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• V4 panel bait design test (2018-03-07)

  Targeted gene screen of FFPEs, cell lines and primary CRC tumours for testing the new V4 Colorectal gene panel. . This dataset contains all the data available for this study on 2018-03-07.

  Dataset EGAD00001004001

• BLUEPRINT release August 2015, DNase-Hypersensitivity for monocyte, on genome GRCh38

  DNase-Hypersensitivity data for 2 monocyte sample(s). 4 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820

  Dataset EGAD00001001560

• BLUEPRINT release January 2015, RNA-Seq for monocyte

  RNA-Seq data for 8 monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001191

• BLUEPRINT release January 2015, DNase-Hypersensitivity for macrophage

  DNase-Hypersensitivity data for 14 macrophage sample(s). 18 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001001198

• DATA FILES FOR Ph-likeALL WES

  DATA FILES FOR Ph-likeALL WES

  Dataset EGAD00001001054

• BLUEPRINT release August 2014, DNase-Hypersensitivity for macrophage

  DNase-Hypersensitivity data for 1 macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001000931

• WGS data for ependymomas (5 tumor-control pairs)

  Whole genome sequencing data for ependymomas (5 tumor-control pairs). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).

  Dataset EGAD00001000950

• WES/WXS data for ependymomas (42 tumor-control pairs)

  Whole exome sequencing data for ependymomas (42 tumor-control pairs). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).

  Dataset EGAD00001000951

• Carcinoid study - WGS dataset

  Fernandez-Cuesta et al., 2014, Nature Communication, Whole genome sequencing was performed using a read length of 2x100 bp for all samples. On average, 110 Gb of sequence were produced per sample, aiming a mean coverage of 30x for both tumour and matched normal.

  Dataset EGAD00001000813

• Whole Exome Sequencing of healthy Spanish individuals - Fastq files

  The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population.

  Dataset EGAD00001001012

• BLUEPRINT September 2016, ATAC-seq for tonsil, on Genome GRCh38

  ATAC-seq data for 7 sample(s) from tonsil, on Genome GRCh38. 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002708

• Whole-genome sequencing data for inflammatory breast cancer patients

  This study reports the whole-genome sequencing data for 20 inflammatory breast cancer patients, each of whom has one normal blood sample and one breast tumor sample. Overall, there are 40 files included in this study, in the format of BAM.

  Dataset EGAD00001005749

• single cell RNASEQ files for Mullighan BiTE RNASEQ3

  single cell RNASEQ files for Mullighan BiTE RNASEQ3 paper titled "Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia"

  Dataset EGAD00001005733

• H3Africa ReMAC Shotgun Metagenomic Phenotype

  Phenotype data for shotgun metagenomic sequencing data of nasopharyngeal fluid for studying nasopharyngeal colonization dynamics with Streptococcus pneumoniae and associated antimicrobial-resistance in a South African birth cohort. https://www.ebi.ac.uk/ena/data/view/PRJEB37312

  Dataset EGAD00001006244

• Breast implant-associated anaplastic large cell lymphoma shallow whole genome sequencing for copy number analysis and Whole exome sequencing data.

  Shallow whole genome sequencing of 29 BIA-ALCL patients for copy number analysis and 24 Alk-negative ALCL samples as control cohort. 7 Whole exome sequencing BIA-ALCL samples.

  Dataset EGAD00001006433

• Clinical data

  This dataset contains demographic, histology, PDL1 IHC, TMB and outcome data (PFS and ORR) for 836 patients, 823 of which had RNAseq, 715 had FMI, with 702 patients having both. The dataset also includes xCell deconvolution scores for patients with RNAseq data.

  Dataset EGAD00001006617

• Genome-wide data for 11 Roma individuals

  This dataset includes genome-wide autosomal array data for 11 Iberian Roma individuals used in the Merchero project.

  Dataset EGAD00001007773

• A Single-cell Atlas of Progressive TKI Resistance in Chronic Myeloid Leukemia

  57 Bone marrow specimens for 5 healthy bone marrow and 24 CML samples profiled with 10X scRNA-seq 5' upon separation using MACS for CD34.

