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• Implementation of the GDPR

  Data Protection 1 About the EGA The European Genome-phenome Archive (EGA) was formally launched in 2008 at the European Bioinformatics Institute (EMBL-EBI), an outstation of the European Molecular Biology Laboratory (EMBL), to address an identified need for archiving and sharing the results of genome-wide association studies from the Wellcome Trust Case Control Consortium. In late 2012, with the signing of a memorandum of understanding (and subsequent formal agreement in 2016) between EMBL-EBI and the Centre for Genomic Regulation (CRG), the EGA formally became a joint project of the two institutes. The two institutes work together to support the EGA services, including supporting submissions, web site, strategic leadership, and data infrastructure developments. 2 EMBL-EBI & GDPR The EGA is co-managed by EMBL-EBI and CRG. EMBL-EBI is an international organisation established by treaty and has certain privileges and immunities (e.g. exemptions from the application of national law) and also may self-regulate its activities (e.g. establish its own institutional legal framework) within the framework of its founding act of 1973. The General Data Protection Regulation (GDPR) is a European Union (EU) regulation that legislates how organisations can share and process personal data of EU citizens. EMBL places great value in maintaining collaboration with researchers who are subject to GDPR. For that reason, it is of utmost importance for EMBL to handle data received from those collaborators in a secure and responsible manner. Mindful of its public mandate and the sensitivity of the data it handles, EMBL has always ensured a high level of data protection in its activities. Since the introduction of GDPR in May 2018, EMBL has established its internal policy on General Data Protection (IP68), exercising its right to self-regulate its operations,., IP 68 establishes a robust personal data protection framework that provides for data protection principles, enforceable data subject rights and oversight and redress mechanisms offering a level of protection comparable with GDPR. 3 CRG & GDPR The Centre for Genomic Regulation (CRG) is an international biomedical research institute of excellence, created in July 2000 and mainly participated by the Catalan Government. It is a non-profit foundation and its mission is to discover and advance knowledge for the benefit of society, public health and economic prosperity. The CRG is a CERCA center. CERCA is the collective organisation for all research centres of excellence in Catalonia. CERCA ensures these centres develop successfully by promoting synergies and strategic cooperation improving their visibility and the impact of their research and promoting the dialogue amongst both public and private stakeholders. As a legal entity based in Spain and operating within the EU, the CRG ensures the compliance with the GDPR and the legal regulations on personal data protection applicable at the national level, as well as any other legislation that may replace, modify or supplement the above-mentioned in terms of personal data protection. 4 EGA & GDPR EGA GDPR Schema 4.1 Genetic and phenotypic data Within GDPR, there are two main actors: data controllers and data processors. Data controllers are persons or entities which determine the purposes and means that the personal data may be processed, e.g. companies, researchers, or universities. For EGA, the data controller is ultimately the data producer and the submitter(s) who submit the data to EGA. The data controller also creates a Data Access Committee (DAC) who will decide on data access permissions at EGA. Data processors are the persons or entities which process the data on behalf of a data controller. With regard to GDPR, EGA is a data processor as it processes data as instructed by the data controller. GDPR applies to any organisation which accesses personal data from an individual within the EU. Under GDPR, personal data is defined as any data that is identifiable, including names and email addresses as well as health-related and genetic data. EGA does not accept personally identifiable data except genetic and phenotypic data, so all other data submitted to EGA, such as names and addresses, must be pseudonymised. GDPR requires that data controllers implement data protection principles, such as data minimisation, to minimise the risk of data leakage, and protect the rights of the data subjects. As a data processor, EGA has a set of security policies that are followed to minimise the risk of unauthorised data access or data loss. In its role as a data processor, EGA requires all submitters to sign a Data Processing Agreement (DPA) when the submission account is first created. This agreement is only required to be signed once per submitter, and will remain valid for future submissions to EGA. 4.2 Other personal data The EGA also collects personal data as part of our interactions with submitters, data access committees, and researchers accessing data distributed by EGA. The below privacy notices explain what personal data is collected by the specific service you are requesting, for what purposes, how it is processed, and how we keep it secure. Privacy Notices for EGA Title Version Last Updated EGA Data Access Committee Account Privacy Notice for EGA Data Access Committee Account 1.0 February 6, 2019 EGA User Account Privacy Notice for EGA User Account 2.0 February 24, 2026 EGA Helpdesk Service Privacy Notice for EGA Helpdesk Service 2.0 February 24, 2026 EGA Website Service Privacy Notice for EGA Website Service 2.0 February 24, 2026 Documentation Title Version Description EGA Security Overview Security Document 1.1 The EGA Security Document provides an overview of EGA’s practices in ensuring the security of data stored at EGA. EGA Data Processing Agreement Data Processing Agreement 1.5 The Data Processing Agreement must be completed and returned as part of the submission process. Please note that this document is non-negotiable. Authorised Submitters Authorised Submitters Formulary 1.0 The Authorised Submitters Form must be completed and returned as part of the submission process. Please list all those that should have access to the submission account in order to submit to the EGA should be detailed here. Dispute Resolution Any controversy or claim arising out of, or relating to, the DPA (including the enforceability or breach thereof, any question regarding its existence, validity or termination) or relating to the EGA Service shall be resolved using the internal dispute resolution mechanisms of EGA including those related to Data Protection. The EGA’s internal dispute resolution mechanism has the following procedure: EGA OPERATIONAL PHASE: Meetings between EGA staff and the Data Controller.LEGAL MANAGEMENT PHASE: Meetings between legal teams of EMBL, CRG and the Data Controller. DIRECTION MANAGEMENT PHASE: Negotiation between the legal representatives of EMBL, the CRG and the Data Controller. If the internal dispute resolution mechanism doesn’t resolve the controversy or claim the next phase is:ARBITRATION PHASE: Resolution by arbitration under the WIPO Expedited Arbitration Rules (“Rules”).

