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• PDAC organoids treated with LGK974

  Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of LGK974 treated pancreatic ductal adenocarcinoma (PDAC) organoids from three different patients for 24h

  Study EGAS50000001542

• RCIDIBAPS001

  DAC created by the Research Computing platform of IDIBAPS for the submission of 2 WES (Whole exome sequencing) samples provided by Sergi Castellví-Bel

  Dac EGAC50000000466

• ITER-FIISC Data Access Committee (FPF)

  DAC for Whole-exome variant calling of individuals from the study of familial pulmonary fibrosis in the Canary Islands.

  Dac EGAC50000000473

• Lymphocyte_PanBody_WGS_H38

  We study lymphocyte somatic evolution through the sequencing of normal healthy lymphocytes. We perform whole-genome sequencing of single-cell derived T and B cell colonies to identify somatic mutations, and perform targeted deep-sequencing of these mutations. The lineages of T and B cells, and the frequencies of these mutations reveals the neutral and non-neutral evolutionary processes underlying lymphocyte growth and function.

  Study EGAS00001003596

• Lymphocyte_Gut_WGS_H38

  We study lymphocyte somatic evolution through the sequencing of normal healthy lymphocytes. We perform whole-genome sequencing of single-cell derived T and B cell colonies to identify somatic mutations, and perform targeted deep-sequencing of these mutations. The lineages of T and B cells, and the frequencies of these mutations reveals the neutral and non-neutral evolutionary processes underlying lymphocyte growth and function.

  Study EGAS00001003594

• Comprehensive de novo variant discovery with HiFi long-read sequencing

  We performed whole-genome sequencing of 8 trios with intellectual disability using Pacbio HiFi long-reads. We then called variants with PBSV and Deepvariant. We filtered for high-quality de novo variants and validated them.

  Study EGAS00001006479

• CRUK Accelerator: oesophageal adenocarcinoma whole exome and RNA-seq raw sequencing data

  Whole exome and RNASeq raw sequencing data for a cohort of 7 male patients with oesophageal adenocarcinoma. Median age at diagnosis was 68. Tumour tissue and PBMCs were used for whole exome sequencing and RNA sequencing. This data was generated as part of a study funded by a Cancer Research UK Centres Network Accelerator Award Grant (A21998).

  Dataset EGAD00001008489

• March 2018 cumulative data release for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2018 cumulative data release (bams,fastqs) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium

  Dataset EGAD00001003963

• Genomic and clinical data from IMmotion010, a phase 3 randomised clinical trial testing adjuvant atezolizumab versus placebo for patients with renal cell carcinoma at increased risk of recurrence following resection

  778 patients were randomized in this study. Pre-treatment bulk RNAseq of primary tumors was conducted for 754 patients. For 80 patients, bulk RNAseq analysis of a metastastic biopsy was conducted. For these 80 pairs, DNA alterations were assessed in pre-treatment and at recurrence using FoundationOne.

  Dataset EGAD50000001827

• SNP data for Ovarian cancer PRS (controls)

  SNP data of 28 sites required for the Ovarian cancer PRS (controls)

  Dataset EGAD00001008145

• Prospective high-throughput genome profiling in advanced cancers:

  Genomics-based tumor profiling in advanced cancers (aC) was recently demonstrated as feasible in clinical practice. After the prospective pilot PANDORA study done on advanced breast cancers, we conducted a prospective monocenter clinical trial called PERMED01 to evaluate the number patients with locally advanced or metastatic cancer for whom identification of molecular alterations in tumor samples could lead to the delivery of a targeted therapy

  Study EGAS00001004554

• Drug-Induced Liver Injury Network (DILIN)

  The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) has established the Drug-Induced Liver Injury Network (DILIN) to collect and analyze cases of severe liver injury caused by prescription drugs, over-the-counter drugs, and alternative medicines, such as herbal products and supplements.