  Dataset EGAD00001007946

• CBD-RAW-REPERTOIRE-B: B cell bulk repertoire sequence files

  fastq and filtered fasta files for B-cell receptor sequencing. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007960

• Single-cell RNA-seq counts and merged data for 28 Hodgkin lymphomas and 5 reactive lymph nodes

  This dataset contains raw count data (10X CellRanger) for 28 Hodgkin lymphoma samples and 5 reactive lymph nodes, and merged data from all samples (RData object) including cell cluster assignments.

  Dataset EGAD00001008270

• RNA-seq for identification of neotranscripts

  This dataset contains RNA-seq data (Fastq files of paired-end data) of 18 patient tumors used for identification of neotranscripts in 18 different types of fusion-driven sarcomas and other cancers as described in Vibert et al., Mol Cell 2022 (PMID: 35550257)

  Dataset EGAD00001008832

• Genotyping of GM samples

  This dataset contains a vcf file for 99 GM individuals genotyped on the Illumina HumanOmni2.5 array . The vcf file is originated after imputation (IMPUTE2) and filtering for minor allele frequency MAF≥0.05, imputation confidence score INFO of >0.4 and Hardy-Weinberg Equilibrium (HWE) p>1e-06, yielding ~6.3 million variants.

  Dataset EGAD00001010255

• 16S bacterial amplicon sequencing data for Guangzhou cohort

  16S bacterial amplicon sequencing data for Guangzhou cohort

  Dataset EGAD00001010268

• WGS of NPC268_Tumor and NPC268_Cell_line

  This dataset contains WGS data in the form of BAM files for NPC268 - "Tumor" derived from snap-frozen tissue while "Cell line" derived from late passage NPC268 cell line. Extracted DNA was sent for 100x and 60x WGS with Novogene via Apical Scientific Sdn Bhd.

  Dataset EGAD00001010292

• Oncoprint GSCCs

  This dataset contains DNA sequencing data from 7 GSCCs (data for BT569 is not available). We performed focused exome sequencing (43 most mutated genes in GBM), combined with OneSeq analysis (Agilent) on the GSCCs and identified both shared and GSCC-specific mutations. For CME038, whole genome sequencing was performed.

  Dataset EGAD00001011276

• SNP Genotype Data: Subpopulations of Filipino, Malaysian, and Papua New Guinea

  In the context of the study 'Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G,' this repository contains 11 VCF files. Each file includes genetic data from 22 autosomes, representing distinct subpopulations. The subpopulations are as follows: Malaysian: Aeta (15 samples) Agta (11 samples) Batak (10 samples) Mamanwa (6 samples) Filipino: Jehai (13 samples) Kintaq (6 samples) Temiar (5 samples) Papua New Guinea: Highlands (2 samples) Koinambe (10 samples) Kosipe (10 samples) Sepik (2 samples) The numbers in parentheses indicate the sample size for each respective subpopulation.

  Study EGAS50000000044

• Genomic Sequencing of Lung Adenocarcinoma

  Lung carcinoma is the leading cause of cancer death in the United States and world-wide; lung adenocarcinoma is the most common cause of lung cancer. Pilot studies of lung adenocarcinoma with hybrid-capture based whole exome sequencing will enable us to identify new targets for therapy and improve diagnosis. We will analyze a blend of whole exome and whole genome sequencing data as well as copy number and somatic mutation calls for 200 tumor and matched normal controls. When completed this study will represent the most comprehensive lung adenocarcinoma genome dataset to date.

  Study phs000488

• Performance Characteristics of Selective Targeted Enrichment in Genetic Diagnostic Testing

  The Nex-StoCT and ACMG recommend that validation of an NGS-based diagnostic test include performance test characteristics for assay accuracy, analytical sensitivity and specificity, reproducibility and repeatability. To measure these parameters for the GEDi capture and sequencing test, 4 samples (three randomly selected patient samples and the NA12878 HapMap sample) were prepared and sequenced in triplicate on each of three separate days. We also performed WES and SNP array genotyping analyses of these 4 samples using Agilent V4+UTR whole exome enrichment kit and Illumina Omni 2.5 SNP arrays, respectively.

