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• Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma -- CA209-025

  Immune checkpoint inhibitors targeting the PD-1 pathway have transformed the management of many advanced malignancies, including clear cell renal cell carcinoma (ccRCC), but the drivers and resistors of PD-1 response remain incompletely elucidated. Here, we analyzed 592 tumors collected from advanced ccRCC patients enrolled in prospective clinical trials of treatment with PD-1 blockade (or mTOR inhibition as control arm) by whole-exome and RNA-sequencing, integrated with immunofluorescence analysis, to define the somatic alteration landscape of late-stage ccRCC and to uncover the immunogenomic determinants of therapeutic response. While conventional genomic markers (tumor mutation burden, neoantigen load) and degree of CD8+ T cell infiltration were not associated with clinical response, we discovered numerous chromosomal alterations in advanced ccRCC associated with response or resistance to PD-1 blockade. These advanced tumors were highly CD8+ T cell infiltrated, with only 22% and 5% with an immune desert and immune excluded phenotype, respectively. Our analysis revealed that CD8+ infiltrated tumors are depleted of favorable PBRM1 mutations and are enriched for unfavorable chromosomal losses of 9p21.3 when compared to non-infiltrated tumors. These data demonstrate how the interplay of somatic alterations and immunophenotypes impacts therapeutic efficacy.

  Dataset EGAD00001006029

• Duplexseq of the interstrand crosslinks_WGS

  One of the most dangerous forms of DNA damage are interstrand crosslinks (ICLs), which covalently crosslink the two strands of the DNA double helix. The repair of these lesions is crucial for cellular survival due to their ability to block transcription and DNA replication. Initially, the major pathway that has been described in ICL repair involves a network of 22 genes that are mutated in a severe human genetic disease known as Fanconi Anemia (FA). Using synthetic lethality screens in the near-haploid human HAP1 cell line, we recently identified two potentially novel regulators of ICL repair, C1orf112 and THAP12. Loss of C1orf112 and THAP12 causes hypersensitivity to ICL-inducing DNA damaging agents, such as Mitomycin C (MMC). Additionally, C1orf112-depleted cells show elevated levels of micronuclei and accumulation of DNA damage in S-phase. To better understand how C1orf112 and THAP12 mediate the repair of ICLs, we want to perform mutational signature analysis, using the BotSeq method. Therefore, WT, C1orf112 and THAP12 knockout cells were cultured in vehicle or MMC treated conditions for 10 days and the genomic DNA was isolated. FANCA and FANCD2 knockout cells are taken along as controls in this experimental setting. . This dataset contains all the data available for this study on 2023-04-20.

  Dataset EGAD00001010298

• Clonal haematopoiesis in patients with AAA (2019-04-03)

  Recent advances in genomics have demonstrated that clonal haemopoiesis driven by leukaemia associated somatic mutations is a relatively common phenomenon that increases in frequency with advancing age. Whilst individuals with clonal haemopoiesis have an increased risk of developing haematological malignancies, they also have an increased mortality from other causes. Additionally, certain mutations are almost exclusively seen in individuals aged 70 years or older, whilst others are seen in individuals with non-haematological cancers including breast and ovarian. Recently, clonal haemopoiesis was found to be associated with a significantly increased risk of atherosclerotic cardiovascular disease. This association is thought to be causative with clonally-derived macrophages showing elevated expression of several chemokine and cytokine genes that contribute to atherosclerosis. Another vascular pathology, abdominal aortic aneurysm (AAA), increases with age and shares risk factors with atherosclerosis (including smoking, male sex, high cholesterol). However, the impact of these risk factors and the overlap between AAA and atherosclerosis is poorly understood. To investigate a possible link between clonal haemopoiesis and AAA, we will study DNA samples from 300 patients with AAA and up to 200 controls for evidence of clonal haemopoiesis. This will be done using target DNA enrichment with biotinylated RNA baits followed by high throughput sequencing. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004895

• Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma -- CA209-009

  Immune checkpoint inhibitors targeting the PD-1 pathway have transformed the management of many advanced malignancies, including clear cell renal cell carcinoma (ccRCC), but the drivers and resistors of PD-1 response remain incompletely elucidated. Here, we analyzed 592 tumors collected from advanced ccRCC patients enrolled in prospective clinical trials of treatment with PD-1 blockade (or mTOR inhibition as control arm) by whole-exome and RNA-sequencing, integrated with immunofluorescence analysis, to define the somatic alteration landscape of late-stage ccRCC and to uncover the immunogenomic determinants of therapeutic response. While conventional genomic markers (tumor mutation burden, neoantigen load) and degree of CD8+ T cell infiltration were not associated with clinical response, we discovered numerous chromosomal alterations in advanced ccRCC associated with response or resistance to PD-1 blockade. These advanced tumors were highly CD8+ T cell infiltrated, with only 22% and 5% with an immune desert and immune excluded phenotype, respectively. Our analysis revealed that CD8+ infiltrated tumors are depleted of favorable PBRM1 mutations and are enriched for unfavorable chromosomal losses of 9p21.3 when compared to non-infiltrated tumors. These data demonstrate how the interplay of somatic alterations and immunophenotypes impacts therapeutic efficacy.

  Dataset EGAD00001006027

• Characterization of mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis

  Multiple signatures of somatic mutations have been identified in human cancer genomes. To investigate whether mutational signatures continue to be generated, and if so their temporal patterns of activity, subsets of cell lines were cultured in vitro for extended periods and subjected to single cell cloning and whole genome or exome sequencing or directly to single cell whole genome sequencing. As expected, signatures of past exogenous exposures, such as tobacco smoke and ultraviolet light, were not generated in vitro. In contrast, signatures of normal and defective DNA repair and replication continued to be generated at essentially constant mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing activity exhibited a distinctive pattern with substantial fluctuations in mutation rate over time and episodic bursts of mutations. The initiating factors for these bursts are unclear although retrotransposon mobilisation may play a role. This cell line set now constitutes a comprehensive resource of live experimental models of mutational processes of both known and unknown aetiologies potentially retaining the patterns of activity and regulatory influences operative in human cells in vivo.

  Dataset EGAD00001004201

• GEDI: A Developmental Model of Gene-Environment Interplay in SUDs: Combined Genotype Dataset from the "Great Smoky Mountains Study" and the "Caring for Children in the Community Study".

  1. Great Smoky Mountains Study (GSMS; Costello et al. 1996, 1997) Three cohorts of boys and girls, aged 9, 11, and 13 years at intake in 1993, were selected from a rural population of some 20,000 children using a household equal probability design. A two-phase procedure was used for White and African-American youth to increase power by oversampling children at risk for psychiatric and SUDs. Parents (usually mothers) of the first stage random population sample completed a questionnaire about their child's behavioral problems. Of 4,195 subjects selected, 95% (N=3,896) of parents completed the screen. All children scoring above a predetermined threshold (the top 25% of the total scores), plus a 10% random sample of the remaining 75%, were recruited for detailed interviews. Results can be back-weighted to population levels for analyses. Half of the sample consists of females, and 6% are African Americans, reflecting the population of the study area. The interviewed sample of white and African-American subjects was 1,070 (80% of those recruited). American Indian youth were oversampled (100%) because they are an understudied group known to be at high risk for stressful events, substance disorders, and mood disorders. Of 431 age-eligible children, 350 (81% boys, 49% girls) participated. Thus, the size of total GSMS sample is 1,070 + 350 = 1,420. Data collection is complete for ages 9-26, and age 30 interviews are in progress. By age 26 a total of 9,858 interviews had been completed; the average number of interviews per subject was seven, and by age 26, 97.3% completed two or more interviews. 2. The Caring for Children in the Community Study (CCC; Angold et al., 2002) This representative study of psychiatric illness and service use in African-American and White youth took place in four rural counties in the southeastern USA. The two-stage sampling design and methods are similar to those used in the GSMS. Of 4,500 youth randomly selected from the 17,117 9- to 17-year-olds in the public school's database, 3,613 (80.0%) were successfully contacted and agreed to complete the behavioral screen. Of the 1,302 selected to participate in the study, 920 (70.7%) interviews were completed. Because CCC was also the only study in GEDI to contain more than a very few African-American participants, these were omitted from the multi-site analyses. Reprinted with permission from Cambridge University Press from Costello et al., 2013: PMID: 23461817 References: Costello et al., 1996: PMID: 8956679 Costello et al., 1997: PMID: 9184514 Angold et al., 2002: PMID: 12365876

