Search Results - EGA European Genome-Phenome Archive

Rare Disease Synthetic Dataset

The purpose of this project is to provide public human datasets for the study of rare diseases. The use of public human genomic background combined with the in-silico insertion of real disease-causing variants enable to have a representative dataset for testing purposes without facing ethical and legal issues associated with the use of human sensitive data. This project aims to help development of technical implementations for rare disease data integration, analysis, discovery, and federated access.

Dataset EGAD00001008392

Whole genome sequencing data of high-grade serous ovarian cancer samples (set 6)

Whole genome sequencing data of 31 high-grade serous carcinoma (HGSC) patients (101 samples) sequenced with HiSeq X Ten and BGISEQ-500

Dataset EGAD00001010202

Drug screen in iPSC-Neurons identifies nucleoside analogs as inhibitors of (G4C2)n expression in C9orf72 ALS/FTD

To investigate the mode of action and potential side-effects we analyzed differential gene expression in Postmitotic C9orf72 iPSC-Neurons by RNAseq. The cells were treated in a 2 dose regime at 10 µm in 0.1 % DMSO for 9 days. Compound treated iPSC-Neurons were washed with PBS, frozen on dry ice and stored at -80°C until RNA isolation. The RNA was isolated using miRNA Mini Kit (Qiagen) using 700 μl of Qiazol. A total of 250 ng of RNA per sample was processed for mRNA library preparation as per the manufacturer’s instructions for Illumina® Stranded mRNA Prep Ligation to be used with the IDT® for Illumina® RNA UD Indexes Set B and sequenced using NextSeq 500/550 High Output Kit v2.5 (Illumina) on NextSeq 550 (Illumina). The data was processed and analyzed using CLC genomics workbench (Version 21.0.3, Qiagen)

Dataset EGAD00001008674

INSPIRE multi-timepoint cfMeDIP dataset

This dataset contains raw sequencing data from multi-timepoint cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq) of plasma samples from the INSPIRE study (NCT02644369). Details about the study, including inclusion/exclusion criteria and interventions are available at https://clinicaltrials.gov/study/NCT02644369. Briefly, five cohorts were included, INS-A (head & neck squamous cell carcinoma), INS-B (triple-negative breast cancer), INS-C (high-grade serous ovarian cancer), INS-D (melanoma), and INS-E (mixed solid tumors). All patients in the study were diagnosed with advanced cancer and received treatment with pembrolizumab. Plasma samples were collected at baseline and every 3 cycles until disease progression, death, loss of follow-up, or completion of the study. Plasma samples were first processed for cell-free DNA mutations and remaining samples were then processed by cfMeDIP-seq, prioritizing baseline and post-cycle 3 samples. In total, data from 204 timepoints from 87 distinct patients are deposited.

Dataset EGAD00001011312

Cancer-independent, second somatic NF1 mutation of normal tissues in neurofibromatosis type 1

Cancer predisposition syndromes mediated by recessive cancer genes generate tumours via somatic variants (second hits) in the unaffected allele. Second hits may or may not be sufficient for neoplastic transformation. Here, we performed whole genome and exome sequencing on 479 tissue biopsies from a child with neurofibromatosis type 1, a multi-system cancer-predisposing syndrome mediated by constitutive monoallelic NF1 inactivation. We identified multiple independent NF1 driver variants in histologically normal tissues, but not in 610 biopsies from two non-predisposed children. We corroborated this finding using targeted duplex sequencing, including a further nine adults with the same syndrome. Overall, truncating NF1 mutations were under positive selection in normal tissues from individuals with neurofibromatosis type 1. We demonstrate that normal tissues in neurofibromatosis type 1 commonly harbour second hits in NF1, the extent and pattern of which may underpin the syndrome's cancer phenotype.

Dataset EGAD00001015398

scDNA-seq for 'Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma'

Neuroblastoma (NB) is one of the most lethal childhood cancers due its propensity to treatment resistance. By spatial mapping of subclone geographies before and after chemotherapy across 89 tumor regions from 12 NBs, we find that densely packed territories of closely related subclones present at diagnosis are replaced under effective treatment by islands of distantly related survivor subclones, originating from a different most recent ancestor compared to lineages dominating before treatment. Conversely, in tumors that progressed under treatment, ancestors of subclones dominating later in disease are present already at diagnosis. Chemotherapy treated xenografts and cell culture models replicates these two contrasting scenarios and shows branching evolution to be a constant feature of proliferating NB cells. Phylogenies based on whole genome sequencing of 505 individual NB cells indicate that a rich repertoire of parallel subclones, emerges already with the first oncogenic mutations and lays the foundation for clonal replacement under treatment.