  Study phs000798

• Transcriptome and TCR Sequencing of T Cells from Metastectomies

  T cells were sorted from metastatic tumors (colon, rectal, breast, anal, melanoma primary histologies) following tumor dissociation and single-cell sequencing was performed (RNAseq and TCRseq). For samples from tumors that had been previously studied, cells were analyzed comparing known neoantigen-reactive TCR-expressing cells to other T cells. For samples without previously identified neoantigen reactivity, TCRs were predicted on the basis of T cell transcriptomic states. To determine candidate neoantigen screening, exome and RNA sequencing were performed on fragments of matched tumors from which T cells were sequenced   

  Study phs002748

• The Vaginal Microbiome in Reproductive Age Women

  The focus of this cross-sectional study was to characterize the vaginal microbiota of asymptomatic, sexually-active, and reproductive-age women representing four self-reported ethnic groups (White, Black, Asian, and Hispanic). Each woman self-collected two mid-vaginal swabs. The first swab was used to prepare a vaginal smear for Nugent gram stain analysis. The second swab was used for DNA extraction, 16S rRNA gene amplicon sequencing, and detection of Candida albicans. In addition, participants measured vaginal pH and completed a detailed questionnaire on sexual health and behaviors.

  Study phs001909

• Identification of Putative Neoantigens in Stage III Melanoma

  This study of three metastatic melanoma patients utilized exome sequencing and RNA sequencing to help identify putative neoantigen peptides that could be further validated by standard immunological assays before design of a personalized vaccine. For each set of neoantigens identified and verified by standard assays, we designed GMP peptides that correspond to the top neoantigens, then used these to condition dendritic cell isolates from each patient. The conditioned dendritic cells were used as the vaccine in three rounds of vaccination, followed by monitoring for T cell memory response to each of the neoantigens.

  Study phs001005

• Fetal Chorioamniotic Membranes Show Molecular Changes in Placenta Previa and Placenta Accreta Spectrum

  Placenta previa and the placenta accreta spectrum (PAS) are understudied pregnancy disorders with serious consequences for both mother and infant. To better understand the molecular and cellular etiologies of these diseases, we performed 3SEQ of formalin-fixed paraffin-embedded (FFPE) fetal chorioamniotic membrane samples from PAS, previa, and gestationally age-matched spontaneous pre-term birth samples to identify molecule signatures of these diseases. These samples were subsequently validated using a second validation cohort of previa, PAS, and control patients. FFPE archival samples provide opportunities for retrospective molecular investigation of many diseases.

  Study phs002075

• Patient Microbiome and Surgical Site Infection in Spine Surgery

  Single center, prospective cohort study on the contribution of the preoperative patient microbiome and resistome to surgical site infection (SSI) and resistance to surgical antibiotic prophylaxis in spine surgery. The samples in this entry comprise a subset of patients for whom paired preoperative microbiome samples and postoperative wound culture isolates were obtained. These samples were analyzed by Illumina-based sequencing of metagenomic libraries enriched for the SSI pathogen of interest using the GenCap-Seq methodology (PMID: 36121157) to identify instances of endogenous infection with strains present in the preoperative microbiome.

  Study phs003358

• NHLBI TOPMed: Women's Health Initiative (WHI)

  This is Whole Genome Sequencing data from the TOPMed participation of the Women's Health Initiative. Approximately 11,100 subjects were involved in this study: approximately 1,100 cases of VTE, 4,000 cases of ischemic stroke, 900 cases of hemorrhagic stroke, and 5,100 controls. Summary level phenotypes for the WHI Cohort study participants can be viewed at the top-level study page phs000200 WHI Cohort. Individual level phenotype data and molecular data for all WHI top-level study and substudies are available by requesting Authorized Access to the WHI Cohort study phs000200.

  Study phs001237

• A Comprehensive Genomic Study of Pediatric Malignancy

  Malignancy remains the leading cause of disease-related death in children. DNA sequencing studies have shown a paucity of actionable genomic alterations and a low mutation burden across pediatric cancers at diagnosis. We perform a comprehensive genomic and epigenomic analysis of pediatric tumor and normal tissues using next-generation sequencing to identify molecular fingerprints and targets for diagnosis, prognosis, and development of novel therapeutic methods. This study also represents one of the largest of its type to date and provides a rich genomic dataset for the pediatric cancer research community.

