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• NIDDK IBD Genetics Consortium Ulcerative Colitis Genome-Wide Association Study

  This dataset contains data for 1,028 white, non-Hispanic, European ancestry individuals with ulcerative colitis who were included in a genome-wide association study published by Silverberg et al. (2009). These individuals were ascertained in North America and selected to have either left-sided or extensive disease (i.e., individuals with proctitis only were excluded). Genotyping was performed using the Illumina HumanHap300v2 (n = 540) and HumanHap550v3 (n = 488) Genotyping BeadChips at the Feinstein Institute for Medical Research. Control data (not included) were obtained from the NIDDK IBD Genetics Consortium's Crohn's Disease GWAS (available from dbGaP) and from studies 64 and 65 deposited in the Illumina iControlDB. Seven hundred eighty individuals in this dataset were taken from the NIDDK IBD Genetics Consortium cell line repository (http://www.niddkrepository.org). These individuals are identified in the file dbGaP_SubjectDS.txt. The subject IDs for these individuals may be used to request corresponding samples for follow-up research through the repository. In addition, complete phenotype data for these individuals are included, collected using the Consortium's forms and phenotyping manual (both included). The remaining 248 individuals were identified from pre-existing collections ascertained by members of the Consortium or their collaborators. For these samples, several of the items in the phenotype file are incomplete. Those who wish to replicate the results in Silverberg et al. should note that 6 individuals with missing genotype rates > 0.07 were excluded from that analysis (leaving 1,022 affected samples total). In addition, the minor allele frequencies (MAFs) reported in the publication were calculated using only those individuals who were included in the allelic association tests (n = 977 for SNPs included in the HumanHap300 and n = 476 for SNPs included only in the HumanHap550). These tests were performed using conditional logistic regression on gender-ancestry strata; individuals who were not placed in a stratum (using the procedure described in the supplementary information for Silverberg et al.) were excluded. The indicator variables hh300 and hh550 in the file dbGaP_PhenotypeDS.txt identify the samples included in the allelic association tests, and may be used to replicate the published MAFs among affected individuals.

  Study phs000345

• Long-read single-cell RNA sequencing uncovers cell-type specific transcript regulation in COVID-19

  SARS-CoV-2 infection leads to extensive host transcriptomic changes, but the role of alternative splicing in shaping the immune response remains underexplored. Here, we present the first application of long-read single-cell RNA sequencing on nasopharyngeal swabs from COVID-19 patients and healthy controls to resolve transcript-level changes across cell types. Leveraging the strengths of long-read sequencing, we characterize alterations in both gene and isoform expression within cell populations of the upper respiratory tract—the primary site of SARS-CoV-2 entry. This approach provides new insights into how transcriptional regulation and splicing shape host immune responses to viral infection.

  Study EGAS50000001290

• The_Causes_of_Clonal_Blood_Cell_Disorders_Study___SCOR

  We will take a bone marrow aspirate and peripheral blood samples from a healthy patient aged around 60, and use flow cytometry to isolate 100 HSCs, 50 MEPs, and 50 GMPs. We will grow these up into colonies, then whole genome sequence each colony. Somatic mutations will act as a unique barcode for each clone. We will then design a panel for targeted resequencing of the mutations that we find. It will then be possible to look for these mutations in the peripheral blood over several years, to see the dynamics of how HSCs contribute to the peripheral blood in health.

  Study EGAS00001002132

• The genomic and radiomic complexity of multifocal prostate cancer

  Multiparametric magnetic resonance imaging (mpMRI) and molecular prognostic tests are emerging to guide screening and prostate cancer (PCa) diagnosis, however their efficacy and cross validation requires further assessment in the context of intraprostatic heterogeneity and patient prognosis. To evaluate the molecular features that make prostate tumors visible to mpMRI, we established an mpMRI-blind multicore collection and performed low pass whole genome, exome, transcriptome and methylation profiling of 14 lesions and 23 representative cores from 6 PCa patients. Our results show that diagnosis based on mpMRI does not capture the genomic complexity of tumors, and reveal that commercial prognostic signature results based on single-biopsy assessments are insufficient to define risk of progression. Altogether, our study supports the use of a multi-biopsy assessment in both mpMRI visible and non-visible areas in order to provide a truly personalised diagnosis

  Study EGAS00001002767

• NHLBI TOPMed - NHGRI CCDG: Atherosclerosis Risk in Communities (ARIC)

