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• Bulk Iso-Seq from brain tissue and exosomes isolated from brain tissue using long-read PacBio sequencing of poly-adenylated transcripts

  Human brain sEVs were isolated from postmortem human brain tissue. RNA was extracted from both the source brain tissue and sEVs and prepared for long-read sequencing. cDNA was sequenced on the PacBio Sequel II. The data provided have undergone processing using the tool ccs (v6.0.0) to generate circula consensus reads. For further processing, it is recommended to follow the guidelines at https://isoseq.how/, starting with using lima to remove cDNA primers.

  Dataset EGAD50000000043

• Association of Age at Diagnosis and Genetic Mutations in Patients with Neuroblastoma

  Neuroblastoma is diagnosed over a wide age range from birth through young adulthood, and older age at diagnosis is associated with a decline in survivability. We performed whole genome sequencing of DNA from diagnostic tumors and their matched germlines from 40 patients with metastatic neuroblastoma obtained between 1987 and 2009. To identify genetic lesions that are associated with age at diagnosis in patients with metastatic neuroblastoma. Age groups at diagnosis included infants (0-18 months), children (18 months-12 years), and adolescents and young adults (>12 years). To confirm the findings from this discovery cohort, validation testing using tumors from an additional 64 patients obtained between 1985 and 2009 was also performed. Formalin-fixed paraffin-embedded tumor tissue was used for immunohistochemistry and fluorescent in situ hybridization. Telomere lengths were analyzed using the whole genome sequencing data, quantitative polymerase chain reaction and fluorescent in situ hybridization

  Study EGAS00001000213

• Acute Respiratory Distress Network (ARDSNet) Studies 06 and 08 Prospective, Randomized, Multicenter Trial of Aerosolized Albuterol Versus Placebo for the Treatment of Acute Lung Injury (ALTA) (ARDSNet-ALTA-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 ARDSNet-ALTA include Plasma, DNA, Urine, and BAL. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives This clinical trial was designed to test the hypothesis that an aerosolized beta-2-agonist, albuterol, would improve clinical outcomes in participants with acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). Background In participants with acute lung injury and acute respiratory distress syndrome (ALI/ARDS), inflammation of the pulmonary circulation increases vascular permeability. Fluid leaks from blood vessels into the pulmonary interstitium and alveoli. Recovery from this form of acute respiratory failure requires that the pulmonary edema resolve. The resolution of alveolar edema is driven by active transport of sodium and chloride ions from the luminal space across both type I and type II alveolar epithelial cells, creating an osmotic gradient for the reabsorption of water. In the ex vivo human lung, the rate of alveolar fluid clearance can be doubled by treatment with a cyclic AMP beta-2 adrenergic receptor agonist. On the basis of the preclinical observations that treatment with beta-2-agonists could reduce pulmonary edema and accelerate the rate of alveolar fluid clearance, the ALTA study was designed and undertaken with the hypothesis that treatment of participants with ALI/ARDS with beta-agonist therapy would accelerate the resolution of alveolar edema and improve clinical outcomes. Participants There were 282 participants. Design Study staff conducted a multicenter, randomized, placebo-controlled clinical trial in which participants were randomized to receive aerosolized albuterol (5 mg) or saline placebo every 4 hours for up to 10 days. The primary outcome variable for the trial was ventilator-free days. Conclusions Ventilator-free days were not significantly different between the albuterol and placebo groups. The results suggest that aerosolized albuterol does not improve clinical outcomes in participants with ALI. Routine use of beta-2 agonist therapy in mechanically ventilated participants with ALI cannot be recommended (Matthay, et al., 2011, PMID: 21562125).

  Study phs003743

• Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer

  Chromosomal instability is a major challenge to patient stratification and targeted drug development for high-grade serous ovarian carcinoma (HGSOC). Here we show that somatic copy number alterations (SCNAs) in frequently amplified HGSOC cancer genes significantly correlate with gene expression and methylation status. We identified five prevalent clonal driver SCNAs (chromosomal amplifications encompassing MYC, PIK3CA, CCNE1, KRAS and TERT) from multi-regional HGSOC data and reasoned that their strong selection should prioritise them as key biomarkers for targeted therapies. We used primary HGSOC spheroid models to test interactions between in vitro targeted therapy and SCNAs. MYC chromosomal copy number was associated with in-vitro and clinical response to paclitaxel and in-vitro response to mTORC1/2 inhibition. Activation of the mTOR survival pathway in the context of MYC-amplified HGSOC was statistically associated with increased prevalence of SCNAs in genes from the PI3K pathway. Co-occurrence of amplifications in MYC and genes from the PI3K pathway was independently observed in squamous lung cancer and triple negative breast cancer. These results suggest that identifying co-occurrence of clonal driver SCNA genes could be used to tailor therapeutics for precision medicine.

  Study EGAS00001006200

• Chip_seq_oesophageal_adenocarcinoma_

  There is complex interplay between underlying genetic sequence and epigenetic factors, however this interplay is still illusive. Massively reconstructed cancer genomes can be used in order to better understand this relationship. Six oesophageal adenocarcinoma organoids will be sequenced using long read sequencing technologies and will be profiled for a range of epigenetic marks. Combination of genetic and epigenetic data will allow the thorough characterisation of reference cancer genomes and will provide novel insights into mechanisms of gene regulation. Description: Chip-seq Sequencing of 5 patient derived organoid cell models. Each model was derived from a piece of patient tumour taken following surgical rescetion of the tumour. All model derivations took place with the CGaP facility in Sanger.