  Study phs001928

• FEGA Sweden Helpdesk

  FEGA Sweden is an archive for storing and sharing all kinds of data resulting from biomedical research projects. As a national node of the Federated European Genome-phenome Archive (FEGA), we enable researchers to store their data in Sweden in a way that meets the requirements of the General Data Protection Regulation (GDPR). Any data submitted to the archive is subject to controlled access, meaning access to the data only will be granted after a formal application procedure. Using FEGA Sweden for storing and sharing data is free of charge for academic users affiliated with a Swedish university. However, the university must have a signed Data Processing Agreement (DPA) with Uppsala University. The current list of universities with a signed DPA can be found here: https://fega.nbis.se/submission/complying-with-gdpr.html. 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. Contact the FEGA Sweden Helpdesk at fega-sweden@nbis.se for further questions.

  Dac EGAC50000000077

• Evaluation of Local Response of Prostate Cancer to Irradiation Using Multiparametric MRI and MR-Guided Biopsies

  The purpose of this study was to determine the rate of local recurrence in patients with intermediate and high risk prostate cancer treated with radiotherapy. In this study, multiparametric MRI was first performed, and biopsy tissue was acquired from cancerous regions detected on MRI. Blood samples were also taken. DNA and RNA were extracted from tissue taken at baseline. DNA was used for whole exome sequencing (WES). RNA was used for gene expression microarray. Each patient then received radiation therapy with androgen deprivation therapy.

  Study phs001821

• Identification of new molecular targets with profiling of malignant mesothelioma

  Aims: Malignant mesothelioma which is associated with asbestos exposure is highly aggressive and refractory to conventional therapeutic modalities. The aim of this study is identification of new targets for molecular target therapy by next generation sequencing and application of the genomic data to new diagnostic and therapeutic strategies for malignant mesothelioma patients. Methods: We extracted genomic DNAs from surgical specimens or established mesothelioma cell lines from Japanese malignant mesothelioma patients. We also extracted control DNAs from peripheral blood of the same patients. We performed whole exome sequencing using these DNAs.

  Study JGAS000062

• Exome Sequencing of familial and sporadic Meniere disease patients

  This study aims to characterize the genetic architecture of spanish patients diagnosed with Meniere disease (MD), focusing on both familial (FMD) and sporadic (SMD) forms, by analyzing coding variants. Whole-exome sequencing was performed on these patients, and variants were called and annotated using the nf-core/sarek bioinformatics pipeline, including alignment to the GRCh38 reference genome. The resulting data provide a curated resource for investigating the potential genetic contribution to the pathophysiology of MD. All data will be made available for reuse under controlled access.

  Study EGAS50000001178

• Sequencing of in vitro generated macrophages and T cells

  Monocyte derived macrophages were polarised into M1 or M2 using IFNg+ ILP or IL-4 respectively (n =4) . Pan T cells were cultured with or without IL-2 for 4 days (n=4 - 6). Pan T cells were co-cultured with THP1 tumour cells for 20 hours in the presence or absence of ImmTAC molecules and in the presence or absence of M2 macrophages. Sorted T cells and macrophage populations prior and post co-culture were analysed by bulk RNA sequencing (60 million reads per sample) using the Illumina NovaSeq system.

  Study EGAS50000000837

• Single-nucleus chromatin accessibility profiling of human fetal liver hematopoiesis (10x Multiome)

  The fetal liver is the primary haematopoietic organ during early human development, yet the timing and regulatory mechanisms governing blood formation remain incompletely understood. To define the cellular, transcriptional, and epigenetic changes underlying human fetal liver hematopoiesis over development, we generated a high-resolution, time-resolved single-nucleus multiome atlas of human fetal liver spanning 5–18 post-conception weeks (PCW) for CD45+CD235- cells. In total, 308,021 high-quality nuclei from 53 donors were profiled using paired chromatin accessibility and transcriptomic modalities. This study is for the chromatin accessibility.

  Study EGAS50000001632

• Single-nucleus gene expression profiling of human fetal liver hematopoiesis (10x Multiome)

  The fetal liver is the primary haematopoietic organ during early human development, yet the timing and regulatory mechanisms governing blood formation remain incompletely understood. To define the cellular, transcriptional, and epigenetic changes underlying human fetal liver hematopoiesis over development, we generated a high-resolution, time-resolved single-nucleus multiome atlas of human fetal liver spanning 5–18 post-conception weeks (PCW) for CD45+CD235- cells. In total, 308,021 high-quality nuclei from 53 donors were profiled using paired chromatin accessibility and transcriptomic modalities. This study is for the gene expression.

