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• Poland WES - The Genomic Map of Poland in Open Access

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Exome Sequencing of 450 samples (227 female, 223 male, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA Prep with Enrichment. Reference Genome: GRCh37.

  Dataset EGAD50000000130

• Exome sequencing of matching primary tumor and venous tumor thrombus (VTT) renal cell carcinoma (RCC) samples

  We performed multiregion whole exome sequencing of a total of 37 samples from five consecutive patients (normal tissue, n=5; primary tumors, n=16; tumor thrombi, n=16) to >35-fold target coverage. Matching primary tumor and venous tumor thrombus samples were analyzed. Four patients had a clear cell RCC, one patient had a poorly differentiated type II papillary RCC (RCC-VTT-04). The latter patient had a friable thrombus, the others were of solid consistency.

  Dataset EGAD00001004887

• Targeted Germline Sequencing of the Leeds Melanoma Cohort

  In this project we performed targeted sequencing of known and suspected melanoma susceptibility genes in a cohort of melanoma patients and matched controls. Our aim was to identify variants that predispose to melanoma development. The melanoma cases used in this study were population ascertained.

  Dataset EGAD00001007520

• Cell-free DNA and bone marrow samples from myelodysplastic syndromes

  We have assessed the molecular profile of a cohort of 70 patients with MDS by next-generation sequencing (NGS) using cfDNA and compared the results to paired bone marrow (BM) DNA.

  Dataset EGAD00001008567

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - dcc_release_24_dataset

  WGS sequencing for cases from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 24

  Dataset EGAD00001003292

• Mitochondrial-Nuclear Mutational Cross-Talk Drives Recurrence of Localized Prostate Cancer

  Prostate cancer remains the most prevalent non-skin cancer in men, but has a remarkably quiet mutational profile. Exome sequencing studies have revealed few recurrent somatic single nucleotide variants (SNVs). Whole-genome sequencing studies have not yet identified highly recurrent driver non-coding SNVs (ncSNVs) or genomic rearrangements (Grs). As a result, the underlying events that drive this frequent disease remain unknown. While mitochondrial mutations have been linked to several tumour types, including prostate cancer, their global frequency and impact has remained unknown. To determine if mitochondrial mutations might drive some prostate cancers, we analyzed the mitochondrial genomes of 216 tumours from patients with the most commonly diagnosed form of prostate cancer. We developed a pipeline that conservatively identified only mitochondrial SNVs (mitoSNVs) that differed in the heteroplasmy fraction as compared to their paired-normal by at least 20%. We identified several features of the mitochondrial genome that were correlated with nuclear genomic mutations, as well as features that were significantly associated with biochemical recurrence.

  Study EGAS00001001782

• Japanese RIKEN liver cancer WGS

  RIKEN collection of WGS reads for 269 liver cancer tumors and matched normal blood or liver tissue from 258 donors. In total there are 1864 paired fastq sets sequenced on Illumina HiSeq 2000 or Genome Analyzer II instruments with paired reads of 75–101 bp. Quality control and duplication removal has not been performed.

  Dataset EGAD00001001881

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

  Dataset EGAD00001010049

• The UCSF Low Grade Glioma Genome Project #2"

  Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor

  Dataset EGAD00001001305

• Single cell multi modal dataset of bone marrow samples from follicular lymphoma patients at diagnosis et one year post treatment

  This dataset contains transcriptome, BCR, TCR and HTO data at the single cell level from follicular lymphoma bone marrow samples at diagnosis (n=19) and one year post rituximab therapy (n=16).

  Dataset EGAD50000001843

• Clonal_analysis_Bcell_activation

  We developed a B cell stimulation protocol that allowed us to expand a smaller number of naive B cells in culture (2,000 B cells at day 0). On day 6, we performed single-cell RNA-and BCR-sequencing on the entire culture, preserving both clonal diversity and size.

  Dataset EGAD50000002114

• Single cell RNAseq, TCRseq, BCRseq and CITE-seq of deep cervical lymph nodes from Multiple sclerosis patients

  These raw sequencing dataset includes 10x Genomics 5' scRNA-seq, TCR-seq, BCR-seq, and CITE-seq profiles of cells isolated from the deep cervical lymph nodes of six Multiple sclerosis (MS) patients.

  Dataset EGAD50000001233

• Exome - Uveal Melanomas

  Whole exome sequencing on 11 uveal melanoma samples and corresponding germline samples. Libraries were prepared using the SureSelectXT2 Clinical Research Exome V2 kit (Agilent, 5190-9500 and G9621B). Paired-end libraries (2 x 100 bp) were sequenced on HiSeq 2000/2500 or NovaSeq 6000 instruments (Illumina).

  Dataset EGAD50000000767

• Whole Exome Sequencing Data of prDLBCL

  We used sequenced 34 prDLBCL samples using whole exome sequencing (WES) data to evaluate possible mutational signatures and driver mutations associated with the patient’s clinical and cytogenetic characteristics.