  Study phs000852

• Inflammatory Bowel Disease Exome Sequencing Study

  The Broad Institute and Massachusetts General Hospital (MGH) are launching a new initiative to perform large-scale exome sequencing in inflammatory bowel disease (Crohn's disease and ulcerative colitis). Given the considerable unmet therapeutic need in inflammatory bowel disease (IBD), the recent emergence of rapid and efficient genome sequencing technologies and the compelling evidence for the role of genetics in these disorders have motivated the founding of a collaborative sequencing effort geared toward the discovery of high-impact genetic variants influencing IBD risk that can serve as guides to future therapeutic development and diagnostic tools. The initiative will be directed by experienced IBD researchers from MGH and the Broad Institute but aims to develop a collaborative exome sequencing network that will partner with researchers worldwide. Two large pilot exome sequencing projects are being launched immediately as part of this initiative based on established genetic study designs that enrich for the discovery of rare, high-impact risk and protective variants. 1) Early-onset pediatric IBD: a major focus of the work will surround full-exome sequencing of the earliest-onset childhood IBD cases. It has long been recognized in many diseases that penetrant genetic risk factors are much more likely to be found in cases with unusually early onset. The Broad Institute has completed more than 50,000 exomes in the past two years; and their technical expertise in generating and processing such sequencing data, along with population genetic variation patterns from these experiments, will provide a foundation for obtaining the best outcome in the interpretation of these cases. Samples with IBD onset before 6 years of age - and in some cases going up to age 10 - collected by IBD researchers around the world are welcomed for inclusion in this study. 2) Adult-onset IBD case-control study: Genetic mapping has provided dramatic insights into IBD pathogenesis in recent years, but a substantial amount of heritability - in particular the role of strong-acting rare mutations - is yet to be elucidated. To deliver those insights, IBD cases with an unusually low burden of known genetic risk factors (particularly emphasizing those with positive family history and/or from isolated or enriched populations) will be contrasted with population controls that have an extremely high burden of known IBD risk factors, enhancing discovery of critical protective variants that may provide the best clues for therapeutic development. This project will also be initiated as an international collaboration, particularly among researchers with sample sets with Immunochip genotyping that will enable the immediate genetic identification of these enriched target populations. This project will be supported by the NHGRI Large-Scale Sequencing Program, with all generated data made publicly available to the research community through standard NIH databases.

  Study phs001076

• Studies of Left Ventricular Dysfunction (SOLVD-BioLINCC)

