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• CLUSTER consortium RNAseq CD19 B cell dataset of UK JIA patients.

  This study examines B cell transcriptomic profiles in Juvenile Idiopathic Arthritis (JIA) patients to investigate molecular mechanisms underlying disease heterogeneity. CD19+ B cells were isolated from peripheral blood samples and subjected to RNA sequencing to characterise gene expression patterns. The dataset includes patients with documented uveitis status to enable investigation of B cell contributions to the common JIA comorbidity.

  Study EGAS50000001123

• Genomic Characteristics of Myeloproliferative Neoplasms in Patients Exposed to Ionizing Radiation following the Chernobyl Nuclear Accident

  The study "Genomic Characteristics of Myeloproliferative Neoplasms in Patients Exposed to Ionizing Radiation following the Chernobyl Nuclear Accident" was designed as case-control study. We studied genomic characteristics of chronic Philadelphia chromosome-negative myeloproliferative neoplasm (MPNs) in Ukrainian patients who were previously exposed to Ionizing Radiation (IR) due to Chernobyl accident in comparison to unexposed MPN patients and controls (previously exposed to IR due to Chernobyl accident and unexposed people who were not diagnosed with any oncological condition at the moment of DNA sampling).

  Study phs001761

• Genomic and Transcriptomic Markers Associated with Response to Immune Checkpoint Blockade

  The neoantigen presentation score (NEOPS) study was designed to better understand molecular determinants of response to immunotherapies, including pembrolizumab and nivolumab in stage III or IV melanoma patients. From this work, we developed a composite approach to predicting neoantigens (NEOPS), which takes into account additional escape mechanisms, including HLA LOH (human leukocyte antigen loss of heterozygosity) and the impact of deleterious mutations to the antigen presentation machinery (APM), yielding an improved prediction of response to immunotherapy compared to TMB (tumor mutational burden) or neoantigen burden alone.

  Study phs002388

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): NIH Digital Health Solutions for COVID-19: SAFER-COVID - Integration of Testing and Digital Health

  SAFER-COVID provides a set of self-management tools to consumers to track symptoms, test results, vaccine record, and environmental factors, such as exposure to others. Consumers may choose to integrate data from wearables and electronic health records (EHR) for self management. These data are used to enable multiple use cases such as return-to-work, activity risk assessment and self-management within SAFER-COVID.DOI: https://rapids.ll.mit.edu/10.57895/cmt5-gh78

  Study phs002540

• INCLUDE: Human Trisome Project

  The INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project is an NIH-wide collaboration that seeks to improve health and quality-of-life for people with Down syndrome. The INCLUDE Project Data Coordinating Center and partners created the INCLUDE Data Hub, a centralized data resource that allows access to large-scale clinical and multi-omics datasets specific to Down syndrome and supports collaborative, cloud-based analysis to accelerate scientific discoveries related to Down syndrome and its co-occurring conditions.

  Study phs002981

• PEACE melanoma 14

  Understanding the evolutionary pathways to metastasis and resistance to immune checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here we present the most comprehensive intra-patient metastatic melanoma dataset assembled to date as part of the PEACE research autopsy programme, including exome, panel-sequenced, RNA-seq, and single-cell whole-genome sequencing samples from 14 ICI-treated patients. The main goals of the project are to decipher the evolutionary dynamics of melanoma metastases and to elucidate mechnisms of resistance to therapies.

  Study EGAS00001007081

• Oral mucosa organoids as a potential model for personalized therapies

  Organoids were established from both tumor and matched wildtype tissue from patients diagnosed with head and neck squamous cell carcinoma (HNSCC). In order to confirm tumor status and identify oncogenic driver mutations, DNA derived of these organoids was sequenced. After validation of tumor identity, organoids were exposed to a range of (targeted) chemotherapeutics and radiotherapy. Differential responses to therapeutics were subsequently correlated to underlying genetic alterations to see if DNA mutation status could be predictive for responses to therapy.