  Dataset EGAD50000000591

• Paired whole genome sequencing of tumor-control pairs of Thymic epithelial tumors -Additional Dataset

  Paired whole genome and exome sequencing of tumor-control pairs of Thymic epithelial tumors, additional samples with paired fastq files, sequenced on Illumina-HiSeq_X_Ten and using the Illumina_TruSeq_Nano_DNA kit.

  Dataset EGAD50000000325

• LITS

  Difference in gene expression values between case and control, log2 values. Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC) Post-genome Cohort taken up to eight years before brest cancer diagnosis. Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip, combined on identical nucleotide universal identifiers.

  Dataset EGAD00010001400

• Transcriptomic origins of mpMRI visibility

  We profiled the transcriptomes (RNA-sequencing) of 40 clinically significant invisible and visible tumors, all with ISUP Grade 2 disease and treated by radical prostatectomy. Twenty tumors were mpMRI invisible (PI-RADSv2: 1-2), while 20 tumors were visible (PI-RADsv2: 5).

  Dataset EGAD00001004397

• Exome sequencing in patients with Oliver McFarlane Syndrome

  In this work, using exome sequencing, we identified biallelic PNLPA6 mutations in patients with childhood blindness due to severe photoreceptor death and clinical features of Leber congenital amaurosis (LCA) and, interestingly, also of the rare Oliver McFarlane Syndrome

  Dataset EGAD00001001042

• Comparison with genomic measurement

  Heatrich-BS was performed on 5 healthy volunteers and 15 CRC patient cell-free DNA. The Heatrich-BS predicted tumor fractions were compared with tumor burden values obtained by genomic methods such as targeted amplicon sequencing and low pass sequencing.

  Dataset EGAD00001008715

• A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell ATAC sequencing

  This datasets contains raw sequencing fastq data of14 samples from 5 donors of single cell ATAC using10x genome technology of human postmenopausal fallopian tube and ovary tissues.

  Dataset EGAD00001010077

• WGS data of paediatric ETV6::RUNX1 B cell acute lymphoblastic leukemia (set3)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of two ETV6::RUNX1 ALL patients (ALLT-397, ALLK-132). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeqX Plus.

  Dataset EGAD50000002287

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of five B-other ALL patients (ALLT-327, ALLT-334, ALLT-357, ALLK-108, ALLT-361). Sequencing library was made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000002157

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of four B-other ALL patients (ALLT-321, ALLT-311, ALLT-314, ALLT-319). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using TruSeq DNA PCRfree library preparation kit v1. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000002156

• scRNA-seq and scATAC-seq data of human cardiac fibroblasts

  6 scRNA-seq and 4 scATAC-seq datasets on cardiac fibroblasts derived from two patients (P1, P2). The sequencing dataset consists of two control samples pretreated with vehicle (resting, only scRNA-seq data available); two samples stimulated with TGFb; and two samples pre-treated with KAT5 inhibitor, followed by stimulation with TGFb (iKAT5).

  Dataset EGAD50000001224

• APCDR AGV Project: Low coverage (4x-8x) sequence data from 3 African populations (VCFs)

  Low coverage (4x-8x) Illumina HiSeq curated sequence data from 3 African populations from the AGV project; 100 Baganda from Uganda (4x), 100 Zulu from South Africa (4x), and 120 Gumuz, Wolayta, Oromo, Somali and Amhara from Ethiopia (8x). Pre-processed, jointly called and filtered with GATK, refined with Beagle3, phased with SHAPEIT2.

  Dataset EGAD00001001663

• Hepatitis B Viral sequence reads

  Deep sequencing of viral samples (average ~9,000x coverage) from patients chronically infected with Hepatitis B (HBV). Whole HBV genome sequencing of 1467 patients (1102 in discovery and 365 in validation cohort) chronically infected with HBV at baseline. The patient population contained HBV genotypes A (98), B (285), C (716), D (356), E (7), and F (5) with 977 HBeAg-positive and 490 HBeAg-negative patients.

  Dataset EGAD00001005075

• V(D)J and 5' Gene Expression data on patients with aplastic anemia

  Chromium V(D)J and 5' Gene Expression platform (10X Genomics) was used to study patients with aplastic anemia. CD45+ cells from two patients (patient AA-3: 3 longitudinal samples from bone marrow and patient AA-4: 3 longitudinal samples from peripheral blood) were analysed. The raw data was processed using Cell Ranger 3.0.1 pipelines.

  Dataset EGAD00001006937

• Dataset contains all Single cell RNAseq data of human neurons from the study Bouwen et al Nat Comm 2025

  These documents contain the patch seq data presented in the Bouwen et al Nat Comm 2025. Human brain samples were gathered during surgery, neurons were isolated using patch clamp glass pipette. Isolated cells were processed using Smartseq2 pipeline, and sequenced using an Illumina 2500. Files are formatted in fastq format. There are a total of 12 patient samples, each with 2 replication runs.