  Data Access NOTE:Please refer to the "Authorized Access" section below for information about how access to the data from this accession. Access differs from many other dbGaP accessions. ObjectivesThis study was initiated in 1986, primarily to evaluate the effects of enalapril, an ACE inhibitor, on long-term mortality and major morbidity in a group of participants with left ventricular dysfunction. Two large separate trials were run concurrently as part of SOLVD: 1) a prevention trial of participants with low ejection fraction but no overt symptoms of CHF and, 2) a treatment trial of participants with low ejection fraction and symptoms of CHF. In addition, participants at selected sites were entered into substudies to evaluate the effect of enalapril on a number of intermediate outcomes such as right and left ventricular function and hemodynamics, LV mass and wall stress, hormones, arrhythmias, exercise capacity, and quality of life in subsets of participants. Lastly, a registry of 6,336 participants with congestive heart failure of LV dysfunction was designed to describe the clinical course of an unselected group of participants. Background Congestive Heart Failure (CHF) is a major and increasingly recognized public health problem. The recognition that participants with CHF often have elevated peripheral vascular resistance has led to the introduction of vasodilator therapy, which has emerged as an important component of its treatment. Of the vasodilators, the angiotensin-converting enzyme (ACE) inhibitors appeared to be the most promising. In 1985, little was known about the impact of any long-term drug treatment on survival. SOLVD Registry: The SOLVD Registry is a hospital-based observational study, conducted at selected SOLVD hospitals, of participants with at least moderate left-ventricular dysfunction (EF ≤ 45%) and/or radiologically confirmed heart failure. It consists of a main study (n=6,273) and a substudy (n=898). Although there is overlap between the Registry and the SOLVD trials, the Registry sample is not a subset of SOLVD nor is it the pool of participants eligible for both trials. Participants A total of 2,569 participants were enrolled into the treatment study and 4,228 participants were enrolled in the prevention study. The dataset available through the NHLBI contains the prevention and treatment study data as well as the registry data. Conclusions In the prevention trial, a significant reduction in the incidence of heart failure and the rate of related hospitalizations was observed for participants in the enalapril arm. A statistically significant reduction in mortality was not observed in the enalapril treatment arm; however, there was a trend toward fewer total deaths and deaths due to cardiovascular causes among the enalapril participants (SOLVD Investigators, et al., 1992, PMID: 1463530).

  Study phs003668

• Sickle Cell Disease Natural History Data Resource (SCD NHDR)

  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. BackgroundThe NHLBI initiated the Sickle Cell Disease Natural History Data Resource (SCD NHDR) to leverage existing SCD studies to build a data resource to provide phenotypic data on contemporaneous control cohorts for gene therapy trials and other studies. The potential uses of the NHDR are broad, including providing matched controls for clinical trials, observing a cohort of untreated patients as part of a natural history study, or conducting comparative effectiveness research on a subpopulation with selected co-morbidities or drug treatment profiles. The SCD NHDR includes two multi-center SCD longitudinal cohort studies with extensive annual clinical data and patient surveys, the Sickle Cell Disease Implementation Consortium (SCDIC-I and SCDIC-II) and the Globin Research Network for Data and Discovery (GRNDaD). The SCDIC-I, initiated in 2017 and concluded in June 2022, enrolled over 2400 patients with SCD from 8 US treatment centers. The SCDIC-II reconsented 1220 of the SCDIC-I patients as well as enrolling an additional 450 new patients from the same 8 centers between September 2022 and October 2023, for a total of 1670 in SCDIC-II. Only two of the many GRNDaD centers are submitting data to the SCD NHDR for deposit into BDC (approximately 122 patients). Data submissions from the SCD NHDR to BDC will be annually starting in early 2024. Description of the Study Data All data obtained for the SCD NHDR are considered common data elements (CDEs) important for studies of SCD. These CDEs were identified from several workgroups of SCD experts convened under the NHLBI's Cure-SC Initiative (https://curesickle.org/cde-catalog). The following types of data elements were abstracted from the medical record – variables that describe the SCD diagnosis, SCD co-morbidities and other clinical complications, elements from the physical examination, medications and transfusions, insurance type, laboratory measurements, healthcare utilization, history of SCD-related procedures, and measurements from cardiac procedures. The following types of data were self-reported on the patient survey – demographics, diagnosis information, pain experience, social and mental health information, other patient reported outcome domains (e.g., sleep, fatigue), and alcohol and smoking history. Standard PRO measures were used from ASCQ-Me, PROMIS and Neuro-QoL. Patient surveys were completed approximately annually. Under SCDIC-I, two medical record abstractions and labs were reported at enrollment and approximately 3 years later. Under SCDIC-II and GRNDaD, all data are collected annually. Patients may refuse to complete the survey.