Dataset EGAD00001015414

RNA-seq dataset

RNAseq FASTq files from 728 bulk pre-treatment tumors from IMvigor010.

Dataset EGAD00001007575

Genomic and transcriptomic landscape of T-cell lymphoblastic lymphoma compared to T-cell acute lymphoblastic leukemia: similar subtypes and different fusions

Due to the lower incidence of T-LBL and difficulties in obtaining diagnostic T-LBL material, extensive research on T-LBL has been hampered whereas genetic aberrations in T-ALL are thoroughly characterized. Given the similarities and differences between T-LBL and T-ALL, the question has been raised whether T-LBL and T-ALL represent two different diseases or different manifestations of the same disease. This study aims to identify the genomic and transcriptomic landscape of T-LBL and compare the findings to what is found T-ALL. Comparison of the molecular aberrations between T-LBL and T-ALL can provide insights into the overlap and differences in malignant development between the two entities, which could lead to improved risk stratification in T-LBL in order to eventually adapt T-LBL treatment protocols based on molecular-genetic prognostic factors.

Dataset EGAD00001015357

Conserved interferon-gamma signaling and decreased immune exclusion programs in responses to immune checkpoint blockade therapy_CM38-RNA

We analyzed baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). Analysis of whole transcriptome data showed that T cell infiltration and interferon-gamma signaling signatures corresponded most highly with clinical response to therapy, with a reciprocal decrease in cell cycle and WNT signaling pathways in responding biopsies. Clinical outcome differences were likely not due to differential melanoma cell responses to interferon-gamma, as 57 human melanoma cell lines exposed in vitro to this cytokine showed a conserved interferon-gamma transcriptome response unless they had mutations that precluded signaling from the interferon-gamma receptor. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream interferon-gamma signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

Dataset EGAD00001006282

Targeted sequencing of Human esophageal epithelium microbiopsies

NOTCH1 mutant clones occupy the majority of normal human esophagus by middle age, but are comparatively rare in esophageal cancers, suggesting NOTCH1 mutations may promote clonal expansion but impede carcinogenesis. Here we test this hypothesis. Visualizing and sequencing NOTCH1 mutant clones in aging normal human esophagus, reveals frequent biallelic mutations that block NOTCH1 signaling. In mouse esophagus, heterozygous Notch1 mutation confers a competitive advantage over wild type cells, an effect enhanced by loss of the second allele. Notch1 loss alters transcription but has minimal effects on epithelial structure and cell dynamics. In a carcinogenesis model, Notch1 mutations were less prevalent in tumors than normal epithelium. Deletion of Notch1 reduced tumor growth, an effect recapitulated by anti-NOTCH1 antibody treatment. We conclude that Notch1 mutations in normal epithelium are beneficial as wild type Notch1 promotes tumor expansion. NOTCH1 blockade has therapeutic potential in esophageal squamous tumors.

Dataset EGAD00001006969

Single-cell RNA sequencing data of peripheral blood mononuclear cells obtained from 30 ATL patients, 11 HTLV-1-infected asymptomatic carriers, and 4 healthy donors.

Single-cell RNA sequencing (scRNA-seq) data of peripheral blood mononuclear cells (PBMCs) obtained from 30 ATL patients (34 samples including 4 sequential ones), 11 HTLV-1-infected asymptomatic carriers, and 4 healthy donors.

Dataset EGAD00001007015

RNA-sequencing of meningiomas for integrative molecular classification.

Dataset EGAD00001007494

Personalized analysis of ctDNA for detection of molecular residual disease and recurrence in a cohort of surgically treated patients with head and neck squamous cell carcinoma

Despite advances in multimodal treatment, survival for patients with advanced head and neck squamous cell carcinoma (HNSCC) has improved only modestly. The recent advent of tumor-informed assays capable of detecting circulating cell-free tumor DNA (ctDNA) has enabled early detection of molecular residual disease (MRD) and recurrence following curative therapy. We assessed ctDNA in plasma from 76 and saliva from 54 HNSCC patients, respectively, who received primary curative-intent surgery.