  Dataset EGAD50000001979

• scRNAseq of fresh CRC punch biopsies

  The dataset includes single-cell RNAseq data generated by Plate-Seq technology from scDiscoveries. The dataset contains samples from a total of 5 different early CRC biobank patients (pt5, pt11, pt13, pt14, pt16) from 4 different sequencing runs. Punch biopsies of different regions of the tumor (Core, Invasive front and, if available, Adenoma) were FACS sorted onto plates prior to sequencing.

  Dataset EGAD50000002203

• DNA-seq FASTQ files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  Paired-end DNA-seq FASTQ files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). Each sample was multiplexed across flowcells and lanes, leading to a total number of 86 FASTQ files.

  Dataset EGAD00001005756

• Somatic mutations reveal embryonic genetic bottlenecks generating placental mosaicism

  The human placenta harbours chromosomal aberrations that are absent from the fetus in one to two percent of pregnancies. This confined mosaicism suggests that embryonic genetic bottlenecks exist, which phylogenetically segregate placental tissue. Here, we studied the somatic genetic landscape of human placentas by whole genome sequencing of 86 placental biopsies and of 106 microdissections.

  Dataset EGAD00001006337

• WGS Dataset of NGS based Aspergillus detection in liquid biopsies of immunocompromised patients

  The dataset comprises plasma and bronchoalveolar lavage (BAL) fluid samples from immunocompromised pediatric patients. Sequencing was performed on the NovaSeq 6000 platform, generating 2x150bp paired-end reads. The samples are provided as raw reads, post-demultiplexing, with no additional processing.

  Dataset EGAD00001015489

• ATAC sequencing of Treg cell subsets

  Within the investigator-initiated clinical trial Charact-IL-2 (ClinicalTrials.gov Identifier: NCT03312335), we treated 12 female systemic lupus erythematosus patients with low-dose interleukin-2. From this study we identified four distinct interleukin-2-driven regulatory T (Treg) cell subsets. This study aimed at defining chromatin accessability and predict transcriptional regulation of HLA-DR– CD38– Treg cells, HLA-DR+ CD38– Treg cells, HLA-DR– CD38+ Treg cells, and HLA-DR+ CD38+ Treg cells. Treg cell subsets were isolated from 500ml blood pooled from four healthy donors by flow cytometry sorting.

  Study EGAS50000000457

• Papua New Guinea Pangenome Project Data Access Policy

  This data policy applies to data access to the PNG15 and PNG16 sequencing data as well as derived genomic variant calls.

  Dac EGAC50000000674

• Mapping the breast cancer metastatic cascade onto circulating tumour DNA using genetic and epigenetic clonal tracking

  Dataset EGAD00001005507

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

  spatial transcriptomics

  Dataset EGAD00001015262

• Multiple paralogues and recombination mechanisms contribute to the high incidence of 22q11.2 Deletion Syndrome

  To enable haplotype-specific assembly and rearrangement mapping in LCR22 clusters, we combined fiber-FISH optical mapping with whole genome (ultra-)long read sequencing or rearrangement-specific long-range PCR on 254 duos families (22q11.2DS patient and parent-of-origin) comprising several different LCR22-mediated rearrangements.

  Study EGAS50000000601

• Adenoma development in familial adenomatous polyposis and MUTYH‐associated polyposis: somatic landscape and driver genes

  Familial adenomatous polyposis (FAP) and MUTYH‐associated polyposis (MAP) are inherited disorders associated with multiple colorectal adenomas that lead to a very high risk of colorectal cancer. The somatic mutations that drive adenoma development in these conditions have not been investigated comprehensively. In this study we performed analysis of paired colorectal adenoma and normal tissue DNA from individuals with FAP or MAP, sequencing 14 adenoma whole exomes (eight MAP, six FAP), 55 adenoma targeted exomes (33 MAP, 22 FAP) and germline DNA from each patient.

  Dataset EGAD00001004332

• Single-cell RNA-seq of matched primary GBM tumours, patient-derived organoids, and gliomasphere lines

  Single-cell RNA-seq of primary GBM tumours and matched patient-derived organoids and gliomasphere lines. Obtained using the 10X Genomics single-cell 3' expression solution (v2 chemistry). Primary samples and PDOs from 12 tumours from 10 patients (10 primary, two recurrent), and gliomasphere lines from a subset of five tumours. Samples were obtained from two spatially distinct regions of each tumour.

  Dataset EGAD00001007936

• single cell RNA sequencing of resting and IAV-stimulated mononuclear phagocytes of Africans and Europeans

  CD14+ monocytes from 4 African and 4 Europeans individuals with varying degree of ex-vivo susceptibility to Influenza, were either stimulated with Influenza A virus, or left resting. Cells from all 16 samples were collected at 4 time points (0, 2, 4, 6h post infection), and pooled across 13 libraries. Samples were processed on the 10x chromium with 3' reagents kits, V3 chemistry and sequenced with Hiseq X ten.

