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• CASCADE germline whole genome sequencing data

  High-coverage whole genome sequencing data (median coverage: 23.5X, range: 14.14X-32.62X)) from white blood cells of the patients from isolated buffy coat of the blood drawn postmortem from patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.

  Dataset EGAD00001009493

• DNA Methylation Profiles of T2D and Control Subjects from the GCAT Cohort Using EPIC v2

  This dataset contains DNA methylation data from 400 individuals (200 Type 2 Diabetes cases and 200 controls) from the GCAT (Genomes for Life) cohort. The methylation profiling was performed using the Illumina Infinium MethylationEPIC v2.0 BeadChip, which offers comprehensive coverage of over 850,000 CpG sites. Data are provided in IDAT file format, enabling raw signal-level analysis and downstream processing.

  Dataset EGAD00010002740

• Visium Spatial tramscriptomics data set

  This data set contains raw FASTQ files and processed files of spatial transcriptomics of 6 EMD samples collected from MM patients. The processed files contain the h5 expression matrices, the Image of the Visium slide, and a TSV of spatial coordinates. Patients included in this data set are PT01A, PT01B, PT02, PT03, PT07, PT08, PT09, PT10, and PT11.

  Dataset EGAD50000000336

• Elucidation of molecular mechanisms of tumorigenesis and development of diagnoses and treatments based on comprehensive genomic analyses in pancreatic tumors, duodenal tumors and biliary tumors

  We performed whole genome and whole exome sequencing analyses of pancreatic tumors, duodenal tumors and biliary tumors and investigated the molecular mechanisms of tumorigenesis based on the comprehensive genome profiling.

  Study JGAS000359

• DNA-seq BAM files from 16 patients affected by acute intermittent porphyria

  Paired-end BAM files from 16 patients affected by acute intermittent porphyria. Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). FASTQ files were processed at the CNAG (Barcelona) using the GEM short-read aligner on the human genome version hs37d5, producing a total of 16 BAM files.

  Dataset EGAD00001006951

• Resolving the Full Spectrum of Human Genome Variation using Linked-Reads

  This dataset contains Linked-Read Whole Exome Sequencing (lrWES) from individuals with known disease-causing variants. The dataset comprises of 30 samples from 10 donors, where multiple samples from the same donor reflect experimental differences assaying the effect of input DNA length on coverage and phasing. Raw data (i.e. BAM files) and variant analysis (i.e. VCF files) for each sample are included in this dataset.

  Dataset EGAD00001004319

• Papua New Guinean Genome Altitude Project Dataset 1

  The PGAP dataset 1 includes 81 whole genome sequences for Papua New Guinean individuals sampled in Daru (N=38) and Mount Wilhelm (N=43). DNA was extrated from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGAP dataset provides Fastq, mapped cram files (GRCh38) and phenotype measurements.

  Dataset EGAD00001010143

• WGS data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors - MUMC

  The dataset includes cram files from WGS of 2 NEN tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue from the corresponding patients are included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.

  Dataset EGAD00001009988

• Tumor Profiler Project - OV cell-free DNA data

  The dataset contains amplicon sequencing data from 48 samples from 35 different patients with ovarian cancers. Cell free DNA was collected from plasma. Sequencing was performed on an Ion Torrent platform and the sequencing data is provided in bam format.

  Dataset EGAD50000001410

• Long-read whole genome sequencing as a tool for variant detection in inherited retinal dystrophies

  WGS sequencing using nanopore long reads sequencing. These data is used for the diagnosis of patients with inherited retinal dystrophies.

  Study EGAS50000000846

• RNA-seq

  RNA sequencing files that were used in our study. The cohort was composed of 39 cases of RNA sequencing data. RNA-seq library was prepared with rRNA depletion method, and the sequence was performed using DNBSEQ sequencer.

  Dataset EGAD50000000971

• Ultra-long whole-genome and Cas9-targeted nanopore sequencing of fibroblasts: FSHD, BAMS, healthy controls

  Data from the D4Z4End2End study (Xiao et al. 2025), for genetic and epigenetic analysis of the D4Z4 macrosatellite in health and disease.

  Dataset EGAD50000001551

• Sequence variation of rs774984872G>T

  This dataset contains the genotypes status of rs774984872G>T, a loss of function variant in ANGPTL8. 8 individuals had the reference allele (G/G), 5 were heterozygous (G/T) and 1 was a knock out (T/T).

  Dataset EGAD50000002135

• WGS for 21 samples

  This dataset contains whole-genome sequencing (WGS) data from 14 acute leukemia cases of the newly identified FOXF1/FENDRR ALL subtype, including diagnosis or relapse samples, as well as 7 matched germline samples. All the 21 samples are in bam file type.

  Dataset EGAD50000001790

• Whole-exome sequencing of breast cancer metastasis and corresponding blood samples

  Whole-exome sequencing (WES) of 216 breast cancer metastasis-normal pairs from patients who underwent a biopsy in the context of the SAFIR01, SAFIR02, SHIVA or MOSCATO prospective trials (France).