  Study EGAS00001003628

• All you need to know about the new Submitter Portal

  In September we launched new services for all EGA users, including a new version of the former Submitter Portal. Our main objective with this Portal is to transform the metadata submission in a simplified and user-friendly method. Although it is possible to find documentation about the Submitter Portal on our website, we wanted to highlight the new features in this article. Enjoy! Credentials: who needs to create a new user to access the Submitter Portal and who doesn't? Users with an old submission account (ega-box) can already access the new Submitter Portal. If it is the first time that you want to access, it is time to request a submitter role linked to the EGA User. In the form, it is mandatory to explain which type of data you want to deposit, the size of your submission, add any comment you’d like us to read, and manage the EGA Data Processing Agreement (DPA) document. This document should be checked by the legal department of your institution and signed by a person with authority to sign contracts on behalf of the institution. Note that we provide a DPA template for new Users; it can be found and downloaded in the Submitter Request section. With the DPA signed and the Submitter Request sent, it is time to wait for our Helpdesk team to validate the request. Metadata submission now can be collaborative It is possible to add collaborator(s) to your submissions. Only registered EGA Users will appear on the search bar. When adding a collaborator, it is mandatory to define the permission granted: Read only: collaborators with this permission can check if the information of the submission is correct but cannot modify anything. Read & write: collaborators with this label can register new objects and modify the registered ones. We wanted to save time for submitters that usually rely on the same collaborators. For that, we have implemented the possibility of adding the same collaborators from previous submissions; all you need to do is to search the submission, and the exact set of EGA users will have access to your submission. You can check the collaborators and their permissions at any point of the submission by going to the collaborators section. Even adding more people to complete the submission is allowed by following the same steps: looking for the EGA User and defining the permission granted (please, note that during the submission it is not possible to add collaborators from previous submissions). Use external links to complement the study information When filling the information about the study we recommend users to enrich the submission with complementary fields such as PubMeds IDs, custom tags and external links. External links are used to connect a study to an external repository. We have implemented an external link to Euro-Bioimaging for a European Project (EuCanImage). Now, we are looking forward to keeping increasing the list of external repositories! Choose the expected release date for your metadata to be searchable on our website Once all the metadata objects are registered it is time to finalise the submission so that the Helpdesk team can approve it. In the new version of the Submitter Portal users can choose the expected release date for the metadata to be searchable on the EGA website. Please, note that the selected date will have a minimum of one week margin from the day of finalisation. This time is necessary for your files to be archived and for the submission to be validated by the Helpdesk Team. Are you looking for the Array submission within the Submitter Portal? Our Submitter Portal does not support array submissions. The submission of Array-based metadata must be done using the EGA programmatic submission. You will find our Array-based format template and all the necessary information on our website, and you can find all the steps in our submission quickguide! More information about the submission process at the EGA Our Team has developed an extended documentation related to metadata submission. A good first step is to take a closer look at the Submission FAQ. To have a general overview of all the metadata submission process we recommend taking a glimpse of our take-the-tour or watching the tutorial available on our YouTube Channel. Don't miss our section on EGA Schemas, to learn more about how the EGA is built. It can be useful to fully ensure that your submissions comply with the EGA's standards and contribute to a valuable and accessible genomic resource.

  Blog new-submitter-portal

• Characterization of patient-derived xenograft models of myxoid liposarcoma either sentitive or resistant to trabectedin

  Two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. The aim of the study was to study the resistance to the drug.

  Study EGAS00001003715

• Phenotypic_characterisation_of_LRRN4CL_over_expression

  This study aims to use RNAseq to identify differentially expressed transcripts in human melanoma cells that over-express the cell surface protein, LRRN4CL, relative to empty-vector control cells, to provide mechanistic insight into how LRRN4CL over-expression confers enhanced pulmonary metastatic colonisation abilities.

  Study EGAS00001003976