  Dataset EGAD00001006938

• Comprehensive molecular profiling with whole-exome sequencing (WES) and RNA sequencing (RNA-seq) of PDX tumors

  To identify biomarkers of the antitumor efficacy of molecular targeted therapies, patient-derived xenograft (PDX) mouse models established from 52 patients with solid tumors were treated.

  Study JGAS000707

• Whone genome DNA methylation profile

  Primary human CD4+ naive T cells were cultured in vitro and sorted based on the defined number of division steps which they have undergone. Of those populations (division 0/div4/div6) EMseq data were generated to assess the whole-genome DNA methylation profile. 2 independent experiments with 2 different donors were conducted

  Dataset EGAD50000001815

• Single-cell RNA sequencing of acute myeloid leukemia patients

  Single-cell RNA sequencing was performed on bone marrow mononuclear cells from 8 acute myeloid leukemia patients at diagnosis. The profiling was performed using 10x Genomics 3' (5 samples) and 5' (3 samples) platforms. The raw data are available as fastq files.

  Dataset EGAD00001006173

• Single cell RNA-sequencing of treatment naïve PDAC patient samples

  Single cell RNA-sequencing of treatment naïve PDAC patient samples. We have 10 samples, sequenced using the 10X genomics chromium platform with 3 prime chemistry. We are submitting FASTQ files representing the index files (I1), Read1 (R1) and Read2 (R2).

  Dataset EGAD00001008961

• Paired RNA-Seq of Tumor Organoids from glioblastoma, 2 patients, treated with different small molecule inhibitors

  Tumor Organoids from glioblastoma, 2 patients, treated with different small molecule inhibitors. Paired RNA-Seq was done on NovaSeq 6000 with the Illumina TruSeq stranded mRNA Kit. The small inhibitors GW2580, BLZ945 and PLX3397 were used. DMSO was used as control.

  Dataset EGAD00001011274

• Single-Cell Mitochondrial Variant Profiling via TAMITO-seq

  This dataset focuses on mitochondrial variant detection using the TAMITO-seq protocol. A pre-designed mitochondrial panel (https://designer.missionbio.com/catalogpanels/Virtual-mtDNA) was spiked into the scTAMseq workflow targeting 200 CpGs and 167 genotyping loci. Data were generated from a peripheral blood sample of a healthy donor, donor X.2, multiplexed with data from another donor.

  Dataset EGAD00001015494

• ATAC_TALL_t_14_16_translocation

  ATAC-sequence for patients with t(14;16) translocated T-ALL and control T-ALL patients

  Dataset EGAD50000001784

• RNAseq data

  Bulk RNAseq data for IMbrave151 (N = 96), including raw counts, transcript per million (TPM), and voom transformed values.

  Dataset EGAD50000000568

• CRC cell line RNA-seq

  RNA-Seq data for C32, CACO2, CL11, HT29, SW403, SW948 MSS CRC cell lines and HCEC-1CT normal colon cell line

  Dataset EGAD50000000297

• CRC cell line ATAC-seq

  ATAC-Seq data for C32, CACO2, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines, and HCEC-1CT normal colon cell line

  Dataset EGAD50000000296

• Sequencing data for oesophageal and related samples - OACs release 5 (RNA)

  Dataset EGAD00001005383

• Sequencing data for oesophageal and related samples - BOs release 6 (RNA)

  Dataset EGAD00001005377

• Sequencing data for oesophageal and related samples - Normals release 6 (RNA)

  Dataset EGAD00001005376

• Sequencing data for oesophageal and related samples - Normals release 2 (RNA)

  Dataset EGAD00001003838

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - pilot normal and pre/post-chemo

  Dataset EGAD00001000704

• Human Embryonic Multi-tissue ChIP-seq (Manchester)

  Histone ChIP-seq of 13 human embryonic tissues from weeks 6-8 of gestation. H3K4me3, H3K27me3 and H3K27ac. Biological replicates (n=2) for 11 tissues. Tissues (n): Brain (2); Retinal Pigmented Epithelium (eye)(2); Palate(2); Tongue (1); Left ventricle (heart)(2); Lung(2); Liver(2); Pancreas (2*); Stomach(1); Upper limb (2); Lower limb (2); Adrenal gland (2); Kidney (2)

  Dataset EGAD00001004335

• Clinal phenotype dataset

  Clinical data from IMvigor010: Clinical data include race, sex, baseline ecog, tumor stage, node status, prior neoadjuvant, PD-L1 status, number lymph nodes resected, pridis, arm, overall survival and disease free survival for 809 patients across IMvigor010.

  Dataset EGAD00001007576

• WXS of 147 lung cancer patients treated with immunotherapy

  We first attempted to predict MHC-binding neoantigens at high accuracy with convolutional neural networks. This prediction model outperformed previous methods in > 70% of test cases. Importantly, our method remarkably increased the predictive value of neoantigen load especially in combination with known resistance parameters. We then developed a classifier that can predict resistance from point mutations that are deleterious to protein function. Notably, genes involved in the adaptive immune response, cytokine signaling,and EGFR signaling held high explanatory power. Furthermore, when integrated with our neoantigen profiling, these anti-immunogenic mutations revealed significantly higher predictive power than known resistance factors.