  Study phs000663

• Breast_Cancer_Exome_Resequencing

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

  Study EGAS00001000207

• Cancer_Genome_Project_Exome_Sequencing

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

  Study EGAS00001000301

• Chondrosarcoma_Validation_Study

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

  Study EGAS00001000181

• DAC for "Copy number variations and fragmentation features in cell-free DNA predict response in advanced non-small cell lung cancer patients under anti-PD-(L)1 therapy"

  DAC for "Copy number variations and fragmentation features in cell-free DNA predict response in advanced non-small cell lung cancer patients under anti-PD-(L)1 therapy" with Florian Janke (f.janke@dkfz-heidelberg.de) and Holger Sültmann (h.sueltmann@dkfz-heidelberg.de)

  Dac EGAC50000000308

• Therapeutic vulnerabilities in the DNA damage response for the treatment of ATRX mutant neuroblastoma

  Whole genome sequencing of ATRX / TP53 knockdown clones of the neuroblastoma cell line SK-N-SH

  Study EGAS00001004550

• ESGI - Whole Genome Sequencing of NSPHS samples (2019-08-19)

  Whole genome sequencing of sampels from the NSPHS cohort. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005267

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  Various peripheral blood immune cell subsets from 89 healthy volunteers and 136 systemic lupus erhythematosus (SLE) donors were collected (Naive_CD4, Mem_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Naive_CD8, EM_CD8, CM_CD8, TEMRA_CD8, NK, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, Neu, LDG). 22 SLE donors were analyzed longitudinally. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.

  Study JGAS000486

• Exome sequencing of 142 gastric cancer and matched normal from Japanese cohorts (UT)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 142 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Dataset EGAD00001004041

• Exome sequencing of 102 gastric cancer and matched normal from Japanese cohorts (YCU)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 102 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Dataset EGAD00001004042

• Inserm U1231 GAD TEAM

  This Data Access Committee reviews requests for access to the data submitted by the Inserm U1231 – Team GAD research team.

  Dac EGAC50000000707

• Mater Research Translational Bioinformatics DAC

  Data Access Committee for controlled-access sequence data published by the Translational Bioinformatics Group at the Mater Research Institute (Brisbane, Australia).

  Dac EGAC50000000755

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): NIH Digital Health Solutions for COVID-19: SAFER-COVID - Integration of Testing and Digital Health

  SAFER-COVID provides a set of self-management tools to consumers to track symptoms, test results, vaccine record, and environmental factors, such as exposure to others. Consumers may choose to integrate data from wearables and electronic health records (EHR) for self management. These data are used to enable multiple use cases such as return-to-work, activity risk assessment and self-management within SAFER-COVID.DOI: https://rapids.ll.mit.edu/10.57895/cmt5-gh78

  Study phs002540

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

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

  Study EGAS00001005342

• Spatiotemporal single-cell analysis reveals a time-dependent immunological modulation by multi-fractionated radiotherapy in esophageal cancer

  Description Here, by integrative spatial and single-cell analyses using spatial transcriptome (VISIUM) and single-cell RNA sequencing (scRNA-seq), we examined the spatiotemporal dynamics of immune-response in the tumor microenvironment of esophageal squamous cell carcinoma (ESCC) before, during and after RT. The comprehensive single-cell analyses demonstrated the infiltration of immune cells into tumor with the dynamic change of immune-stimulatory and -suppressive gene expression after RT. ScRNA-seq analysis uncovered the time- and cell-type-dependent alteration of gene expression profile from during to after RT. This datasets in the present study will provide the information of RT-induced gene signature to seek an appropriate target of personalized immunotherapy combined with radiotherapy and of determining the timing of the combination therapy.

  Study JGAS000712

• Separation, characterization, and identification of individuals from multi-person blood mixtures with single cell transcriptome sequencing and a novel bioinformatics pipeline

  We report a deconvolution and identification strategy of scRNA-seq datasets using mixed PMBCs data. After sequencing the data were processed with the de-goulash pipeline and analyzed with aim to identify and aquire biogeogrpahical ancestry of the involved individuals. The study includes samples of biological mixtures and in silico mixtures.

  Study EGAS00001006202

• Genetic analysis in an inherited cardiac arrhythmia

  To identify a causative gene for an inherited cardiac arrhythmia, exome sequence analysis was conducted in 6 patients and 5 controls.

  Study JGAS000041

• Central Africa whole genome sequencing (rainforest hunter-gatherers and neighboring populations)

  High-coverage (>30X) whole genome data (FASTQ) for 29 central African rainforest hunter-gatherer individuals (from five populations) and for 20 central African rainforest hunter-gatherer neighbor individuals (from four populations).