  Participants from the Atherosclerosis Risk in Communities (ARIC) Study, a large population-based longitudinal cohort study, have been included in this Project and whole genome sequencing will be performed to contribute to analyses of early-onset atrial fibrillation and venous thromboembolism. Additional phenotype and genotype data are available for these individuals on dbGaP and can be accessed through the parent ARIC Cohort accession (phs000280). The National Heart, Lung and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) program is designed to generate scientific resources to enhance understanding of fundamental biological processes that underlie heart, lung, blood and sleep disorders (HLBS). It is part of a broader Precision Medicine Initiative, which aims to provide disease treatments that are tailored to an individual's unique genes and environment. TOPMed will contribute to this initiative through the integration of whole genome sequencing (WGS) and other -omics (e.g., metabolic profiles, protein and RNA expression patterns) data with molecular, behavioral, imaging, environmental, and clinical data. In doing so, this program seeks to uncover factors that increase or decrease the risk of disease, identify subtypes of disease, and develop more targeted and personalized treatments. The Whole Genome Sequencing (WGS) Project is part of NHLBI's TOPMed program and serves as an initial step for the larger initiative.

  Study phs001211

• Determinants of Asthma Following RSV Bronchiolitis in Early Life

  The goal of the RSV Bronchiolitis in Early Life (RBEL) study is to determine how specific genetic, biologic, and immunologic characteristics interact to predispose individuals to develop asthma. Participants were carefully recruited by selecting a prospective cohort of 206 infants with severe respiratory syncytial virus (RSV) bronchiolitis who were at substantial risk of developing asthma.

  Study phs001009

• The European MAPPYACTS trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

  MAPPYACTS (NCT02613962) is an international prospective precision medicine trial aiming to define tumor molecular profiles in pediatric patients with recurrent/refractory malignancies, in order to suggest the most adapted salvage treatment. From February 2016 to July 2020, 787 patients were included in France, Italy, Ireland and Spain. At least one genetic alteration leading to targeted treatment suggestion was identified in 436 patients (69%) with successful sequencing; 10% of these were considered "ready for routine use". Of 356 patients with follow-up beyond 12 months, 107 (30%) received one or more matched targeted therapies, 56% of them within early clinical trials, mainly in the AcSé-ESMART platform trial (NCT02813135). Overall, matched treatment resulted in a 17% objective response rate, those of patients with "ready for routine use" alterations was 38%. In patients with extra-cerebral tumors, 76% of actionable alterations detected in tumor tissue were also identified in circulating cell free DNA (cfDNA).

  Study EGAS00001005935

• NHLBI TOPMed: Childhood Asthma Management Program (CAMP)

  The Childhood Asthma Management Program (CAMP) was designed to evaluate whether continuous, long-term treatment (over a period of four to six years) with either an inhaled corticosteroid (budesonide) or an inhaled noncorticosteroid drug (nedocromil) safely produces an improvement in lung growth as compared with treatment for symptoms only (with albuterol and, if necessary, prednisone, administered as needed). The primary outcome in the study was lung growth, as assessed by the change in forced expiratory volume in one second (FEV1, expressed as a percentage of the predicted value) after the administration of a bronchodilator. Secondary outcomes included the degree of airway responsiveness, morbidity, physical growth, and psychological development.