  Study EGAS00001003781

• Mutation signatures in melanocytic nevi reveal characteristics of defective DNA repair

  Nevi are common benign melanocytic neoplasms that can be found on any skin location and share many of the genomic hallmarks of melanoma. In our recent report involving whole-exome sequencing of acquired nevi (Stark et al., 2018), ultra-violet radiation (UVR) related somatic mutation signatures (“signature 7”) (Alexandrov et al., 2013) were frequently observed in all lesions that were located on sun-exposed sites. In the study presented herein, we sought to investigate whether an independent Spanish cohort (Valencia, Spain) of minimally sun exposed nevi had genomic features consistent with our previous findings.

  Study EGAS00001004274

• Metatranscriptomic Sequencing of Pulmonary Fluid in Immunocompromised Children

  Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. In version 1.0 of this study, we performed RNA-based next generation sequencing (mNGS) on 41 lower respiratory samples collected from 34 children. We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Potential pathogens were detected in half of samples previously negative by clinical diagnostics. In version 2.0, we included an addition 278 samples from 229 pediatric stem cell transplant patients with pulmonary disease.

  Study phs001684

• Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin

  Study EGAS00001004660

• STAG1-ChIP-Seq of STAG2-mutated and cohesin wildtype adult AMLs

  ChIPseq targeting the cohesin subunit STAG1 in STAG2-mutated AMLs or cohesin wildtype AMLs

  Dataset EGAD00001011206

• Plasma whole genome sequencing from patients with stage IV colorectal cancer and microsatellite instability

  This study aims to explore genomic features of cancer in plasma WGS data from patients with advanced colorectal cancer. Cell-free DNA (cfDNA) was extracted from plasma using the QIAamp Circulating Nucleic Acid Kit. Libraries were prepared with 5 to 250 ng of cfDNA using the NEBNext DNA Library Prep Kit.

  Study EGAS00001006377

• 24 Chordoma samples (WES,WGS)

  Case series of the rare tumor entity chordoma. 9 cases sequenced with Whole Exome Sequencing (WES) and 2 cases sequenced with Whole Genome Sequencing (WGS) were recruited from the personalized oncology program NCT-MASTER/DKTK-MASTER at the German Cancer Research Center. One of the WES patients was re-sequenced at a later time point when he relapsed, this resequencing was done by WGS. Therefore there are 11 patients, one of which with two samples, all of which were sequenced with matched normal controls, amounting to a total number of 24 NGS samples.

  Dataset EGAD00001004825

• RNA-seq of high-grade serous ovarian cancer in long-term survivors (MOCOG study)

  RNA-seq dataset of high-grade serous ovarian cancer (HGSC) tumours from long-term survivors performed as part of the Multidisciplinary Ovarian Cancer Outcomes Group (MOCOG) study. The dataset includes fastq files from 56 HGSC tumours (53 primary tumours and 3 recurrent tumours) from 53 long-term survivor patients. Libraries were generated using the Illumina Stranded mRNA Prep and 150 bp paired-end sequencing was performed to a minimum of 100 million reads on Illumina NovaSeq 6000 instruments.

  Dataset EGAD00001008537

• STREP GENE: Genetics and Severe Streptococcal Infections

  This study investigated host genetic susceptibility to invasive group A streptococcal disease in the UK. Cases were either survivors recruited retrospectively through a patient group or identified from the a tissue bank at Imperial College London. Those recruited through the patient group had survived an episode of invasive GAS disease at a UK hospital since 1980 with microbiological confirmation obtained either through Public Health England or from the treating hospital. Those identified from the tissue bank had been diagnosed with invasive GAS disease at the Hammersmith Hospital, London, UK, since 2006. All cases aged less than 65 years without long-term medical conditions genome-wide genotyped using either the Illumina HumanCore or the Global Screening Array platform.

  Study EGAS00001003421

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set5)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of four hyperdiploid ALL patients (ALLT-502, ALLK-130, ALLK-137, ALLK-139). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq X Plus.

  Dataset EGAD50000002428

• Case Report: Pre-Clinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma

  We report a rare case of a young patient (VENUS 167) initially diagnosed with grade 1 endometrioid endometrial cancer, which, following endocrine treatment, presented with mixed aggressive carcinoma with three distinct histologic patterns: grade 1 endometrioid, large cell neuroendocrine, and undifferentiated carcinoma. The NGS fastq data are WES, RNAseq and ATAC

  Dataset EGAD50000002397

• Spatial CosMx Human 6K

  we profiled the cellular composition and TME spatial organization in 4 ICB-resistant HCC patients using single-cell spatial transcriptomics (CosMx Human 6K Discovery Panel). We identified 397 fields-of-view (0.51 mm by 0.51 mm) of hematoxylin and eosin (H&E)-defined tumor and stromal regions followed by cell segmentation using a nuclear stain plus 4 protein markers, yielding 485,209 high-confidence single-cell profiles that were subsequently categorized into distinct cell types based on marker gene annotation.

