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• A Genome-Wide Association Study of Peripheral Arterial Disease

  The Electronic Medical Record Phenotypes and Community-engaged Genomic Association Study aims to identify genetic variants mediating susceptibility to peripheral arterial disease (PAD). The study leverages a biorepository of blood samples of 1688 PAD cases and 1649 controls, and the electronic medical record (EMR) to annotate the biorepository. PAD cases were identified from the vascular laboratory database as having an ankle brachial index (ABI) <0.9 at rest or after exercise or having non-compressible vessels. Controls were without prior history of atherosclerotic vascular disease and when tested, no evidence of ischemia on a stress test. Phenotypes and environmental exposures including age, ethnicity, demographic and anthropometric data are derived from the Mayo Electronic Medical Record (EMR). Comorbidities were determined using algorithms for diabetes and hypertension based on ICD-9 codes and medication use. Relevant laboratory data, including lipid levels, fasting blood sugar and serum creatinine at index date or within a 1-year window of the index date were extracted. Medication classes at index date were identified using Mayo's Natural Language Processing-based system with RxNorm codification and NDF-RT terminologies mapping. Smoking status was confirmed by natural language processing of clinical notes. Genotyping of ~600,000 SNPs across the genome is being conducted at the Broad Institute using the Illumina 660W platform. Statistical analyses will be conducted to identify genetic variants associated with susceptibility to PAD.

  Study phs000203

• NIH RECOVER: A Multi-Site Pathology Study of Post-Acute Sequelae of SARS-CoV-2 Infection

  The RECOVER tissue pathology study is a cross-sectional study designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection in a diverse population representative of the general COVID-19 population in the US. The autopsy study will characterize the pathology of PASC in decedents who die more than 60 days after initial onset or after hospital discharge, whether in-hospital or out-of-hospital at time of death, and who meet the working definition of PASC as defined by the recent World Health Organization publication given in Section 5.4. The autopsy study will also explore the pathology of acute SARS-CoV-2 infection in a smaller subset of decedents who died between15-60 days from symptom onset. This protocol defines the common set of clinical data elements, autopsy procedures for tissue collection, core measures, pathology protocols, shared pathology tissues, data elements, and methodology. Each investigator site is expected to perform autopsies on the decedents to address the pathophysiology of the potential long-term effects of SARS-CoV-2 infection on human health. The Consortium analysis plan aims to address research questions by incorporating: 1) tissue obtained from autopsies performed at each Phase II participant's site; and 2) tissue available from other pathology investigators/autopsy sites within the Consortium.

  Study phs003768

• A prognostic human brain network for diffuse midline glioma

  Diffuse midline glioma (DMG) are near-universally lethal tumours of the paediatric central nervous system. In animal models, DMG form brain-wide, integrated networks through neuron-to-glioma synapses and glioma-to-glioma gap junctional coupling. This extensive connectivity robustly promotes the growth and invasion of DMG and other glial malignancies through paracrine mechanisms and direct neuron-to-glioma synapses. The organisation and clinical implications of these connections in the living human brain, however, remain to be elucidated. Here, we develop tumour network mapping to compute the brain-wide connectivity profile of DMG: defining a conserved brain network across pontine and thalamic DMG associated with patient short-term survival (DMG network). Tumour functional connectivity with the DMG network was independently predictive of patient overall survival across two external validation cohorts. Tumour growth mapped to DMG network-specific trajectories and peak, in-network neurometabolic changes across development spatiotemporally aligned with the peak age incidence of DMG. Single-nucleus RNA-sequencing confirmed diverse synaptic gene enrichment in high-connectivity DMG. Strikingly, incidental surgical resection of high-connectivity thalamic DMG tissue conferred a significant survival advantage. Collectively, these data define a conserved and prognostically important brain network in children with DMG, consistent with the hypothesis that DMG exploit otherwise healthy brain circuits to promote tumour growth.