  Dataset EGAD50000001560

• BLUEPRINT: WGBS-seq for monocytes and neutrophils

  WGBS-seq for monocytes and neutrophils

  Dataset EGAD00001000673

• Dataset for whole exome sequencing of 113 pairs of tumor and normal DNA samples along with 8 cell lines

  Dataset for whole exome sequencing of 113 pairs of tumor and normal DNA samples along with 8 cell lines.

  Dataset EGAD00001001006

• RNA-seq data from paired tumour and germline samples from mesothelioma patients for study EGAS00001005196

  RNA-seq data from paired tumour and germline samples from mesothelioma patients for study EGAS00001005196

  Dataset EGAD00001007874

• Separation, characterization, and identification of individuals from multi-person blood mixtures with single cell ATAC-seq

  We report a deconvolution and identification strategy of scATAC-seq datasets using mixed PMBCs data. After sequencing the data were processed with the de-goulash pipeline and analyzed with aim to identify and acquire biogeogrpahical ancestry of the involved individuals. The study includes samples of biological mixtures and in silico mixtures in different mixed ration and cell volumes.

  Study EGAS00001007380

• Whole-genome variant calling of individuals from the study of allergic diseases in the Canary Islands

  Research study of genetic susceptibility and analyses of polygenic risk scores in allergic diseases. The historic influences in the Canary Islanders have resulted in an admixture of European, North Africans and Sub-saharan African genetic ancestries. Genetic risks linked to any of these ancestries could underlie disease peculiarities in the current inhabitants. To leverage genectic ancestry to identify and assess genetic risks in allergic diseases in the Canary Islands, we combine different genomic technologies in case-control studies and reference samples from the three parental populations to characterize and identify genetic risks factors and the intersection with ancestry.

  Study EGAS50000000299

• Roifman DAC

  This Data Access Committee will oversee all requests for data submitted by Dr. Chaim Roifman at the Hospital for Sick Children in Toronto, Canada. Requests should be directed by email to chaim.roifman@sickkids.ca.

  Dac EGAC50000000396

• Thymic epithelial transplantation for complete DiGeorge syndrome Spatial (2025-07-28)

  Spatial transcriptomics study of thymic transplant biopsies . This dataset contains all the data available for this study on 2025-07-28.

  Dataset EGAD00001015659

• RNASeq files for Mullighan ECOG2993 data

  RNASeq files for paper titled "Molecular classification improves risk assessment in adult B-lineage ALL: Patients on the international UKALLXII-ECOG2993 trial."

  Dataset EGAD00001006380

• STARR-seq of ERa binding sites in MCF7 and Ishikawa cell lines

  A oligo-captured STARR-seq library was generated using as targets ERa binding regions indetified by ChIP-seq in Ishikawa (Endometrial cancer) and T47D (breast cancer) cell lines and, breast cancer primary tissues. STARR-seq assays have been performed in MCF-7 and Ishikawa cell lines. Cells have been cultured for 3 days in hormone deprivated (phenol-red free) media and stimulated for 6 hours by 10nM estradiol (E2) or DMSO (negative control).

  Dataset EGAD50000000015

• ERBB2/HER2 transmembrane and juxtamembrane domain mutations in cancer

  In this study, we identified several recurrent activating HER2 somatic mutations in transmembrane and juxtamembrane domain in multiple cancers and demonstrate that patients carryingthese mutations are candidates for anti-HER2 therapy. We have also identified a germline mutation in HER2 transmembrane domain.

  Study EGAS00001003213

• DAC for the study EGAS00001003572

  Dac EGAC00001001174

• APS-1 Immune Panel Sequencing

  Single cell sequencing of expanded regulatory T cells (Tregs) in 8 APS-1 patients and 8 age and gender matched controls (same patients and controls as for global gene expression and TCR sequencing, excluding one for each group (control sample and patient sample #13)). Each Sample has two technical repeats. 10x Genomics Target Hybridization Kit and Human Immunology Panel was used with GEX libraries.