  Documentation about/privacy-notice

• Whole-Exome Sequencing of Tumor Biopsies from a Colorectal Cancer Patient with Two Distinct Primary Tumors and Matched Metastases

  Colorectal cancer (CRC) is a heterogeneous disease in which rare genetic alterations, such as neurotrophic receptor tyrosine kinase (NTRK) fusions, have emerged as clinically relevant therapeutic targets. Here, we report the case of a 69-year-old man with an advanced colorectal carcinoma comprising two intermixed but histologically distinct components: a predominant (>90%) poorly differentiated solid carcinoma and a conventional adenocarcinoma with mucinous features. Whole-exome sequencing (WES) of microdissected tumor regions (two primary tumors and two matched metastases) along with germline DNA analysis revealed profound genetic divergence between the two tumor components. This case illustrates the coexistence of two genetically independent yet spatially inseparable CRCs following distinct evolutionary trajectories—one driven by an NTRK1 fusion and microsatellite instability (MSI), and the other by canonical KRAS and SMAD4 alterations.

  Study EGAS50000001385

• Distinct immune and genomic signatures predict resistance to ibrutinib therapy in Waldenström macroglobulinemia

  In this data, we investigate the complex interplay between tumour-acquired genetic features and the composition of the microenvironment in the promotion of ibrutinib resistance in WM patients by integrating single-cell RNA sequencing (scRNAseq) and whole-genome sequencing (WGS), to examine bone marrow tumour and immune compartments from 37 symptomatic WM patients treated with ibrutinib.

  Dataset EGAD50000002267

• Plasma CTCF ChIP-seq Reveals Cancer-Associated cfDNA Binding Profiles

  Cell-free DNA (cfDNA) in plasma predominantly exists as nucleoprotein complexes. Although circulating CTCF-bound cfDNA (cfCTCF-DNA) has previously been reported, the occupancy of individual CTCF binding sites in plasma has not been systematically characterised. This study describes the isolation of endogenous plasma cfCTCF-DNA by chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) in samples obtained from cancer patients and healthy individuals. A two-step enrichment strategy was employed, combining physical removal of background cfDNA by immunoprecipitation with bioinformatic filtering to remove residual non-CTCF-derived sequences. Sequencing reads were aligned to the UCSC hg38 reference genome using BWA-MEM v0.7.17 and processed to generate CRAM files containing alignments restricted to the primary chromosomes (chr1–chr22, chrX, chrY and chrM). CTCF-associated cfDNA fragments were classified according to their similarity to a consensus CTCF binding motif, enabling discrimination between low-affinity and high-affinity CTCF binding sites. Comparative analyses identified quantitative and qualitative differences in plasma cfCTCF-DNA profiles between healthy individuals and patients with cancer. The deposited dataset comprises plasma cfCTCF-DNA ChIP-seq data from four clinical cohorts and includes both CTCF-enriched and total cfDNA samples where applicable. These data support the investigation of CTCF occupancy patterns as a novel class of liquid biopsy biomarkers for cancer detection and monitoring.