  Study phs003529

• Providing safe access to sensitive human data across borders: Federated EGA becomes a reality

  Enabling discovery and access to sensitive data across national boundaries is vital for improving human health. It enables more powerful and efficient research by increasing the volume and diversity of data available for analysis. It allows us to better understand the causes of diseases – cancer, rare diseases, infectious diseases like COVID-19 – and develop new medicines and treatments. Sensitive human omics data are typically generated by research initiatives and shared using specialist repositories which provide services for data submission, discovery, and access. The EGA is one such repository. Established in 2008 at EMBL’s European Bioinformatics Institute (EMBL-EBI) in the UK, since 2012 the EGA (“Central EGA”) has been jointly managed by EMBL-EBI and the Centre for Genomic Regulation (CRG) in Spain. Many countries have emerging personalised medicine programmes which generate data from national initiatives. These programmes are driving a transition in human genomics from being research-driven to receiving funding through healthcare. Data generated in a clinical context are subject to stricter governance than research data and must follow national data protection legislation. To solve these challenges, the Federated EGA provides a network of connected resources to enable transnational discovery of and access to human omics data for research, while also respecting jurisdictional data protection regulations. In this way, the Federated EGA infrastructure supports the goals of European initiatives such as the 1+ Million Genomes initiative (1+MG), the European Health Data Space, and a number of EU-funded 1+MG implementation projects including Beyond 1 Million Genomes. The Federated EGA is made up of “Nodes” – typically nationally funded and operated – which store and manage data locally while allowing global discovery within the Federated EGA network. Since 2016, multiple parallel efforts, supported by ELIXIR and other transnational and national initiatives, have created technical and legal frameworks for establishing the Federated EGA. In 2022, the first five Nodes – Finland, Germany, Norway, Spain, and Sweden – officially joined the Federated EGA by signing Federated EGA Collaboration Agreements with Central EGA. The Finnish FEGA Node is operated by CSC - IT Center for Science and provides data management services according to national laws and the requirements of the EU General Data Protection Regulation (GDPR). These services provide tools and support for the whole life-cycle of sensitive research data from collating to analysis, publication, and authorised re-use. The development of the services has been a joint effort with the other Nordic nodes within NeIC's Tryggve and Heilsa projects, and funded by Finnish Ministry of Education and Culture and projects coordinated by ELIXIR Finland. Read more about Finnish FEGA signing. The German Human Genome-Phenome Archive (GHGA) strives to provide a national infrastructure as well as an ethical and legal framework that balances FAIR omics data usage and data protection needs for Germany. As a Germany-wide consortium funded by the German Research Foundation under the umbrella of the NFDI association, GHGA combines the expertise of 21 universities and research institutions to form a federated national infrastructure. Read more about GHGA signing. The German Human Genome-Phenome Archive (GHGA) strives to provide a national infrastructure as well as an ethical and legal framework that balances FAIR omics data usage and data protection needs for Germany. As a Germany-wide consortium funded by the German Research Foundation under the umbrella of the NFDI association, GHGA combines the expertise of 21 universities and research institutions to form a federated national infrastructure. Read more about GHGA signing. In Norway, a key component of the infrastructure is the services of The Sensitive Data Service (TSD) offered by USIT at University of Oslo. The Federated EGA Norway Node is developed by ELIXIR Norway and operated by the University of Oslo as the responsible legal entity. Core software modules are developed jointly with the other Nordic nodes in the NeIC Tryggve and Heilsa projects. Read more about FEGA Norway signing. The Spanish FEGA (es-FEGA) is a national service for storing sensitive biomedical data in Spain. Supported by the Spanish Institute of Bioinformatics (INB) in collaboration with Central EGA, sensitive research datasets are primarily hosted at the Barcelona Supercomputing Centre facilities. The Swedish Sensitive Data Archive is a secure data archive and sharing platform for sensitive datasets. It was developed by the National Bioinformatics Infrastructure Sweden (NBIS) in collaboration with other Nordic ELIXIR Nodes through the Tryggve and Heilsa projects funded by NeIC and coordinated with Central EGA through ELIXIR. Read more about the Swedish Node signing. The Swedish Sensitive Data Archive is a secure data archive and sharing platform for sensitive datasets. It was developed by the National Bioinformatics Infrastructure Sweden (NBIS) in collaboration with other Nordic ELIXIR Nodes through the Tryggve and Heilsa projects funded by NeIC and coordinated with Central EGA through ELIXIR. Read more about the Swedish Node signing. By providing a solution for secure and efficient management of human omics data, the Federated EGA aims to foster data reuse, enable reproducibility, accelerate biomedical research, and improve human health. Find out more Interested in setting up your own Federated EGA Node? Check out the FEGA Onboarding Knowledge Base for more information. The ELIXIR Federated Human Data Community is a great entry point for anyone interested in learning more about the Federated EGA. You can: Join the ELIXIR Federated Human Data Community mailing list (select “Human Data”) Attend the ELIXIR Federated Human Data Community calls

