm. Conclusions In participants with NYHA class II or III CHF and LVEF of 35% or less, amiodarone had no favorable effect on survival, whereas single-lead, shock-only ICD therapy reduced overall mortality by 23%.

Study phs003654

14382 results for ""Pennsylvania+German"+ACS+study+'Socius'+open+access"

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