  Dataset EGAD50000002052

• M116 Whole Genome Sequencing

  Whole Genome Sequencing (WGS) was performed using DNA extracted from M116’s blood, saliva, and urine samples. DNA was fragmented to 350 bp, followed by library preparation, paired-end 150 bp WGS, and variant calling, all conducted by Novogene®. Sequencing was carried out with a 10X coverage (approximately 60 Gb and 200 million reads per sample) using the NovaSeq X Plus platform (Illumina). Files types included in this dataset are raw Fastq files.

  Dataset EGAD50000001286

• Whole-genome cfDNA TAPS sequencing data from 91 people with various types of cancer and from non-cancer controls

  TAPS data in the form of BAM files from 214 samples: plasma (at 80x) and matched germline (at 30x) pairs from 61 cancer and 30 non-cancer subjects, fresh-frozen matched tumour biopsies (at 80x) from 16 subjects, as well as several follow-up plasma samples (at 80x) from 10 subjects with colorectal cancer.

  Dataset EGAD50000000996

• ICR TYA WES

  Whole exome sequencing of high grade gliomas occurring in teenagers and young adults between the ages of 13 and 30. This study combines methylation array profiling, whole exome sequencing and fusion panel sequencing to provide an integrated molecular description of brain tumours in this age group. Dataset contains 96 BAM files aligned with BWA to GRCh37 from 88 tumours. Tumour DNA was isolated from FFPE material in most cases. 8 germline sequences from peripheral blood DNA are also included.

  Dataset EGAD50000000904

• The spatio-temporal evolution of lymph node spread in early breast cancer

  Set of multi-region sequenced breast cancer primary samples, lymph nodes and ctDNA. We collected samples from 11 breast cancer patients with lymph node involvement but no sign of distant metastasis. We performed a mix of whole-exome sequencing, targeted capture sequencing, and whole-genome sequencing of primary tumour samples and lymph nodes, as well as targeted capture sequencing of circulating tumour DNA.

  Dataset EGAD00001004122

• Bulk RNASeq on CD8+CD69+CD103+ and CD8+CD69+CD103- T cells form breast cancer.

  CD8+CD69+CD103+ and CD8+CD69+CD103- T cells were flow sorted from 1 primary triple negative breast cancer, 1 primary HER2 amplified breast cancer, and 1 triple negative liver metastasis. Prior to flow sorting, fresh tumor samples were digested to produce single cell homogenates on the day of surgery. Following RNA extraction, RNASeq was performed using polyA selection.

  Dataset EGAD00001003964

• BulkTCR-sequencing data from different human intestinal CD8 T cell subsets.

  5000 cells of each subset of CD8 T cells (CD103-KLRG1+, CD103-KLRG1- and CD103+ from LP and CD103+ IELs) were sorted into tubes. A modified SMART protocol was used in first-strand cDNA synthesis, and TCRalpha / TCRbeta genes were amplified in two rounds of semi-nested PCR reaction, following the method described in detail in Risnes et al., 2018.

  Dataset EGAD00001005049

• AT-AML samples dataset

  Serial samples from one AT-AML patient as described in publication Goldgraben et al Pediatric Blood & Cancer 2020. Whole exome sequencing of a AT-'germline' blood sample, one bone marrow sample (at AML diagnosis) and 3 AML blood samples. Library preped using the Illumina Nextera Rapid Capture Exome Enrichment Kit, and sequenced as PE150 on HiSeq4000. Provided: 5 BAM files (GRCh37); 2 VCF analyses (germline and somatic)

  Dataset EGAD00001006090

• Assessment of cannabidiol and Δ9-tetrahydrocannabiol in mouse models of medulloblastoma

  These data were used in the following publication: Andradas, C.; Byrne, J.; Kuchibhotla, M.; Ancliffe, M.; Jones, A.C.; Carline, B.; Hii, H.; Truong, A.; Storer, L.C.D.; Ritzmann, T.A.; et al. Assessment of Cannabidiol and delta9-Tetrahydrocannabiol in Mouse Models of Medulloblastoma and Ependymoma. Cancers 2021, 13, 330. https://doi.org/10.3390/cancers13020330 There are 4 paired-end RNA-seq samples from paediatric brain cancer cell lines.

  Dataset EGAD00001006923

• NEC

  This multi-centre, non-randomized, open-label, phase II trial (NCT03016338), assessed niraparib monotherapy (cohort 1, C1), or niraparib and dostarlimab (cohort 2, C2) in patients with recurrent serous or endometrioid endometrial carcinoma. The primary endpoint was clinical benefit rate (CBR). Secondary outcomes were safety and objective response rate (ORR). Translational research was an exploratory outcome. Potential biomarkers were evaluated in archival tissue by immunohistochemistry and next generation sequencing panel. Feasibility of liquid biopsy by ctDNA was assessed.

