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• The genomic landscape of childhood acute lymphoblastic leukaemia with intrachromosomal amplification of chromosome 21 (iAMP21-ALL)

  Intrachromosomal amplification of chromosome 21 (iAMP21) results from breakage-fusion-bridge cycles and chromothripsis defines a cytogenetic subgroup of childhood B-cell precursor acute lymphoblastic leukemia (B-ALL) cases associated with a poor prognosis. To systematically characterize the mechanism of somatic alternations in iAMP21, we perform integrated genomic, cytogenetic and transcriptomic analysis of 128 cases.

  Study EGAS00001004998

• Intellance-2: omics data on recurrent glioblastoma patients participating in the Intellance-2 clinical trial, prior to treatment.

  This study contains omics data from patients from the Intellance-2 clinical trial, in which effectiveness of ABT414 in EGFR amplified recurrent glioblastoma patients was tested. Patients were randomly assigned to one of three arms: (1) standard of care treatement (TMZ or CCNU), (2) Only ABT414 and (3) ABT414 + (TMZ|CCNU)

  Study EGAS00001005437

• High-powered complex trait association mapping through whole genome sequencing of a selected subpopulation of the INGI-Val Borbera genetic isolate

  The VBSEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Up to 100 Val Borbera samples will be sequenced to a 6x depth.

  Dataset EGAD00001000730

• Genome and transcriptome sequence data from a metastatic clear cell carcinoma of the ovary patient

  Genome and transcriptome sequence data from a metastatic clear cell carcinoma of the ovary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005906

• COVID-19 progression and resolution in common variable immunodeficiency patients

  116,958 single-cell transcriptomes from samples of peripheral blood mononuclear cells (PBMCs) from five CVID patients at three distinct stages of the SARS-CoV-2 infection: 1) baseline, before viral infection, 2) progression, during viral infection, and 3) convalescence, once the viral infection had been resolved and the patient was PCR negative. CVID patients were under regular immunoglobulin replacement therapy and displayed only mild symptoms during SARS-CoV-2 infection.

  Dataset EGAD00001009773

• Single cell RNA-seq, TCR-seq and bulk TCR-seq on HNSCC patients treated with ICB

  We performed single cell RNA- and TCR-sequencing (10x Genomics) on immune infiltrates (CD45+ cells) from 18 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021). Viable immune cells were isolated from pre-treatment and post-treatment primary tumor biopsies of 10 patients responding (1 partial pathological response and 9 major pathological responses) and 7 patients non-responding to anti-PD-1 and anti-CTLA4 combination immunotherapy. One patient treated with anti-PD-1 monotherapy (1 major pathological response) was included in the dataset. Bulk TCR-seq was performed on the PBMCs of responding patients, pre- and post-treatment.

  Dataset EGAD00001011311

• RNA-seq dataset of Characterization of UV DNA damage in B-cell precursor acute lymphoblastic leukemia

  Extensive characterization of mutational signature SBS7a in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) samples. We aimed to describe the presentation of SBS7a in BCP-ALL, identify other pediatric cancers presenting with SBS7a, look into the link of SBS7a and UV-light in the context of BCP-ALL and cancers with provable UV exposure, and pinpoint when SBS7a was acquired.

  Dataset EGAD00001015598

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library for library A95728A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 844 samples; filetype=bam

  Dataset EGAD00001004758

• A108879A

  Whole genome sequencing for single cells for library A108879A 1567 cells; filetype=bam

  Dataset EGAD00001007093

• A96165A

  Whole genome sequencing for single cells for library A96165A 779 samples; filetype=bam

  Dataset EGAD00001008239

• A96228B

  Whole genome sequencing for single cells for library A96228B 1125 samples; filetype=bam

  Dataset EGAD00001008218

• A95707A

  Whole genome sequencing for single cells for library A95707A 1359 samples; filetype=bam

  Dataset EGAD00001008228

• A95732B

  Whole genome sequencing for single cells for library A95732B 655 samples; filetype=bam

  Dataset EGAD00001008231

• A96145A

  Whole genome sequencing for single cells for library A96145A 642 samples; filetype=bam