  Study EGAS50000001752

• A genomic approach towards an understanding of clonal evolution and disease progression in multiple myeloma

  Multiple Myeloma (MM) is a largely incurable haematological malignancy defined by the clonal proliferation of malignant plasma cells within the bone marrow. Clonal heterogeneity has recently been established as a feature in MM, however, the subclonal evolution associated with disease progression has not been described. We used whole exome sequencing to analyse 10 paired patient samples, providing new insights into the progression from Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smouldering MM (SMM), to symptomatic MM. We confirm that clonal heterogeneity is a common feature at diagnosis and that the driving events involved in disease progression are more complex than previously reported. While we observe some previously identified known “drivers” of MM, we find that the driving events involved in progression are complex and not limited to the known SNVs or CNVs. The RAS/MAPK pathway was found to be the most frequently deregulated pathway, with recurrent mutations in KRAS and NRAS observed in patients at both MGUS/SMM and MM stages. We reveal that MM evolution is mainly characterised by the phenomenon of clonal stability, where the subclonal plasma cell populations identified at MM progression are already present in the asymptomatic MGUS/SMM stages. These subclonal populations could be amenable to therapeutic intervention to arrest transformation to MM.

  Study EGAS00001002850

• PAX5 biallelic genomic alterations define a novel subgroup of B cell precursor acute lymphoblastic leukemia

  Chromosomal rearrangements and specific aneuploidy patterns are initiating events and define subgroups in B cell precursor acute lymphoblastic leukemia (BCP-ALL). Here we analyzed 250 BCP-ALL cases and identified a novel subgroup (‘PAX5-plus’, n=19) by distinct DNA methylation and gene expression profiles. All patients in this subgroup harbored mutations in the B-lineage transcription factor PAX5, with p.P80R as hotspot. Mutations either affected two independent codons, consistent with compound heterozygosity, or suffered LOH predominantly through chromosome 9p aberrations. These biallelic events resulted in disruption of PAX5 transcriptional programs regulating B cell differentiation and tumor suppressor functions. Homozygous CDKN2A/B deletions and RAS activating hotspot mutations were highly enriched as cooperating events in the genomic profile of PAX5-plus ALL. Together this defined a specific pattern of triple alterations, exclusive to the novel subgroup. PAX5-plus ALL was observed in pediatric and adult patients. Although restricted by the limited sample size, a tendency for more favorable clinical outcome was observed with 10 of 12 adult PAX5-plus patients achieving long-term survival. PAX5-plus represents the first BCP-ALL subgroup defined by sequence alterations in contrast to gross chromosomal events and exemplifies how deregulated differentiation (PAX5), impaired cell cycle control (CDKN2A/B) together with sustained proliferative signaling (RAS) cooperatively drives leukemogenesis.

  Study EGAS00001003209

• Single cell transcriptomics of hESC-derived midbrain dopaminergic neurons generated by a new human development-based protocol

  Recent advances in stem cell technologies provide new opportunities for regenerative medicine and Parkinson’s disease modelling. However, the precise composition and quality of human embryonic stem cell (hESC)-derived preparations at the single cell level, compared to endogenous brain standards, remains to be determined. In addition, multiple developmental pathways important for midbrain dopaminergic (mDA) neuron development remain to be implemented in hESCs. Here we use mouse developmental knowledge and human single cell RNA-sequencing (scRNA-seq) data to generate a new development-based protocol to differentiate hESCs into mDA neurons. We found that Laminin 511, dual WNT activation with CHIR99021 and WNT5A, together with FGF8b, improved different aspects of midbrain patterning. Moreover, mDA neurogenesis and differentiation were enhanced by activation of liver X receptors and inhibition of fibroblast growth factor signaling. Analysis of hESC-derived midbrain cultures by scRNA-seq revealed multiple hESC-derived clusters, which resembled those in the endogenous human ventral midbrain. Moreover, high quality mDA neurons were detected and found to progressively acquire functionality in vitro. Thus, we hereby provide a hESC differentiation protocol that recapitulates several aspects of endogenous mDA neuron development, and a strategy to determine cell composition and quality of hESC-derived preparations that can be useful for disease modeling and cell therapy.

