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• ORCADES_WGA

  The ORCADES Whole Genome Sequence Study plans to sequence the genomes of 400 subjects from the Orkney Complex Disease Study (ORCADES) at low coverage, each with data on up to 300 quantitative traits and other risk factors associated with cardiovascular, metabolic and other complex diseases

  Study EGAS00001000068

• FRCC_Exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from FRCC patients. one lane of Illumina Hiseq sequencing will be performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000176

• Molecular evolution of classic Hodgkin lymphoma revealed through whole genome sequencing of Hodgkin and Reed Sternberg cells

  Here we leveraged whole genome structural variant copy number analysis to report the first whole genome sequencing landscape of HRS cells and reconstruct the chronology and likely etiology of pathogenic events prior to the clinical diagnosis of cHL.

  Study EGAS00001006884

• Chromothripsis in Small Cell Lung Carcinoma Associated with Carcinoid Transformation

  Small cell lung carcinoma (SCLC) is typically associated with tobacco exposure and inactivation of RB1 and TP53 genes. We performed detailed clinicopathologic, genomic, and transcriptomic profiling of an atypical subset of SCLC in never/light smokers that lacked RB1 and TP53 co-inactivation and found that most cases were associated with chromothripsis – massive, localized chromosome shattering, recurrently involving chromosomes 11 or 12, among other findings. Uniquely, these clinically aggressive tumors exhibited genomic and pathologic links to pulmonary carcinoids. Conversely, SCLC never smokers harboring inactivated RB1 and TP53 exhibited hallmarks of adenocarcinoma-to-SCLC derivation, supporting two distinct pathways of plasticity-mediated pathogenesis of SCLC in never smokers.

  Study phs003676

• Discovery of genetic factors associated with thiopurine-induced severe adverse events

  Despite NUDT15 variants showing significant association with thiopurine-induced adverse events (AEs) in Asians, it remains unclear whether additional genetic variants should be tested to predict AEs. To clarify it, we performed a genome-wide association study to discover additional variants associated with thiopurine-induced severe AEs, alopecia and leukopenia. GWASs of these AEs were performed with 1221 Japanese patients with inflammatory bowel disease using population-optimized genotyping array and imputation.

  Study JGAS000661

• Understanding the Progression of Metastatic Colorectal Cancer

  This study is to understand (1) the clonal evolution of metastatic colorectal cancer using DNA sequencing and (2) long non-coding RNAs associated with metastatic colon cancer using RNA sequencing. Our goal is to better understand the progression of aggressive colorectal cancer.

  Study phs001722

• Spatial tumor microenvironment characterization and outcome of relapsed/refractory classic Hodgkin lymphoma

  About half of relapsed or refractory classic Hodgkin lymphoma (r/r CHL) patients succumb to their disease after high dose chemotherapy followed by autologous stem cell transplantation (HDT/ASCT). Here, we aimed at describing spatially resolved tumor microenvironment (TME) ecosystems to establish novel biomarkers associated with treatment failure in r/r CHL.

  Study EGAS00001007261

• Using human induced pluripotent stem cells (iPSC) and iPSC-derived neurons to explore cellular phenotypes associated with schizophrenia.

  Schizophrenia and major mental illness are common devastating conditions. Whilst partially effective treatments are available, none are disease-modifying. Notwithstanding important insights provided by animal models there is a need for novel models of mental illness to develop more effective therapies. A study of sporadic schizophrenia-derived human induced pluripotent stem cells (hiPS) has demonstrated a neuronal phenotype representing a powerful proof of concept of in vitro disease modeling, even for diseases with complex causation such as schizophrenia. These techniques have been used here to examine the behaviour of neural stem cells and neurons derived from fibroblasts from subjects carrying NDE1 copy number variations (CNVs) associated with increased risk of major mental illness. Using hiPS from individuals with and without disease-associated CNVs we have investigated how disease risk is conferred at a cellular and molecular level through detailed comparative studies of neural progenitor proliferation, neuronal morphology, physiology, cytoskeletal organization, synaptic function, glutamate (NMDA) receptor expression and also RNA sequencing and proteomic studies of these patient-derived cells.