  Dataset EGAD00001008232

• A96149A

  Whole genome sequencing for single cells for library A96149A 751 samples; filetype=bam

  Dataset EGAD00001008234

• A96155B

  Whole genome sequencing for single cells for library A96155B 1028 samples; filetype=bam

  Dataset EGAD00001008236

• A96157C

  Whole genome sequencing for single cells for library A96157C 938 samples; filetype=bam

  Dataset EGAD00001008237

• A96174B

  Whole genome sequencing for single cells for library A96174B 1447 samples; filetype=bam

  Dataset EGAD00001008242

• A96177B

  Whole genome sequencing for single cells for library A96177B 683 samples; filetype=bam

  Dataset EGAD00001008244

• Recurrent COPA mutation drives R-spondin-independent Wnt activation in intestinal tumors

  The majority of intestinal tumors harbor mutations in canonical Wnt pathway genes such as APC, whereas the lack of such alterations in a subset of tumors implies alternative tumorigenic routes. Here, we identify recurrent in-frame deletion in COPA, frequently co-occurring with USP9X truncating mutation, in small intestinal adenoma and adenocarcinoma. Patient-derived and CRISPR-engineered small intestinal organoids carrying COPA in-frame deletions exhibit R-spondin-independent yet Wnt ligand-dependent growth, maintaining LGR5 expression without canonical Wnt drivers. Mechanistically, COPA mutation stabilizes frizzled co-receptor LRP6 irrespective of R-spondin, sustaining Wnt pathway activation under growth factor-restricted conditions. USP9X loss further potentiates this phenotype. Unlike canonical Wnt pathway members, COPA encodes the alpha-subunit of coatomer complex I, which engages in vesicle trafficking with little prior linkage to intestinal tumorigenesis. Our findings establish COPA mutation as a novel and atypical intestinal tumor driver and implicate USP9X loss as a cooperating lesion.

  Study JGAS000868

• Oncogenic cooperation in a human de novo T-ALL model

  We previously modelled T-cell acute lymphoblastic leukemia (T-ALL) by over-expressing four oncogenes (activated NOTCH1, LMO2, TAL1, and BMI1) in healthy human umbilical cord blood cells through lentiviral transduction (Kusakabe et al, Nat Commun 10, 2913 (2019). https://doi.org/10.1038/s41467-019-10510-8). We have now tested individual effects of the four oncogenes by transducing human cells with all possible combinations of one, two, three, and four oncogenes. We also tested the effects of additional known T-ALL oncogenes including HOXA9, LYL1, MEF2C, NXK2.1, TLX1, and TLX3. In addition to culture in vitro on OP9-DL1 feeders, we also injected transduced cells into immunodeficient NSG mice. We observed differing abilities of the various oncogene combinations to support growth in vitro and frank leukemia in vivo. This study includes RNA-seq data from samples of transduced cells cultured in vitro as well as cells harvested from clinically moribund mice after development of leukemia in vivo.

  Study EGAS00001006055

• Somatic Mutations in Variant and IGHV4-34 Expressing Hairy Cell Leukemia

  To understand the genetic mechanisms driving variant and IGHV4-34 expressing hairy-cell leukemia, we performed whole exome sequencing of tumor/normal pairs from ten patients.

  Study phs000671

• Genetic History of Neandertal and Denisovan Introgression into Melanesian Individuals

  This study describes high-coverage whole-genome sequencing of 35 individuals sampled from the Bismarck Archipelago of Northern Island Melanesia, Papua New Guinea as described in PMID: 26989198

  Study phs001085

• Genetic Heterogeneity of Diffuse Large B Cell Lymphoma

  We sequenced exomes of 94 DLBCL tumors and cell lines. 34 of the tumors had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in DLBCL.

  Study phs000573

• MDACC Lymphoma & Myeloma scRNAseq of Plasma Cells in Multiple Myeloma

  FastQ files from Chromium single cell 5' gene expression and B-cell receptor sequencing of plasma cells from patients diagnosed with a monoclonal gammopathy of the multiple myeloma spectrum, including the precursor stages MGUS (n =13) and SMM (n = 22); newly diagnosed (n = 17); relapsed (n = 15); and plasma cell leukemia (n = 2); and 3 controls.