  Dataset EGAD00001010056

• Single-cell RNA and TCR sequencing of 37 PBMC pools of advanced HCC patients.

  scRNAseq and scTCRseq of serial peripheral blood mononuclear cell (PBMC) samples (n=72) taken at various timepoints before and during treatment (Week 0 (W0), Week 3 (W3), Week 6 (W6)). PBMC samples were pooled together into 37 pools, loading 2 or three samples per lane in the 10X Genomics chip, in equal proportions, according to a pre-designed pooling matrix.

  Dataset EGAD00001011345

• Chromosome Segregation Errors Promote a Diverse Spectrum of Simple and Complex Genomic Rearrangements

  Cancer genomes are frequently characterized by numerical and structural karyotypic abnormalities. Here we combined an inducible centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy we term ‘CEN-SELECT’, and show that single-chromosome missegregation during cell division can directly drive a broad spectrum of structural rearrangement types. Cytogenetic profiling revealed that missegregated chromosomes are 120-fold more susceptible to developing seven major categories of structural variants, including translocations, insertions, deletions, and reassembly into chromothriptically rearranged chromosomes. Whole-genome sequencing of clones with genetically propagatable derivative chromosomes identified complex rearrangements and copy-number alterations that can result in gene inactivation or extrachromosomal gene amplification. We conclude that chromosome segregation errors are sufficient to drive extensive structural variation that recapitulates those commonly associated with human cancers.

  Dataset EGAD00001004163

• Prostate Cancer and Normal Adjacent Prostate RNA-seq samples, NGS-ProToCol

  The dataset "Prostate Cancer and Normal Adjacent Prostate RNA-seq samples, NGS-ProToCol" includes 41 Normal Adjacent Prostate and 51 ribo-depleted Prostate Cancer RNA-seq samples. ---- Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data Youri Hoogstrate, Malgorzata A. Komor, René Böttcher, Job van Riet, Harmen J. G. van de Werken, Stef van Lieshout, Ralf Hoffmann, Evert van den Broek, Anne S. Bolijn, Natasja Dits, Daoud Sie, David van der Meer, Floor Pepers, Chris H. Bangma, Geert J. L. H. van Leenders, Marcel Smid, Pim French, John W.M. Martens, Wilbert van Workum, Peter J. van der Spek, Bart Janssen, Eric Caldenhoven, Christian Rausch, Mark de Jong, Andrew P. Stubbs, Gerrit A. Meijer, Remond J.A. Fijneman, Guido Jenster

  Study EGAS00001002816

• Shallow Whole-Genome Sequencing of Plasma ctDNA in Relapsed/Refractory Germ Cell Tumors

  This dataset comprises shallow whole-genome sequencing data (~3× coverage) of circulating tumor DNA extracted from baseline and on-treatment plasma samples of patients with relapsed or refractory germ cell tumors treated with salvage high-dose chemotherapy. Libraries were generated from 20 ng of cfDNA using the KAPA Hyper Prep protocol with unique dual indexing and sequenced on an Illumina NovaSeq 6000 platform to enable genome-wide copy number and biomarker analyses associated with treatment response and clinical outcome.

  Dataset EGAD50000002183

• Quantitative Exploratory Proteomics Analysis of Glioblastoma in Initial and Recurrent Tumors

  Shotgun Proteomics; Glioblastoma samples from 11 patients were obtained at initial and recurrent tumor stages. Proteins were extracted, identified and quantified via tandem mass spectrometry based on a TMT isobaric labelling approach. Quatitative proteomics reveals 146 differentially abundant proteins using a patient-matched statistical modelling. Analysis of proteolytic processing reveals differential proteolytic patterns in recurrent tumors. Proteogenomics reveals the presense of 30 single-amino acid variants present in glioblastoma tumor and 1 of those as increased in recurrent tumor.

  Dataset EGAD00010002350

• Dataset Plasma-seq

  We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9).

  Dataset EGAD00001000364

• Genomic and Transcriptomic Profile of Paired Primary-Metastasis Colorectal Tumors

  Samples encompass primary colorectal tumors, adjacent normal colonic mucosa and metastasis of 12 patients, collected by Medical Pathologists from surgically removed specimens. Normal mucosa samples were taken more than 2 cm away from the tumor. Tissues were embedded in optimal cutting temperature (OCT) medium, snapshot frozen in liquid nitrogen within 40 minutes of collection and preserved at -80ºC. Samples were collected between June 2010 and October 2017 as part of a prospective biobanking project.

  Dataset EGAD00001007686

• Ither NB in Organoids WGS dataset - Exploring high-throughput drug sensitivity testing in neuroblastoma cell lines and patient-derived tumor organoids in the era of precision medicine

  Ither NB in Organoids WGS dataset - We aimed to launch an online repository integrating genomics and transcriptomics with high-throughput drug screening (HTS) of nineteen commonly used neuroblastoma cell lines and fourteen generated neuroblastoma patient-derived organoids (NBL-PDOs) to improve identification of molecularly matched therapies and support clinical uptake.