  Study EGAS50000001631

• Epigenetic profiling of primary human thymocyte subsets

  Dynamic changes of the DNA methylation (DNAmeth) landscape drive differentiation of mature T lymphocytes. However, the role of DNAmeth-mediated regulation in thymocyte development remains unclear. Thus, we generated genome-wide DNAmeth and transcriptomic profiles of eight defined, ex vivo isolated primary human thymocyte subsets, to assess the epigenetic remodling taking place during human thymic T cell development. The generated data may also serve as a reference for the analysis of T cell-based inborn errors of immunity or for quality control purposes of in vitro generated T cell populations.

  Study EGAS50000001106

• Papua New Guinean Lowlanders Dataset

  High-coverage whole genome sequences were collected to study patterns of genomic variation across the southern lowland of Papua New Guinea. This region has experienced an extremely complex demographic history, including repeated bouts of admixture with archaic and modern human groups. This dataset reports whole genome sequences for 41 individuals from this region. Particular attention has been paid in the original study to genomic signals that are informative for population history, including admixture with archaic hominins and the role of modern human admixture during the late Pleistocene and Holocene.

  Study EGAS50000000033

• Comprehensive peripheral blood immunoprofiling reveals five immunotypes with immunotherapy response characteristics in cancer patients

  The lack of comprehensive diagnostics and consensus analytical models for evaluating the status of a patient’s immune system has hindered a wider adoption of immunoprofiling for treatment monitoring and response prediction in cancer patients. To address this unmet need, we developed an immunoprofiling platform that uses multiparameter flow cytometry and RNA-seq to characterize immune cell heterogeneity in the peripheral blood of healthy donors and patients with advanced cancers. Using unsupervised clustering, we identified five immunotypes with unique distributions of different cell types, and gene expression profiles.

  Study EGAS50000000286

• T cell repertorie analysis fom a Spanish cohort of mild and severe cases of COVID-19 recovered patients

  The cohort included 98 mild and 75 severe cases with a median age of 53 years. We amplified and sequenced the T Cell Receptor (TCR β) chain complementary determining region 3 (CDR3b) and performed bioinformatic analyses to assess repertoire diversity, clonality, allelic usage, and epitope affinity CDR3b clustering. CDR3b sequences were amplified by multiplex PCR and sequenced by Illumina. The resulting raw files were processed for clonotype assembly, filtering for coding clonotypes, removal of non-TRB alleles, and downsampling.

  Study EGAS50000000331

• Single-cell targeted DNA-sequencing and protein sequencing

  We performed single-cell targeted DNA sequencing (MissionBio) on 13 high hyperdiploid B-ALL patients at diagnosis to study the genetic heterogeneity. For a number of patients single-cell surface protein antibody sequencing was added (DAB-seq) to better characterize the different cell types. Furthermore, additional samples during treatment were collected and analysed for some patients. In this way we want to study the clonal heterogeneity of these B-ALL samples, based both on mutations and CNVs, and identify resistant clones that could be targeted after relapse.

  Study EGAS50000000580

• Arcagen - Extra-pulmonary neuroendocrine tumour or cancer grade 3 (NET / NEC G3) domain

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here were are submitting the dataset that contains NGS files from patients with extra-pulmonary neuroendocrine tumour or cancer grade 3 (NET / NEC G3) (n=85).

  Study EGAS50000000644

• Genome-wide NanoRCS of cfDNA from plasma of healthy individuals

  Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant molecules, extremely sensitive sequencing methods are required. We adapted a new technique, NanoRCS, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule for genome-wide sequencing, and applied this to plasma of healthy controls.

  Study EGAS50000000695

• Human scMultiome data (GEX and ATAC paired) from CD34+ Bone Marrow (BM) and mobilized peripheral blood (mPB), including CITE-Seq data from mPB CD34+ samples

  We analyzed healthy CD34+ samples from Bone Marrow (BM) and mobilized Peripheral Blood (mPB) in gene therapy experiments within the X-PAND project. BM samples underwent scMultiome analysis, providing paired GEX and ATAC data. For the mPB samples, both scMultiome and CITE-Seq were performed on the same donors, offering additional protein marker information. These datasets allow for an in-depth exploration of chromatin accessibility, gene expression, and surface protein profiling in hematopoietic progenitor cells from healthy donors.

  Study EGAS50000000750