  Study EGAS00001002895

• Tracing early predictors of glioma evolution under therapy

  Clonal evolution drives cancer progression and therapeutic resistance. Recent studies revealed divergent longitudinal trajectories in gliomas, but early molecular traits steering post-treatment cancer evolution remain unclear. We analyzed sequencing data of 544 initial-recurrent adult diffuse glioma pairs to identify genomic and transcriptomic early predictors of tumor evolution in each molecular subtype.

  Study EGAS00001006894

• PBMC scRNA-seq data using 10X Genomics platform

  Matrices of counts from single-cell RNA-seq data and single-cell CITE-seq data collected from 16 patients enrolled in GO30103 trial, and the cell level annotation. Specifically, PBMCs at C1D1, C1D15 (2 weeks after treatment), C2D1 (3 weeks after treatment) and C4D1 (9 weeks after treatment) were collected and subject to 10x Genomics protocol. Associated metadata also included.

  Dataset EGAD50000000370

• Whole-exome sequencing of tumor samples

  Whole exome sequencing of DNA samples from tumor samples of patients in the Neo-Pembro trial. For each patient, up to four samples were sequenced; one tumor biopsy at baseline, one tumor biopsy after induction chemotherapy, a tumor sample from resection material at cytoreductive surgery, and a reference normal DNA sample isolated from whole blood. DNA was obtained from fresh-frozen samples where possible, or formalin-fixed paraffin-embedded when no fresh-frozen sample was available.

  Dataset EGAD50000001150

• Whole-transcriptome sequencing of tumor samples

  Whole transcriptome sequencing of RNA samples from tumor samples of patients in the Neo-Pembro trial. For each patient, up to three samples were sequenced; one tumor biopsy at baseline, one tumor biopsy after induction chemotherapy, and a tumor sample from resection material at cytoreductive surgery. RNA was obtained from fresh-frozen samples where possible, or formalin-fixed paraffin-embedded when no fresh-frozen sample was available.

  Dataset EGAD50000001151

• Human Single-Oocyte Transcriptome - Control and Cannabis Treated

  RNAseq data of human single oocytes exposed to THC and its metabolites, (mean concentration measured in the follicular fluid, THC1, n=95, 25 ng/mL Δ9-THC, 5 ng/mL 11-OH-THC, 50 ng/mL 11-COOH-THC) or a supraphysiologic, THC2, n=93, 100 ng/mL Δ9-THC, 50 ng/mL 11-OH-THC, 200 ng/mL 11-COOH-THC).

  Dataset EGAD50000001534

• 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

• Omics data of advanced bladder cancer

  To identify the therapeutic targets in a treatment-refractory cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

  Dataset EGAD00001005978

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

  Paired-end DNA-seq FASTQ 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). Each sample was multiplexed across flowcells and lanes, leading to a total number of 83 pairs of FASTQ files.

  Dataset EGAD00001006950

• Stage-specific gene and transcript dynamics in human male germ cells

  To study global transcriptional dynamics during human spermatogenesis we sequenced total RNA of human testicular biopsies with 5 specific histological phenotypes: Sertoli cell-only (SCO, n=3), spermatogenic arrests at the spermatogonial (SPG, n=4), spermatocyte (SPC, n=3), and spermatid (SPD, n=3) level, as well as normal spermatogenesis (Normal, n=3).

  Dataset EGAD00001008652

• Dataset for leiomyosarcoma-EXON

  Rare cancer sequencing data of 96 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008885

• Dataset for synovial_sarcoma-RNA

  Rare cancer sequencing data of 23 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008844

• Dataset for bone_cancer-EXON

  Rare cancer sequencing data of 87 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008865

• Dataset for hematopoietic_malignancy-WHOLE_GENOME

  Rare cancer sequencing data of 49 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008881

• Dataset for leiomyosarcoma-WHOLE_GENOME

  Rare cancer sequencing data of 66 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008887

• Dataset for upper_gastrointestinal_tumor-EXON

  Rare cancer sequencing data of 85 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008902

• Dataset for other_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 49 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008895

• RNA-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011819