  Dataset EGAD00001010282

• The evolution of ovarian high grade serous carcinoma from STIC lesions

  We performed shallow whole genome sequencing of normal fallopian tube, stroma, p53 signatures, STIL/STIC, invasive and metastasis carcinoma from 5 high grade serous carcinoma cases.

  Study EGAS50000000360

• Targeted capture sequencing data from 107 classical Hodgkin Lymphoma tumors and 25 corresponding normal samples.

  To delineate the mutational landscape of classical Hodgkin Lymphoma targeted sequencing using a capture panel ("medistinal lymphoma panel") targeting 217 genes was performed on HRS cells isolated from classical Hodgkin Lymphoma tumors (n=107) and corresponding normal samples (n=25)

  Dataset EGAD50000002163

• Long-read Nanopore data EVOFLUx

  Bam files with all reads covering 976 fCpGs identified in Gabbutt and Duran-Ferrer 2025 to develop the EVOFLUx methodology. These include 10 samples, 6 normal B cells, and 2 CLL patients developing RT.

  Dataset EGAD50000001697

• Single-cell RNA-sequencing data of human iPSC-derived (hiPSC-derived) astrocytes, both alone and in co-culture with neurons, to define the molecular response of astrocytes to misfolded alpha-synuclein.

  Samples were derived from an human iPSC-derived astrocyte line, both alone and in co-culture with neurons +/- alpha-synuclein oligomer treatment.

  Dataset EGAD50000001110

• Distinct immune cell infiltration patterns in pancreatic ductal adenocarcinoma (PDAC) exhibit divergent immune cell selection and immunosuppressive mechanisms

  To elucidate the heterogeneity of tumour immune cell infiltration, we performed single cell RNAseq sequencing on CD45+ cells enriched from matched fresh tumour tissue following surgical resection of 12 treatment-naïve patients and matched PBMCs.

  Dataset EGAD50000001008

• EPITREAT pilot cohort

  Benchmark data set containing five tumor/normal pairs of non-small cell lung cancer (NSCLC) patients. Tissue pairs were screened with bisulfite (BS) sequencing, MeDIP methylation enrichment sequencing and RNA sequencing in order to identify differentially methylated and expressed spots in the genomes.

  Dataset EGAD00001003116

• 5WGS and 35WES sample pairs belongs to COCA-CN

  There are 5WGS and 35WES sample pairs from the first affiliated hospital of kunming medical university, which belongs to ICGC projects COCA-CN.

  Dataset EGAD00001003456

• Exome Sequencing of Spanish Patients with rare genetic diseases.

  Whole Exome sequencing of a set of Spanish patients suffering rare genetic diseases. The set consists of 3 patients, two were diagnosed with Aniridia (ANI-0006 and ANI-0023) and another one was diagnosed with Retinitis Pigmentosa (RP-0247).

  Dataset EGAD00001005498

• WES_localized non-small cell lung cancer (540 samples)_MDACC

  Whole exome sequencing of tumors and paired adjacent uninvolved tissues from 222 early stage NSCLC patients, in order to identify genomic drivers present in early-stage non-small cell lung cancer and determine the overall tumor mutational burden in early-stage non-small cell lung cancer.

  Dataset EGAD00001005956

• Single-Nuclei RNA-seq of healthy (post-mortem) and temporal lobe epilepsy (biopsy) subjects.

  To identify dysfunctional neuronal subtypes underlying seizure activity in the human brain, we have performed single-nucleus transcriptomics analysis of >110,000 neuronal transcriptomes derived from temporal cortex samples of multiple temporal lobe epilepsy and non-epileptic subjects.

  Dataset EGAD00001006575

• T cell receptors of pathogenic CD4 T cells isolated by using distinct phenotypic markers in celiac disease

  The dataset contains rearranged TCR‐α and TCR‐β genes of Ttet+/Tpat+, Ttet-/Tpat+ and Ttet-/Tpat- CD4+ cells from gut biopsies (exvivo) or that of T cell clones generated from gut biopsies (invitro) from 12 CeD patients.

  Dataset EGAD00001008098

• TransplantLines Gut Microbiome study

  The TransplantLines Gut Microbiome study includes raw data generated by shotgun metagenomic sequencing of fecal samples of solid organ transplant recipients and basic phenotypes (age and sex, BMI).

  Dataset EGAD00001008907

• A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA

  This datasets contains raw sequencing fastq data of 17 samples from 7 donors of single cell RNA using10x genome technology of human postmenopausal fallopian tube and ovary tissues.

  Dataset EGAD00001010076

• Sequencing Data of Leukemic Samples

  Sequencing data of leukemic samples included in study. Including WES, WGS and targeted sequencing files from patients at diagnosis, remission and at relapse. The dataset includes samples from 52 pediatric patients, totaling 311 samples.

  Dataset EGAD00001015662