Study EGAS50000001018

VariantMedium: Sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental confirmation data

This study contains whole-exome sequencing (WES) and results of targeted deep-sequencing data of three matched tumor and normal cell lines, with two technical WES replicates each. The calls by Mutect2, Strelka2, and VariantMedium were confirmed using targeted deep sequencing on Illumina Miseq The targeted deep sequencing was performed in three runs and the results are summarized under VCF files, with labels determined for 1663 point mutations and 201 insertion-deletions.

Study EGAS00001007633

Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease

A comprehensive clinical and multi-omic profiling for 199 patients with acute coronary syndrome (ACS), an acute subcategory of CAD, that we recruited in two major Israeli hospitals. We demonstrate that ACS has distinct serum metabolome and gut microbial signatures, as compared to a control cohort. Metabolic aberrations linked with microbiome and diet show a gradual trend with significant metabolite deviations in control participants with metabolic impairment suggesting their involvement in earlier dysmetabolic phases preceding clinically overt CAD.

Study EGAS00001005342

H3Africa - Consortium WGS

To address gaps in sequence data for some of the African populations being studied in H3Africa projects, additional sequencing has been carried out through various projects and the data are being made available. The first dataset includes a high coverage whole genome sequence dataset generated at the Baylor College of Medicine with samples provided by H3Africa PIs and collaborators, funded by the National Institutes of Health. The sequence data files are accompanied by minimal metadata, including country, ethnic group (where available) and sex.

Study EGAS00001005972

Chromosomal instability shapes the tumor microenvironment of oesophageal adenocarcinoma via a cGAS–chemokine–myeloid axis

This study employed whole-genome sequencing (WGS) to investigate genomic alterations in oesophagogastric adenocarcinoma, with a focus on mechanisms of chromosomal instability. Twelve tumour samples were analysed, including specimens obtained prior to neoadjuvant chemotherapy and at surgical resection. WGS was used to identify structural variants, quantify tumour mutational burden, and detect potential driver mutations across samples. The study aimed to correlate genomic measures of chromosomal instability with clinicopathological features to improve understanding of tumour biology.