  Blog safe-access-to-sensitive-human-data-federated-ega

• Comprehensive NGS Profiling to Enable Detection of ALK Gene Rearrangements and MET Amplifications in Non-Small Cell Lung Cancer

  We evaluate the analytical performance of the PGDx™ elio™ tissue complete assay, a 505 gene next-generation sequencing (NGS) tissue-based assay, that has now been FDA-cleared for use by physicians to help guide treatment decisions for cancer patients, using a NSCLC cohort of 38 patients.

  Study EGAS50000000010

• Enhanced resolution profiling in twins reveals differential methylation signatures of Type 2 Diabetes with links to its complications

  We profiled DNA methylation in blood samples from participants of European ancestry from 7 twin cohorts using a methylation sequencing platform targeting regulatory genomic regions encompassing 2,048,698 CpG sites. The results help to improve our understanding of T2D disease pathogenesis and progression and may provide biomarkers for its complications.

  Study EGAS50000000197

• Tumor Normal Pair for SV mosaic

  Simulated (based on real world data) tumor normal pair designed for benchmarking and optimisation of structural variation callers. The calls are derived from 12 patients in the hartwig database requested by the EUCANCan project. Paired-end sequencing data was imputed into the normal reference data to simulate real world variation like purity as well as technical impact of sequencing technologies. The dataset contains a tumor sequenced to ±90x depth and a normal control sequenced to ±30 x depth of these imputed events. The break junctions of all detected SVs in the original cases are imputed in this data from diagnostic WGS sequencing data.

  Dataset EGAD50000000668

• scRNA-seq to study interactions between HSPCs, BMSCs and immune microenvironment

  Mechanisms of clonal evolution in myeloid neoplasms remain incompletely understood. Darwinian theory predicts that the (micro)environment of clone-propagating stem cells may contribute to clonal selection. Here, we provide data fitting this model, establishing a relationship between stromal niche inflammation, inflammatory stress in HSPCs, clonal resistance and leukemic evolution in human MDS.

  Study EGAS00001008181

• Test dataset with ligh-weight files

  This is a test dataset derived from public data of the 1000 Genomes Project. Its purpose is not to allow for any inference about cohort data or results, but to aid bioinformaticians in the technical development and testing of tools, as well as data consumers in learning how to access information. This dataset consists of 3 pairs of light-weight (sliced) files: BAM + BAI, CRAM + CRAI and VCF + TBI. These files can be downloaded directly through the EGA-download-client PyEGA3 (https://github.com/EGA-archive/ega-download-client). For any further questions, please contact the DAC (Helpdesk - email: helpdesk [at] ega-archive [dot] org).