  Study phs001726

• The EGA Helpdesk team: 2025 in review and what we are building next

  Behind every dataset submitted, every access request processed, and every technical question answered, there is a team working quietly to keep things moving: the Helpdesk (HD). With the onset of 2026, this feels like the right moment to look back on what 2025 has been like for the HD team: the challenges we faced, how we adapted, and where we're heading next. Why the Helpdesk matters to EGA The EGA Helpdesk is more than a support channel. It plays a key role in maintaining trust in the EGA ecosystem. By supporting data submitters, researchers, Data Access Committees (DACs), and institutional partners, the HD helps ensure that data can flow securely, efficiently, and reliably. When issues arise, the Helpdesk is often the first place where their impact is felt and addressed. In that sense, the HD sits at the intersection of technology, policy, and people. One Helpdesk, two locations, one shared mission The EGA Helpdesk is a joint, distributed team working closely across two locations: CRG (Barcelona, Spain) and EMBL-EBI (Cambridge, UK). Although we are based in different institutions, we operate as a single Helpdesk, with shared workflows, priorities, and responsibility towards users. At CRG, the HD team is formed by: Andrea Max Àlex and me At EMBL-EBI, we work closely with: Silvia Coline Aravind What defines us as a team is simple: we work user-first, even under pressure. In a highly technical environment, clarity, empathy, and consistency matter just as much as tools and processes. A close collaboration across sites is essential to making that happen. What does the EGA Helpdesk do? The HD supports users across the full lifecycle of data in EGA. This includes: Data submissions, uploads, and encryption workflows. Data access requests and permissions. Questions around policies, consent, and data usage. Technical and system-related issues. Coordination between users, internal teams, and external partners. 2025: growth, change, and recalibration 2025 was a year of growth, but not always a predictable one. Early in the year, several technical and system-related challenges required us to adjust our original plans. Priorities shifted, timelines changed, and some improvements had to be rethought. For the HD team, this is often the hardest part of the job: we see delays through the eyes of users and understand the real impact they can have on ongoing research. One of the key lessons from 2025 was that stability is not only a technical challenge, but also an organisational one. Teamwork proved to be essential: anticipating peak periods, sharing context early, and coordinating closely across teams made a tangible difference. When things became complex, working together across roles and locations was what allowed us to keep moving forward. In 2025, the Helpdesk received 5.313 tickets and resolved 5.511 requests, reflecting both increased adoption of EGA and the team’s ability to absorb higher demand. At the same time, demand continued to grow. Compared to 2024, ticket creation increased by over 6%, while resolution capacity grew by more than 11%. The team not only kept up with incoming requests but also resolved part of the accumulated backlog, finishing the year having solved more tickets than were created. The real challenge of 2025 was not overall performance, but how the workload was concentrated during peak months. Seasonality and demand spikes placed pressure on the system, even while overall efficiency remained strong. On a team level, 2025 was also a year of transition. I joined the HD leadership role in January 2025, stepping into a period of change and rapid learning. Later in the year, in October, we said goodbye to Raül, and in January 2026, we welcomed Àlex, strengthening the team for the next phase. What users needed most in 2025 While requests vary widely, some themes stood out throughout the year: Support with data submissions and uploads Data access requests and permissions Technical and system-related issues As EGA matures, day-to-day operations have become more complex. Many long-running tickets are not delayed due to a lack of follow-up, but because they depend on external approvals, cross-institutional coordination, or multi-step processes. Understanding these patterns helps us focus not just on resolving tickets, but on improving how work flows through the system. Looking ahead to 2026 With a reinforced team and clearer insights from 2025, our focus for 2026 shifts from throughput to flow. Key priorities include: Strengthening our web content and documentation Reducing structural backlog Improving cross-team and cross-system coordination Anticipating peak demand earlier and planning capacity accordingly Challenges will continue to arise in 2026, as they always do. However, 2025 reinforced something important: a stable, empathetic, and well-aligned Helpdesk team is essential to supporting EGA's mission at scale. Supporting users well means supporting research, and that remains at the core of what we do.

  Blog ega-helpdesk-team-2025-in-review-and-upcoming-improvements

• Rituximab-treated lymphoma patients show correlated deficiency in serological and T cell Spike-specific response after SARS-CoV-2 vaccination: insights from the CORSA Study.

  This study is part of the CORSA trial (NCT04345315), a prospective multicentric research project conducted by the Istituto Romagnolo per lo Studio dei Tumori “Dino Amadori” to investigate the immunologic response to mRNA SARS-CoV-2 vaccines in patients with hematologic malignancies (HM) and healthy individuals as controls (HC). The data in this repository refer to two subcohorts: 7 healthy controls and 10 lymphoma patients, randomly selected. Whole blood samples were collected to characterize T cell receptor (TCR) repertoire specificity against SARS-CoV-2 proteins before and after two BNT162b2 vaccination cycles, at baseline (before vaccination), 50 days after the first dose (V1), and 6 months after the first dose (V3). All participants were vaccinated under the Italian national campaign and provided informed consent following the Declaration of Helsinki. We investigated SARS-CoV-2-specific T cell responses through TCR repertoire profiling and examined correlations between serological and cellular responses in both patient and control groups. Using Next-Generation Sequencing (NGS) to characterize the CDR3 sequences of TCR β-chains from peripheral blood, we assessed clonal expansion (depth) and diversification (breadth) of SARS-CoV-2-specific T cell clonotypes over time, aiming to understand how cancer and its treatment influence vaccine-induced immunity in immunocompromised individuals.

  Study EGAS50000001205