  Dataset EGAD00001002747

• Sporadic and endemic Burkitt lymphoma have frequent FOXO1 mutations but distinct hotspots in the AKT recognition motif

  Sample set of 74 whole-exome sequencing samples from sporadic Burkitt lymphoma patients from the UK. 33 of these samples have matched constitutional data, giving a total number of 107 samples

  Dataset EGAD00001005105

• Data files for PCGP SJACT WES

  This dataset contains WES files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing.

  Dataset EGAD00001002679

• CNA vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004440

• PSC-IBD-CRC

  Formalin-fixed, paraffin-embedded samples from 19 PSC-IBD-CRCs, 15 adjacent (non-tumour) mucosa samples and 18 non-mucosal DNA samples were collected via the nationwide network and registry of histo- and cytopathology in the Netherlands (PALGA). DNA was extracted for molecular analysis.

  Dataset EGAD00001006226

• CNA vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  CNA calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004442

• SNV vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  SNV calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004432

• SNV vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004434

• CNA vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  CNA calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004443

• SNV vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  SNV calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004431

• CNA vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004441

• Whole Transcriptome Sequencing

  RNA-seq data of 15 snap-frozen tissue of peritoneal mesothelioma. The strand specific RNA library prepared using TruSeq (Illumina) and pair-end sequencing performed in Illumina HiSeq 4000. The datasets contains paired fastq files for each of 15 tumor samples.

  Dataset EGAD00001004504

• SNV vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  SNV calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004433

• The natural history of clonal haematopoiesis: phase 6 targeted

  Deep targeted sequencing of 56 genes associated with clonal haematopoiesis and haematological malignancy in peripheral blood-derived DNA from 11 older adults, each previously sampled 2-5 times over the preceding ~13 years.

  Dataset EGAD00001007683

• Exome sequencing of 7-member healthy family (father, mother, their three biological daughters and monozygotic twin sons)

  The dataset contains exome sequencing data of seven healthy family members, all in FASTQ format. The samples were taken from peripheral blood mononuclear cells. Furthermore, corresponding proteomics data are available as well.

  Dataset EGAD00001004949

• Whole-genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from long-term survivors.

  Whole-genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from long-term survivors performed as part of the Multidisciplinary Ovarian Cancer Outcomes Group (MOCOG) study. The dataset includes fastq files from 58 HGSC tumours (53 primary tumours and 5 recurrent tumours) and 53 matched normals from 53 long-term survivor patients. Sequence libraries were generated from tumour and matched normal genomic DNA using the KAPA HyperPrep PCR-free library preparation kit (Roche) according to manufacturer’s instructions. Sequencing was carried out by the Kinghorn Centre for Clinical Genomics Sequencing Laboratory (Sydney, Australia) on the HiSeq X Ten System (Illumina) to a minimum base coverage of 30-fold for normal DNA and 60-fold for tumour DNA samples.

  Dataset EGAD00001009398

• ScRNA-seq of 6 human FL

  Follicular lymphoma (FL) is an indolent cancer of mature B-cells but carries increased risk of transformation to a more aggressive histology over time. We present here comprehensive profiling both tumor and immune compartments in 6 diagnostic FL biopsies by single-cell RNA sequencing. This confirmed results from 155 FL tumors characterized by mass cytometry (CyTOF) which revealed two distinct evolutionary trajectories with disparate risk of transformation and alternate biologies.

  Dataset EGAD00001007691

• Genome-wide 5-mC profiling in plasma of metastatic ALK-rearranged non-small cell lung cancer (NSCLC) patients receiving tyrosine kinase inhibitor therapy.

  Longitudinal plasma samples (n = 79) of 21 ALK-positive NSCLC patients and 13 healthy donors were collected alongside 15 ALK-positive tumor tissue and 10 healthy lung tissue specimens. All plasma and tissue samples were analyzed by cell-free DNA methylation immunoprecipitation sequencing to generate genome-wide 5-mC profiles. Paired cfMeDIP on NextSeq 550 using KAPA Hyper Prep Kit was done.

  Dataset EGAD00001009412

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence

  ChIP-seq for AR, FOXA1 and H3K27ac in primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment. RNA-seq expression data of primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment.

  Dataset EGAD00001008562

• Methylation profiling of human lung fibroblasts in COPD

  Primary lung fibroblast were isolated from well-matched control donors (no COPD, n=3) and patients with COPD (GOLD stage I-IV, n=8). Genomic DNA of cultured human lung fibroblast was isolated at passage 3, fragmented by tagmentation, and subjected to bisulfite treatment. 100 bp paired-end reads were generated from DNA libraries on Illumina HiSeq2500 platform.

  Dataset EGAD00001009406

• Whole blood RNA-sequencing of covid-19 patients and healthy controls

  This dataset contains whole blood transcriptome data generated from 93 patients with COVID-19 across a range of severities and 23 healthy controls. All patients were PCR positive for SARS-CoV-2 and disease severity ranged from asymptomatic to severe disease requiring ventilation. Individuals without symptoms, or with mild symptoms, were recruited from routine screening of healthcare workers, while COVID-19 patients were recruited at or soon after admission to Addenbrooke’s or Royal Papworth hospitals. Blood samples were taken at recruitment and then again four weeks later. Further details of the cohort and the generation of the RNA-Sequencing data can be obtained from Bergamaschi, L. et al. Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease. Immunity 54, 1257-1275 e8 (2021).