  Dataset EGAD00001009826

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (Targeted) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 30 women who mastectomies due to Breast Cancer. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005923

• Single MII oocyte mRNA expression from women

  This dataset contains 14 paired-end FASTQ sequences from mRNA-Seq on single human M-II stage oocytes that were collected from ovarian tissue from unstimulated patients undergoing fertility preservation treatments due to cancer diagnoses, which did not influence ovarian function. Cumulus-oocyte-complexes were matured in vitro according Gruhn et al (Science 365: 1466-1469) and short term flash frozen prior to lysis, RNA extraction, full length cDNA preparation and amplification using the Ultra-low-input SMART-Seq2 v4 kit from Takara Clonetech. Further, these cDNA were used to prepare libraries for sequencing according the Nextera XT DNA library preparation kit from Illumina

  Dataset EGAD00001005971

• MutWP5: CRUK Mutographs of Cancer: Breast: BRCA Carriers (Targeted) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005920

• COMPARE study: participants typed during UK Biobank version 2 array development phase

  The COMPARE study enrolled 29,066 British blood between donors between February 2016 and March 2017, the study aim is to find the optimum technology for haemoglobin screening (ISRCTN 90871183). All participants were at the time of recruitment active blood donors. The 4,796 participants in this dataset have consented to join the NIHR BioResource. Genotyping data was produced using the Thermo Fisher Scientific Axiom Genotyping platform. The UK Biobank version 2 array design was used, content on this array has been added to allow for accurate DNA based identification of human blood group antigens.

  Dataset EGAD00001005023

• MutWP5: CRUK Mutographs of Cancer: Breast: BRCA Carriers (Exome) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005921

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (Exome) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 30 women who underwent mastectomies due to a breast cancer diagnosis. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005924

• Embryonic tumour transmission in monozygotic twins

  We have a case of two siblings (twins) who were born with nodular blue rashes over their body. The first twin had a large periorbital subcutaneous mass which was diagnosed as infantile undifferentiated sarcoma. This baby was too systematically unwell for chemotherapy and died at 12 days of age. The second sibling received two cycles of emergency chemotherapy however died due to disease progression and secondary haemorrhage at 2 months of age. Post-mortem normal and tumour samples have been taken. In addition to placental tissue and parental germline DNA, the goal will be to investigate intra-uterine transfer of sarcoma and the phylogenetic relationship of tumours in both twins.

  Dataset EGAD00001015681

• Chordoma Sequencing Project Whole Genome

  This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

  Dataset EGAD00001000721

• Whole genome sequence of third generation family member (SFHS)

  Previously we performed deep WGS on 6 parents and 13 children from 3 large families from the Scottish Family Health Study to identify de novo mutations. This prelim is cover the additional sequencing of one grandchild from one of these three families. The inclusion of a third generation individual will provide additional experimental validation for the de novo mutations found in the initial trio. As in the previous study, the DNA will be WGS to a depth of approximately 25X to achieve this purpose.These data can only be used for the investigation of the genetic causes of the reported clinical phenotypes in these patients