  Study EGAS50000001937

• Polynesian Founder Effects

  Founder effects can lead to strong, population-specific allele frequency differentiation, including autosomal recessive conditions. Their characterization in European-descent groups such as the Finnish and Amish has resulted in actionable genetic tests for each. We show that Polynesians experienced an order-of-magnitude stronger cumulative founder effects during their settlement of Eastern Polynesia. Using whole genome sequences spanning Polynesia, we show that two of the most bottlenecked populations are Hawaiʻi and Easter Island (Rapa Nui), and that these two most closely genetically related yet geographically distant islands were likely settled by the same ultra-voyagers with earlier ancestral roots in Mangareva. We identify clinical genetic variation generated by this sequence of successive oceanic founder events, including a loss-of-function FAN1 mutation common in Eastern Polynesia (>1%) but entirely absent from gnomAD.

  Study EGAS50000002085

• Transcriptomic and epigenetic characterization of ex vivo expanded T cells

  In this study, we investigated the transcriptomic and epigenetic landscape of primary human T cells stimulated ex vivo under various conditions. Naïve CD8+ T cells isolated from healthy donor PBMCs were subjected to ex vivo stimulation and used for bulk RNA-seq and ATAC-seq library preparation. These datasets were generated to characterize global changes in gene expression and chromatin accessibility associated with ex vivo T-cell stimulation. The data may support comparative analyses of molecular states arising under distinct culture conditions.

  Study EGAS50000001718

• Machine Learning Uncovers Previously Undetectable Genetic Deletions in Cancer Panel Sequencing

  We developed a novel machine-learning pipeline for detection of genetic deletions and zygosity evaluation within MASTERsg, a precision oncology program using the TSO500 DNA gene panel to identify targetable alterations in advanced cancers. The TSO500 pipeline detects copy number variations (CNVs) through bin count averaging but may miss focal CNVs not meeting thresholds. As a proof-of-concept we used deletions in PTEN, which confer sensitivity to mTOR and Akt inhibition. An Extreme Gradient Boosting model trained on tumor samples with PTEN deletions and PTEN wild-type status enabled the correct identification of missed focal deletions, which were subsequently confirmed by immunohistochemistry. Additional cases of PTEN loss could be identified in 34 of 204 previously profiled, seemingly uneventful samples, which were validated in 75% of stainable cases. The findings underscore the substantial clinical potential of this method to uncover therapeutically relevant alterations beyond established diagnostic pipelines.

  Study EGAS00001008324

• DLGG sequencing

  NGS panel based sequencing of disseminated pediatric low-grade glioma (DLGG). This is a dataset from the international DLGG consortium of patients from 0-44 years of age at diagnosis, and diagnosed between 1988-2024. Sequencing was done at the Hospital for Sick Children (Toronto, Canada). The goal of this study was to define the genetic drivers in DLGG and compare them to non-disseminated pediatric low-grade gliomas.

  Study EGAS50000000841

• Prehistoric global migration of vanishing gut microbes with humans

  The gut microbiome is crucial for health and is affected strongly by lifestyle. Many microorganisms commonly found in non-industrialized populations are disappearing or have become extinct in industrialized populations. Studying which microorganisms have been long-term residents of the human gut and may have co-evolved with humans could provide insights into how microbial biodiversity loss affects human health. However, the genetic complexities of microbial evolution and the plasticity of gut microbiome composition have made it challenging to resolve the evolutionary history of these long-term associations. Here we performed deep metagenomic sequencing of the Tsimane horticulturalists of Bolivia and compared their gut microbiomes with those of the Hadza hunter-gatherers of Tanzania. These two populations, whose ancestors have been separated for tens of thousands of years, share 1,231 microbial species, most of which are rare in or absent from industrialized populations. Population genetic analyses of 636 of the shared species revealed patterns of microbial divergence and gene flow consistent with prehistoric human co-migration, with estimated split times that approximately align with human migration out of Africa and into the Americas. Our findings indicate that a diverse gut microbiome co-migrated with humans worldwide and has persisted over millennia. However, many of these species are now vanishing from industrialized populations and the consequences for human health remain uncertain.

  Study EGAS50000002215

• Genetic landscape of kidney failure in Israel

  Kidney failure is a major cause of morbidity and mortality, and a substantial fraction of cases has an underlying monogenic cause that often remains undiagnosed. This study aimed to characterise the genetic landscape of kidney failure and to estimate the diagnostic yield of exome sequencing in a nationwide cohort of dialysis-treated patients in Israel. Proband exome sequencing was performed and variants were interpreted according to ACMG/AMP guidelines to identify molecular diagnoses in known kidney disease genes.

  Study EGAS50000002227