  Dataset EGAD00001007776

• Raw data (FASTQ) and processed data (VCF) of 7 patient-derived Sézary Syndrome (SS) cells

  We profile the whole-transcriptome (bulk RNAseq) of 7 patient-derived Sézary Syndrome (SS) cells to identify expression patterns, functional programs and expressed gene mutations that may provide clues on new therapeutic options for SS patients. The libraries were sequenced on NextSeq500 (Illumina) with a paired-end read length of 2x75bp. Raw data (FASTQ) and obtained processed data (VCF) including all called raw variants are available.

  Dataset EGAD50000001646

• Targeted exome DNA sequencing of matched brain tumor-normal pairs (ICGC)

  Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.

  Dataset EGAD00001000699

• Evolution of four ER+ breast cancers

  The evolution of four breast cancers was analyzed using longitudinal samples collected over 2-15 years. Whole-genome sequencing and single-cell RNA-Seq were used to analyze evolution. We have deposited VCF files for SNV, indel, and structural variant calls from WGS data, and a text file showing transcripts per million (TPM) expression for the single-cell RNA-Seq data.

  Dataset EGAD00001003303

• RNA sequencing of multiple tumor biopsies and patient-derived spheroids from five colorectal cancer patients (BAM files)

  Whole transcriptome, strand-specific RNA-seq libraries were prepared from total RNA purified using RNeasy mini kit (Qiagen) using Ribo-Zero technology (Epicentre, an Illumina company) for depletion of rRNA followed by library preparation using ScriptSeq ScriptSeq RNA-Seq Library preparation Kit from Illumina. The paired raw sequence reads were processed using TopHat2 and mapped to the humane reference genome HG19.

  Dataset EGAD00001003820

• RNA-seq of hepatocellular carcinoma xenografts established from needle biopsies

  RNA-sequencing of human hepatocellular carcinoma biopsies (n=14), 44 HCC xenografts derived from 11 HCC biopsies and 3 lymphoma xenografts derived from 3 HCC biopsies. RNA-sequencing was performed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (lllumina). SR126 sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry according to the manufacturer’s guidelines.

  Dataset EGAD00001004541

• sWGS of OV cell lines for ACN rascal study

  This dataset contains 60 .bam files of shallow WGS data (~0.1X) from ovarian cancer cell lines. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008118

• RNAseq and ATACseq data

  RNAseq and ATACseq data for the FMF patients and healthy control. The RNAseq data was sequenced on a BGI MGI G400 machine, with PE100 reads. ATAC-seq libraries were prepared with Illumina Nextera primers and sequenced on NovaSeq 6000 platform with 50bp paired-end sequencing, where each sample was sequenced to approximate 60 million reads.

  Dataset EGAD00001010304

• Single cell RNA sequencing of colorectal cancer

  To understand intrinsic cancer cell signatures and the surrounding microenvironemt and their interactions, we performed single-cell RNA sequencing on 63,689 cells from 23 patients with 23 primary colorectal cancer and 10 matched normal mucosa samples. Analyzing of primary colorectal cancer and normal mucosa samples show a comprehensive cellular landscape of colon cancer, which is a valuable resource for the development of therapeutic strategies.

  Dataset EGAD00001005198

• Total RNA sequencing from the TNT trial (NCT00532727)

  Primary tumours from 186 TNT participants (13 matched recurrences) were profiled using total RNA-sequencing. Four transcriptional DDR-related and 25 immune-related signatures were evaluated. We assessed their association with objective-response-rate (ORR) and progression-free-survival (PFS) and performed conditional inference forest clustering to integrate multi-modal data.

  Study EGAS00001007398

• Germline genome sequencing samples from the Hereditary Cancer Syndromes (ICCon) Cancer Flagship

  A prospective study of individuals with suspicion of a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or was not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing and a comprehensive cancer virtual gene panel analysis were undertaken.

  Study EGAS00001007045

• VCF file, post sample QC

  This VCF contains the full sequence data post QC. This consists of 41,911 individuals. All polymorphic sites are present in this VCF.

  Dataset EGAD00001000623

• GabonDiv_SNP_genotyping

  Genome-wide SNP genotyping data for 1,235 western Africans by Illumina HumanOmniExpress-12 array, used in the EGAS00001002078 study

  Dataset EGAD00010001209

• VCF dataset of Colorectal Cancer Synthetic genomes

  This dataset contains genomic variants data from VCF files of four patients synthetically generated in the EOSC4Cancer project

  Dataset EGAD50000000314

• HIV Viremic Non-Progressors (VNPs) and HIV Progressors Data Access Committee

  Data Access Committe for the project: Analyzing exome sequencing in HIV Viremic Non-Progressors (VNPs) and HIV Progressors

  Dac EGAC50000000062

• Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

  spatial transcriptomics

  Dataset EGAD00001015262