  Dataset EGAD00001001454

• Federated EGA

  Federated EGA Federated EGA Index Overview Map of FEGA status across the world Current status of the FEGA Network Documentation Overview Federated EGA is a global network of repositories enabling secure discovery and access to sensitive human data. Our vision is to accelerate scientific discovery and healthcare breakthroughs by creating the go-to worldwide sensitive human data resource. Our values are: Privacy & Trust: Ensuring privacy of data subjects, security of services and acting with integrity to build community trust.FAIRness: Driving reuse of data through standardisation of metadata and clear access policies.Diversity: Expanding our network and representing global diversity in the data we host to bring benefits worldwide. Federated EGA - European by name, global by nature Federated EGA collaborates with European and global initiatives (GA4GH, ELIXIR, 1+ Million Genomes Framework, GDI), demonstrating that a network for transnational discovery of and access to human data is possible. By providing a solution to emerging challenges around secure and efficient management of human omics and associated data, the FEGA Network fosters data reuse, enables reproducibility, and accelerates biomedical research. For general enquiries or to request more information about Federated EGA, please send an email to fega-info [at] lists [dot] ega-archive [dot] org. Read more about the Federated EGA in our commentary in Nature Genetics! Learn more about setting up a Federated EGA Node in our onboarding documentation. Map of FEGA status across the world Current status of the FEGA Network Node Description Joined CEGA Central EGA is managed by the Centre for Genomic Regulation (CRG) and EMBL-EBI. The EGA has been a trusted repository for sensitive data since 2008. CEGA coordinates the FEGA network, hosts central services and the EGA catalogue. 2022 Finland FEGA Finland is hosted by CSC - IT Center for Science Ltd., which is the national ELIXIR Node in Finland. CSC is a state-owned company specialising in providing high-quality IT infrastructure and services for Finnish higher education and research. 2022 Germany The German Human Genome-Phenome archive (GHGA) is part of the German National Research Data Infrastructure (NFDI). It is coordinated by the German Cancer Research Center (DKFZ) and includes over 20 academic partners. 2022 Norway FEGA Norway is a service by ELIXIR Norway, the Norwegian node of the European organisation ELIXIR. University of Oslo as a partner institution in ELIXIR Norway is hosting the service relying on the TSD infrastructure for sensitive data. ELIXIR Norway is a consortium of 5 Norwegian universities and is coordinated by University of Bergen. 2022 Spain FEGA Spain is co-hosted by the Barcelona Supercomputer Center (BSC) and the Centre for Genomic Regulation (CRG), both part of ELIXIR Spain and the Spanish National Infrastructure for Personalised Medicine associated with Science and Technology (IMPaCT). 2022 Sweden 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. 2022 Poland FEGA Poland is hosted by Biobank Lodz, which is part of University of Lodz. Biobank Lodz is an element of the infrastructure of the Regional Digital Medicine Centers established by the Medical Research Agency. 2022 Portugal FEGA Portugal is managed by BioData.pt, the distributed infrastructure for Life and Health data for Portugal. This entity is a non-profit association of 15 life sciences R&I organisations spread across the country, and the home of ELIXIR Node in Portugal. 2023 Canada Canadian Genome-phenome Archive is part of the Pan Canadian Genome Library, with the mandate to allow the secure and responsible sharing and analysis of Canadian genomic information. 2024 Switzerland Swiss FEGA is hosted by SIB Swiss Institute of Bioinformatics, which is the national ELIXIR Node in Switzerland, on behalf of the Swiss FEGA Partnership which includes 4 other key partners (ETH Zurich, Health 2030 Genome Center, Swiss Data Science Center and Switch). 2025 Documentation Title Version Description Mission, vision, values Federated EGA Mission, vision, values 1.0 The official Mission-Vision-Values statement for FEGA, produced and formally approved by the FEGA Strategic Committee in September 2025. Structure and Organisation Federated EGA Structure and Organisation 2.0 The structure of the FEGA network and service expectations, responsibilities and commitments. FEGA is organised into three tiers: Central EGA, FEGA Nodes and FEGA Affiliates. Strategic Committee Federated EGA Strategic Committee 1.1 Terms of reference for the FEGA Strategic Committee describe the purpose and objectives of the committee, which is to provide direction and strategic planning for the FEGA network. The committee receives input from, and provides feedback for the EGA Strategic Committee. Operations Committee Federated EGA Operations Committee 1.1 Terms of reference for the FEGA Operations Committee describe the purpose and objectives of the committee, which is to review operational performance and coordinate technical roadmaps of FEGA Nodes and Central EGA. The committee receives advice from, and provides operational reporting to the FEGA Strategic Committee. Guidelines Node Operations guidelines 2.1 An overview of the operational areas which require resources in order to create a FEGA Node. The document is based on more than 15 years' experience of EMBL-EBI and CRG operating the EGA and initial expericences of the inaugural FEGA Nodes. The operational areas of responsability are in line with the FEGA Maturity Model, which guides establishment and operation of FEGA Nodes. Collaboration Federated EGA Node Collaboration Agreement 1.3 Nodes are welcome to make a copy of this current version of the CA to start its review with their legal teams and understand the responsibilities of joining FEGA. Nevertheless, this version (the one with a watermark) shall not be signed: the official version needs to be obtained from FEGA prior signing through its official channels.

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