  Dac EGAC50000000271

• Sahel Data Access Committee

  Genome-wide genotype array data of Fulani populations presented in Fortes-Lima et al. 2025. Citation: Population History and Admixture of the Fulani People from the Sahel. Cesar A. Fortes-Lima, Mame Y. Diallo, Václav Janoušek, Viktor Černý, and Carina M. Schlebusch. American Journal of Human Genetics 112(2), February 6, 2025. doi: https://doi.org/10.1016/j.ajhg.2024.12.015

  Dac EGAC50000000290

• ABHD11 Autoimmunity Study DAC

  This DAC oversees controlled access to human RNA-seq data generated as part of the project “ABHD11 inhibition and T cell function in autoimmunity” at Swansea University. The DAC will evaluate and approve access requests based on scientific merit and alignment with participant consent. Data requests will be considered from academic researchers and healthcare professionals working on immunology or autoimmunity.

  Dac EGAC50000000750

• Target sequencing of ROS1-rearranged lung cancer patients

  We performed target capture sequencing of ROS1-rearranged non-small cell lung cancer patients to develop and examine the efficacy of new molecular targeted drug against ROS1 tyrosine kinase.

  Study JGAS000189

• Elucidation of disease state by multi-layered omics analysis

  We performed a comprehensive metagenome-wide association study by utilizing whole-genome shotgun sequencing. We elucidated a gut microbiome???s role in human biology of the Japanese population.

  Study JGAS000205

• Tanzania dietary intervention study 2019-2020

  We performed a dietary intervention study comparing western diet, traditional diet and the supplementation of fermented banana beverage in a cohort of 66 individuals (22 in each study arm)

  Study EGAS50000000317

• ACUITI

  This study assessed the feasibility and performance of a tumor-informed circulating tumor DNA (ctDNA) assay in patients with metastatic HR+/HER2- breast cancer receiving endocrine therapy and CDK4/6 inhibitors.

  Study EGAS50000000962

• BCAC TIIC Data

  Data on spatially-resolved tissue infiltrating immune cells (TIICs) from 17,265 breast cancer patients of European descent, from studies participating in the Breast Cancer Association Consortium, together with linked clinical data.

  Study EGAS50000001477

• Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  This study explores the evolution of tumor and blood immune microenvironment and related mechanisms that shape breast cancer progression, culminating in a heterogeneous lethal cancer.

  Study EGAS00001004956

• Clinical and molecular features of early onset pancreatic cancer

  A retrospective cohort study on the clinical and molecular features of early onset pancreatic cancers (i. e. diagnosed at <50 years old) in comparison with later onset tumors.

  Study EGAS50000000362

• RNA dataset of ALK study

  Here we sequenced biopsies from a patient with ALK-positive NSCLC progressing on first-line lorlatinib. This dataset contains one mRNA-seq and one Total-RNAseq. This aims to investigate the impact of the K1150dup mutation on lorlatinib progression and to explore potential therapeutic strategies to overcome resistance.

  Dataset EGAD50000002553

• LUAD dataset

  This dataset includes 25 LUAD samples consisting of control samples derived from lymph node and tumor tissues samples, which were either untreated or treated with formalin and/or the NEBNext FFPE DNA Repair v2 Module. Sequencing was performed on the Illumina NovaSeq X platform using a 2×150 nt configuration, yielding approximately 18 Gbp per sample.

  Dataset EGAD50000001950

• Cell-free DNA methylation profiling of sepsis patients

  This data set contains paired-end NGS files (in FASTQ format) generated from a methylation profiling experiment of cell-free DNA derived from the plasma of sepsis patients and healthy controls. Methylation profiling was performed using the TET-assisted pyridine borane sequencing (TAPS) protocol.