  Dataset EGAD50000000262

• Yemen_Somali.Omni5

  The individuals were assayed for genome-wide SNP genotypes using the Illumina Human Omni5 Bead Chip (Illumina), which surveys 4,284,426 single nucleotide markers regularly spaced across the genome

  Dataset EGAD00010001651

• FASTQ Data from In Situ Hi-C on Medulloblastoma Tissue Samples

  29 Hi-C datasets [8 G3 (MB3667, MB3687, MB3690, MB3692, MB3693, MB4010, MB4037, MB4141), 13 G4 (MB0558, MB3510, MB3670, MB3689, MB3716, MB3760, MB3761, MB3807, MB4079, MB4132, MB4174, MBSF7, SNC_2_5), 7 SHH (MB3612, MB3661, MB3662, MB3695, MB3697, MB3724, MB4143), and 1 WNT (MB4036)]. Fresh tissue samples were obtained from The Hospital for Sick Children (Toronto, ON). In situ Hi-C libraries were generated using approximately 2.5 million dissociated cells as input. All Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).

  Dataset EGAD50000000771

• RNA-seq data from 121 tumor samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). RNA-seq was performed using the QuantSeq kit FWD HT kit (Lexogen) using 500 ng input RNA from 121 tumor samples. Data provided here consist of 780 fastq files for RNA-seq.

  Dataset EGAD00001006238

• Somatic Mosaicism in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia

  The study was designed to investigate the role of somatic mosaic mutations in the pathogenesis of sporadic amyotrophic lateral sclerosis (sALS) and frontotemporal dementia (sFTD). A panel of molecular inversion probes (MIP) were used to target the exons and exon-intron junctions of 88 neurodegeneration-related genes. The panel included 34 ALS/FTD genes, 10 Alzheimer's disease genes, 28 Parkinson's disease genes, and 16 genes associated with other rare neurodegenerative disorders. The panel was used to perform ultra-deep sequencing on postmortem brain and spinal cord from 404 individuals with sALS or sFTD and 144 age-matched neurotypical controls. Known pathogenic germline mutations were found in 20.6% of ALS cases and 26.5% of FTD cases. Predicted pathogenic somatic mutations were observed in 2.7% of sALS and sFTD cases that did not have known germline mutations. The somatic variants had low variant allele fraction and region-specific enrichment, particularly in the primary motor cortex of sALS cases and prefrontal cortex of sFTD cases.

  Study phs003530

• Platelet response in aspirin adherent pregnant women

  We conducted an unbiased genome-wide assessment of genomic factors that may influence response to low-dose aspirin in pregnant women at high risk of pre-eclampsia in two pregnancy cohorts: Liverpool (n=91) and Dublin (n=91). We applied UK Axiom microarray technology for GWAS investigations. We specified tight phenotyping with COX-selective urinary 11-dehydrothromboxane B2 (pg/mg creatinine) and accounted for adherence/platelet exposure to aspirin by detection of aspirin’s principal urinary metabolite, SUA, with nuclear magnetic resonance (NMR).

  Study EGAS00001005188

• 160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN

  160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN

  Dataset EGAD00001003205

• Whole Genome sequencing of Angolan and Mozambican individuals

  To support the continued discovery and cataloguing of genomic variation in human populations and to further our understanding of the Bantu Expansion, we sequenced the genomes of 291 individuals from Cabinda, a northern exclave of Angola, and 49 individuals from Maputo, the capital of Mozambique. Utilising the power and flexibility of these whole-genome sequencing datasets, we discover rare variation, fine-scale population structure, and perform analyses using haplotype-based inference tools and our own model-based simulation framework to reconstruct complex dispersals of Bantu speak-ing populations across sub-Saharan Africa.

  Study EGAS00001007458

• The Genetic and Transcriptomic Evolution of Melanoma

  The overarching goal of the study was to better understand the evolution of melanoma. To do this, we collected archival tissue of melanomas adjacent to their intact, remnant precursor lesions. We also collected archival tissue of primary melanomas and their matching metastases. From the formalin-fixed paraffin-embedded (FFPE) blocks, we microdissected non-neoplastic (normal), precursor, and descendent portions of tissue. Both RNA and DNA were extracted from the microdissected tissues and subjected to next generation sequencing. In summary, we performed matched DNA/RNA sequencing of melanoma/precursor/normal trios, allowing us to trace the genetic and transcriptomic evolution of melanoma.

  Study phs001550

• DAC Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  Data access committee for Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  Dac EGAC50000000527