Study EGAS50000001561

Privacy Notice for the Account User

Privacy Notice for EGA User Account This Privacy Notice explains 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. Note that this service collects personal data directly provided by the user, and also collects personal data from users that is provided by other organisations. 1. Who controls your personal data and how to contact us? European Genome- Phenome Archive - EGA offers a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects, jointly managed by European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI) and Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG). EMBL-EBI and CRG represent joint Data Controllers’ of processing of your personal data. They and their Data protection officers may be contacted for data protection queries and for exercising your rights under Section 8. You may contact EMBL-EBI, represented by dr. Thomas Keane, by: email at: tk2@ebi.ac.uk or post at EMBL-EBI, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridgeshire, UK. EMBL’s Data Protection Officer may be contacted by: telephone at +49 6221 387-8590, email at dpo@embl.org, or post at EMBL Heidelberg, Data protection officer, Meyerhofstraße 1, 69117 Heidelberg, Germany. You may contact CRG, whose EGA team is represented by dr. Jordi Rambla de Argila, by: email at jordi.rambla@crg.eu, or post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), Dr.Aiguader 88, PRBB Building, 08003 Barcelona, Spain. CRG Data protection officer may be contacted by: email at dpo@crg.eu post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, PRBB Building, 08003 Barcelona, Spain. 2. Which is the lawful basis for processing personal data? We process your personal data on the grounds of important public interest. For monitoring your activities on the website, we process your personal data on the grounds of important public interest. Such legal basis is found in Article 5(1)(a) of EMBL Internal Policy No 68 on General Data Protection (hereinafter IP 68), which is equivalent to Article 6 (1)(e) of the EU General Data Protection Regulation (hereinafter GDPR) and upon which personal data are processed for the achievement of the aims laid down in 1973 agreement establishing EMBL, such as the promotion of the cooperation in the fundamental research, in the development of advanced instrumentation and in advanced teaching in molecular biology and dissemination of information. 3. What personal data is collected from users of the service? How do we use this personal data? We collect the following personal data from you: Name Email address Title/Position Organisation Organisational affiliation Username and password (to authenticate access to the system) IP Address (for anonymous usage statistics) We process your personal data: to provide you with the authenticated access to the EGA service (opening and managing submission and distribution account), to publicly publish some aggregate data to facilitate scientific research (e.g. number of accounts, geographic distribution), to better understand the needs of the users and to guide future improvements of the service, to create anonymous usage statistics. If you do not provide us with your personal data we will not be able to open the user account and offer you our services or we will only provide you a subset of functionalities available within the service. 4. Who will have access to your personal data? The personal data will be disclosed to: Authorised staff in the data controller’s institutions acting on data controller`s behalf and instructions (for all user account data), Requested dataset Data access committee – DAC will have access to the name, email, organization, affiliation, title/position of the distribution user account, using it for their own purpose of granting access to their datasets. 5. Will your personal data be transferred to third countries (i.e. countries not part of EU/EEA) and/or international organisations? Distribution user account data are in the process of granting access disclosed to dataset(s) DAC, which might be a recipient in countries outside of the European Economic Area. Insofar as the second joint controller may be subject to GDPR, data transfer to and from the first joint controller (EMBL-EBI) is necessary for important reasons of public interest embedded in the aims of the EMBL and justified in the Article 9(4) of IP 68 (equivalent to Article 49(1)(d) of GDPR) read in conjunction with EMBL`s 1973 establishing agreement and Article 179(2) of the Treaty on the Functioning of the European Union. 6. How long do we keep your personal data? All data are stored for as long as you have the account open. Thereafter the storage is prolonged for as long as our service is live, even if you stop using our services. This prolongation is necessary for further scientific research, to ensure legal compliance and security and to facilitate internal and external audits it they arise. By contrast, the log files for the data categories related to anonymous usage statistics (raw web service logs) are processed only for 30 days and thereafter erased. 7. The joint Data Controllers provide these rights regarding your personal data You have the right to: Not be subject to decisions based solely on an automated processing of data (i.e. without human intervention) without you having your views taken into consideration. Request at reasonable intervals and without excessive delay or expense, information about the personal data processed about you. Under your request we will inform you in writing about, for example, the origin of the personal data or the preservation period. Request information to understand data processing activities when the results of these activities are applied to you. It must be clarified that rights under points 4 and 5 are only available whenever you need support whilst using our website. For other processing based on the grounds of important public interest you cannot exercise your rights to object, rectify or erase your personal data according to the Article 13(2)(a)(b) of IP 68 (equivalent to Article 17(3)(b)(d) and Article 21(6) of the GDPR). 8. Supervisory authority If you wish to complain against the processing of your personal data, you may do so by post at: EMBL Heidelberg, Data Protection Committee, Meyerhofstraße 1, 69117 Heidelberg, Germany, or Autoritat Catalana de Protecció de Dades (Catalan Data Protection Authority), C/Rosselló 214, Esc A, 1r 1a, Barcelona 08008, Spain. Published at: February 6, 2019