  Dataset EGAD50000001505

• 10x single-nucleus RNA-seq of postoperative human FCD II brain tissues

  This dataset contains 10x Genomics single-nucleus RNA sequencing data from postoperative brain tissues of patients with focal cortical dysplasia type II (FCD II). The samples were processed using the Chromium platform.

  Dataset EGAD50000001403

• 104 CRLM patients RNA-seq

  This dataset consists of RNA-seq data from 104 CRLM patients. Reads were mapped to the GRCh37 genome version using STAR. The data include patients with no treatment, as well as those treated with FOLFOX, FOLFOX-bevacizumab, atezolizumab, and FOLFOX-bevacizumab-atezolizumab.

  Dataset EGAD50000000954

• snRNA and snATAC analysis of human cocaine use disorder in caudate nucleus

  The dataset contains raw data from 10x Multiome derived single-nuclei RNA and single-nuclei ATAC sequencing in the same cells

  Dataset EGAD50000000691

• Multi-omics analysis of cocaine use disorder in postmortem brain tissue of the ventral striatum

  The dataset contains raw sequencing data from miRNA-seq, RNA-seq and single-nuclei RNA-seq experiments to investigate transcriptomic changes in cocaine use disorder.

  Dataset EGAD50000000881

• WES data from primary CRC

  Whole exome sequencing from ffpe samples DNA was extracted from FFPE tissue samples from colorectal cancer biopsies. Exome libraries where prepared using the KAPA Hyper Plus Kit (Roche Diagnostics) followed by target enrichment by hybridisation capture using the Roche Hyper Exome Kit. Sequenced on NovaSeq6000 to generated 2x 151 paired-end reads.

  Dataset EGAD50000000924

• Disease recurrence after pathologic response

  In this study we aim to gain insight into the mechanisms of immune evasion after initial pathologic response to neoadjuvant immune checkpoint inhibition in macroscopic stage III melanoma by pooling data of the neoadjuvant OpACIN, OpACIN-neo and PRADO trials. Here we used RNAseq data from 21 patients(paired end)

  Dataset EGAD50000000698

• BELLINI clinical trial bulk WES data: cohorts A & B

  WES data of 30 breast cancer primary tumors obtained from 30 unique patients from BELLINI clinical trial (cohorts A & B) and 30 matched blood samples. The data includes pretreatment samples. The included raw WES sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000809

• IBS-D RNA-seq raw data

  The data set consists of fastq raw files from RNA-seq of seven mucosal biopsies of the colon from seven patients, among them three patients with irritable bowel syndrome with diarrhea-predominant symptoms. Paired end sequencing on Illumina NovaSeq 6000 was used.

  Dataset EGAD50000000063

• Combined genetic and transcriptome analysis of patients with Systemic Lupus Erythematosus (SLE)

  A comprehensive profiling of the genomic architecture of Systemic Lupus Erythematosus (SLE) by combining genetic and transscriptomic analysis by RNA-seq.

  Study EGAS00001003662

• GWAS of tuberculosis in Russia

  Genome-wide association study of cases of tuberculosis from St Petersburg and Samara, in Russia, compared to healthy controls from the same two cities. Genotype data from Affy6 array.

  Study EGAS00001001090

• Mutations of whole genome sequencing in single cells in normal esophageal epithelium

  In order to obtain insight into the mutations in normal esophageal epithelium, we performed whole genome sequencing of 13 single cell-derived colonies isolated from 7 cases.

  Study EGAS00001003281

• Cabozantinib Response in ETV6-NTRK3 G623R Positive Carcinoma HIPO-021

  We report a case of marked response to cabozantinib in a secondary entrectinib-resistant tumor harboring the ETV6-NTRK3 fusion with a G623R solvent-front mutation.

  Study EGAS00001004494

• Whole Genome Sequencing of Mutifocal HCC tisue

  The differentiation of distinct multifocal hepatocellular carcinoma (HCC): multicentric disease vs. intrahepatic metastases, in which the management and prognosis varies substantively, remains problematic. We aim to stratify multifocal HCC and identify novel diagnostic and prognostic biomarkers by performing whole genome and transcriptome sequencing, as part of a multi-omics strategy.

  Dataset EGAD00001003348