  Study EGAS00001007180

• National Cancer Institute (NCI) Genome-Wide Association Study (GWAS) of Renal Cell Carcinoma in African Americans

  The NCI GWAS of renal cell carcinoma (RCC) in African Americans was undertaken to provide insight into genetic loci affecting susceptibility to this malignancy in a racial group known to be at elevated risk. We genotyped 1,136,723 single-nucleotide polymorphisms (SNPs) among 255 cases and 375 controls of African ancestry from the NCI Kidney Cancer Study, and further investigated 16 SNPs in a replication set consisting of 140 cases and 543 controls from a case-control study conducted at the University of Texas MD Anderson Cancer Center. The variant rs10771279 located on 12p11, 77kb from a European-ancestry RCC risk marker, was associated with RCC risk in the GWAS (P=1.2 x 10-7) but did not replicate (P=0.99). The variant 7105934 on 11q13.3, previously associated with RCC in a GWAS using European-ancestry samples, was associated with risk in both studies [meta-analysis odds ratio (OR)=0.76, 95% confidence interval (CI)=0.64-0.91; P=0.0022]. The frequency of this allele was higher than that observed in the European-ancestry GWAS (0.56 and 0.07 respectively among controls). The rs7105934 association was stronger for clear cell RCC (ccRCC: OR=0.56; P=7.4 x 10-7) and absent for cases of other or unknown histology (OR=1.02; P=0.86). In conclusion, this study provides evidence that rs7105934 is a susceptibility locus for RCC, and clear-cell RCC in particular, among African Americans.

  Study phs000863

• 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

• Whole Exome Sequencing for Familial Intracranial Aneurysm (FIA I-II) Study

  The goal of this study is to identify the genes underlying the risk of intracranial aneurysm (IA). The FIA Study initially recruited families appropriate for linkage analysis. Therefore, the recruitment focus was not only on probands with a family history of IA but also required that biological samples be obtained for at least two affected family members. Family members underwent detailed interviews for medical, social and family history, and provided blood samples for DNA extraction. Over 400 multiplex IA families were recruited and enrolled. The whole exome sequencing project aims to identify novel and rare (in the general population) genetic variants that are enriched in seven extended multiplex families with a strong familial aggregation of intracranial aneurysms.

  Study phs000636

• Whole exome and transcriptome analysis of UV-exposed epidermis and carcinoma in situ reveals early drivers of carcinogenesis

  Squamous cell carcinoma in situ (SCCIS) is a prevalent precancerous lesion that can progress to cutaneous squamous cell carcinoma (cSCC). Although SCCIS is common, its pathogenesis remains poorly understood. To better understand SCCIS development, we performed laser-captured microdissection of human SCCIS and adjacent epidermis to isolate genomic DNA and RNA for next generation sequencing. Whole exome sequencing (WES) identified UV-signature mutations in multiple genes including Notch 1-3 (GeneID:4851, GeneID:4853, GeneID:4854) in the epidermis and SCCIS and oncogenic TP53 (GeneID:7157) mutations in SCCIS. Novel gene families, including SCHLAFEN genes, contained UV/oxidative-signature disruptive (UVD) epidermal mutations that manifested positive selection in SCCIS. The frequency and distribution of NOTCH and TP53 mutations indicate that NOTCH mutations may precede TP53 mutations. RNA sequencing identified 1166 differentially expressed genes; the top 5 enriched GO biological processes included: 1) immune response, 2) epidermal development, 3) protein phosphorylation, 4) regulation of catalytic activity, and 5) cytoskeletal regulation. The NEURL1 ubiquitin ligase, which targets Notch ligands for degradation, was upregulated in SCCIS. Neuralized 1 protein was found to be elevated in SCCIS suggesting that increased levels could represent a novel mechanism for downregulating Notch during UV-induced carcinogenesis. The data from DNA and RNA sequencing of epidermis and SCCIS provide insights regarding SCCIS formation.

  Study phs002019

• The clinicopathologic spectrum and genomic landscape of de-/trans-differentiated melanoma

  De- and trans-differentiation is a rare and only poorly understood phenomenon in cutaneous melanoma. To study this disease more comprehensively we have retrieved 11 primary cutaneous melanomas from our pathology archives showing biphasic features characterized by a conventional melanoma and additional areas of de-/trans-differentiation as defined by a lack of immunohistochemical expression of all conventional melanocytic markers (S-100 protein, SOX10, Melan-A and HMB-45). The clinical, histologic and immunohistochemical findings were recorded and follow-up was obtained. The patients were mostly elderly (median: 81 years; range: 42-86 years) without significant gender predilection, and the sun-exposed skin of the head and neck area was most commonly affected. The tumors were deeply invasive with a mean tumor thickness of 7 mm (range: 4-80 mm). The dedifferentiated component showed atypical fibroxanthoma-like features in the majority (7), while additional rhabdomyosarcomatous and epithelial transdifferentiation was noted histologically and/or immunohistochemically in two tumors each. The background conventional melanoma component was of desmoplastic (4), superficial spreading (3), nodular (2), lentigo maligna (1) or spindle cell (1) types. For the 7 patients with available follow-up data (median follow-up period of 25 months; range: 8-36 months), 2 died from their disease and 3 developed metastases. Next-generation sequencing of the cohort revealed somatic mutation of established melanoma drivers including mainly NF1 mutations in the conventional component (5 cases), which were also detected in the corresponding de-/trans-differentiated components. In summary, the diagnosis of de-/trans-differentiated melanoma is challenging and depends on the morphologic identification of the conventional melanoma component. Molecular analysis is diagnostically helpful as the mutated gene profile is shared between the conventional and de-/trans-differentiated components. Importantly, de-/trans-differentiation does not appear to confer a more aggressive behavior.

  Dataset EGAD00001007033