Documentation data-protection/privacy-notice/ega-user-account

Privacy Notice for Helpdesk service

Privacy Notice for EGA Helpdesk service This Privacy Notice explains 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. Note that this service collects personal data directly provided by the user, and also collects personal data from users that is provided by other organisations. 1. Who controls your personal data and how to contact us? European Genome- Phenome Archive - EGA offers a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects, jointly managed by European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI) and Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG). EMBL-EBI and CRG represent joint Data Controllers’ of processing of your personal data. They and their Data protection officers may be contacted for data protection queries and for exercising your rights under Section 8. You may contact EMBL-EBI, represented by dr. Thomas Keane, by: email at: tk2@ebi.ac.uk or post at EMBL-EBI, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridgeshire, UK. EMBL’s Data Protection Officer may be contacted by: telephone at +49 6221 387-8590, email at dpo@embl.org , or post at EMBL Heidelberg, Data protection officer, Meyerhofstraße 1, 69117 Heidelberg, Germany. You may contact CRG, whose EGA team is represented by dr. Jordi Rambla de Argila, by: email at jordi.rambla@crg.eu, or post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), Dr.Aiguader 88, PRBB Building, 08003 Barcelona, Spain. CRG Data protection officer may be contacted by: email at dpo@crg.eu post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, PRBB Building, 08003 Barcelona, Spain. 2. Which is the lawful basis for processing personal data? We process your personal data on the grounds of important public interest. For monitoring your activities on the website, we process your personal data on the grounds of important public interest. Such legal basis is found in Article 5(1)(a) of EMBL Internal Policy No 68 on General Data Protection (hereinafter IP 68), which is equivalent to Article 6 (1)(e) of the EU General Data Protection Regulation (hereinafter GDPR) and upon which personal data are processed for the achievement of the aims laid down in 1973 agreement establishing EMBL, such as the promotion of the cooperation in the fundamental research, in the development of advanced instrumentation and in advanced teaching in molecular biology and dissemination of information. 3. What personal data is collected from users of the service? How do we use this personal data? We collect the following personal data from users of the service: Name Email address Job title Date and time when the support request was sent We will use your personal data for the following purposes: To provide uninterrupted user access to the service To better understand the needs of the users and guide future improvements of the service To create anonymous usage statistics 4. Who will have access to your personal data? The personal data will be disclosed to: Authorised staff in the data controller’s institutions acting on data controller`s behalf and instructions. 5. Will your personal data be transferred to third countries (i.e. countries not part of EU/EEA) and/or international organisations? There are no personal data transfers to third countries or international organizations. 6. How long do we keep your personal data? Any personal data directly obtained from you will be retained as long as the service is live. Such duration serves the purpose of enabling scientific research and ensures legal compliance and facilitates internal and external audits if they arise. By contrast, the log files for the data categories related to anonymous usage statistics (raw web service logs) are processed only for 30 days and thereafter erased. 7. The joint Data Controllers provide these rights regarding your personal data You have the right to: Not be subject to decisions based solely on an automated processing of data (i.e. without human intervention) without you having your views taken into consideration. Request at reasonable intervals and without excessive delay or expense, information about the personal data processed about you. Under your request we will inform you in writing about, for example, the origin of the personal data or the preservation period. Request information to understand data processing activities when the results of these activities are applied to you. It must be clarified that rights under points 4 and 5 are only available whenever you need support whilst using our website. For other processing based on the grounds of important public interest you cannot exercise your rights to object, rectify or erase your personal data according to the Article 13(2)(a)(b) of IP 68 (equivalent to Article 17(3)(b)(d) and Article 21(6) of the GDPR). 8. Supervisory authority If you wish to complain against the processing of your personal data, you may do so by post at: EMBL Heidelberg, Data Protection Committee, Meyerhofstraße 1, 69117 Heidelberg, Germany, or Autoritat Catalana de Protecció de Dades (Catalan Data Protection Authority), C/Rosselló 214, Esc A, 1r 1a, Barcelona 08008, Spain. Published at: February 6, 2019

Documentation data-protection/privacy-notice/ega-helpdesk

Profiling RNA Translation in Pediatric Medulloblastoma

This study provides RNA-sequencing and ribosome profiling data for patient-derived cell lines and patient tissue samples for children with medulloblastoma. Ribosome profiling is a variant protocol of RNA-sequencing that directly sequences ribosome-bound RNA fragments only. Associated RNA-seq and Ribo-seq data obtained separately for some cancer cell lines can be found on the NCBI SRA as PRJNA957428. Samples were processed for poly-A mRNA sequencing using the Roche Kapa Kit. Ribosome profiling was performed as described in the manuscript referenced below (Hofman et al.) and based on the article by McGlincy et al., Methods (2017). Ribo-seq data were analyzed for sample quality using RiboseQC (Calviello, Nat Struct Mol Biol, 2020). These data were used to quantify P-sites of open reading frames. RNAseq and ribo-seq data were integrated and compared to determine translational efficiency values using TPM (Ribo-seq) over TPM (RNA-seq) as the metric. Ribo-seq data on 14 samples and RNAseq data on 21 samples derived from 16 fresh-frozen surgical samples for medulloblastoma and 5 autopsy samples are available through dbGaP. A second cohort of 4 medulloblastoma samples (RNAseq, Ribo-seq) related to this study can be found on the EGA at EGAS00001007426.

Study phs003446

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