  Study EGAS00001006313

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - ExomeNanoSeq

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016058

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - TargetedNanoSeq

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016059

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - TargetedEMSeq

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016060

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - PTA_WGS

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016061

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - PTA_DNAHyb

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016062

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - PTA_RNA

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016063

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - LCMB_WGS

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016064

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - LCMB_WES

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016065

• Long-term organoid culture of a small intestinal neuroendocrine tumor

  Dac EGAC00001003157

• Validation of a targeted sequencing panel for multiple myeloma

  Study EGAS00001006164

• Molecular characterization of a renal cell carcinoma PDX cohort

  Study EGAS00001006249

• Hepatoblastoma tumoroid biobank as a key resource for tumour genetics

  Study EGAS00001008251

• Idiopathic Pulmonary Fibrosis Network (IPFnet) Prednisone, Azathioprine, and N-Acetylcysteine: A Study That Evaluates Response in Idiopathic Pulmonary Fibrosis (IPFNet-Panther-IPF-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: The initial objective of the PANTHER-IPF study was to evaluate the effectiveness of a drug combination of prednisone, azathioprine, and N-acetylcysteine in the treatment of mild-to-moderate idiopathic pulmonary fibrosis (IPF) compared to N-acetylcysteine alone or placebo. After interim analysis presented safety concerns regarding the three drug regimen, the protocol was modified to evaluate only N-acetylcysteine effectiveness. Background: IPF is a chronic, progressive lung disease of unknown cause that is characterized by the histopathological or radiologic patterns of usual interstitial pneumonia in a typical clinical setting. The median survival of participants with idiopathic pulmonary fibrosis after diagnosis is 2 to 5 years. To date, no pharmacologic therapies have been shown to improve survival. Acetylcysteine has been suggested as a beneficial treatment for idiopathic pulmonary fibrosis, although data from placebo-controlled studies are lacking.Design: Patients with mild-to-moderate impairment in pulmonary function were randomly assigned to receive a three-drug regimen (prednisone, azathioprine, and acetylcysteine), acetylcysteine alone (plus matched placebos for prednisone and azathioprine), or matched placebos for each of the active therapies. After the planned midpoint interim analysis, the data and safety monitoring board recommended discontinuation of the three-drug regimen because of an excess in the number of deaths, hospitalizations, and serious adverse events among patients in the combination-therapy group, as compared with the placebo group. After NHLBI accepted this recommendation on October 14, 2011, the three-drug regimen was discontinued and patients were recruited for only the acetylcysteine group and the placebo group. Patients were seen at the clinical centers for screening, at baseline, and at 4, 15, 30, 45, and 60 weeks. The primary outcome measure was change in FVC over 60 weeks.Conclusions: As compared with placebo, acetylcysteine offered no significant benefit with respect to the preservation of FVC in patients with idiopathic pulmonary fibrosis with mild-to-moderate impairment in lung function. In addition, there were no significant differences between the acetylcysteine group and the placebo group in the rates of death or acute exacerbation.

  Study phs004071

• A Case Controlled Etiologic Study of Sarcoidosis (ACCESS-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions. Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from (ACCESS) include Bronchial Lavage, DNA, Peripheral Blood Mononuclear Cells, and Plasma. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: To determine the etiology of sarcoidosis by establishing a case control, multi-center study. In addition to etiology, this study also sought to examine socioeconomic variables and the clinical course of patients with sarcoidosis, including quality of life.Background: Sarcoidosis is a chronic granulomatous disorder of unknown cause that is characterized by activation of T-lymphocytes and macrophages. For many years, sarcoidosis was presumed to be an atypical manifestation of tuberculosis because of the similarity between the inflammatory responses of the two diseases. However, as culture techniques became more widely employed to diagnose tuberculosis and it became less common, it became clear that sarcoidosis was not simply a variation of tuberculosis. Data on the etiology of sarcoidosis have come from diverse sources: in clinical investigations, alveolitis has been found to precede granulomatous inflammation; in case control studies, familial aggregation has been identified; and in case reports, recurrence of granulomatous inflammation has been observed after lung transplantation. The cause may not prove to be a single, known exposure. Interactions of exposures with genetic dispositions could have important implications for our understanding of immune responses as well as the pathogenesis of sarcoidosis.Participants: 736 participants with sarcoidosis enrolled within 6 months of diagnosis from 10 clinical centers in the U.S. Using the ACCESS sarcoidosis assessment system, organ involvement was determined for the whole group and for subgroups differentiated by sex, race, and age (Conclusions: The initial presentation of sarcoidosis is related to sex, race and age, and it tends to remain stable over two years in the majority of patients. The etiology is probably multifactoral with both genetic and environmental factors contributing.Specimen Details: The PBMC for this study are pelleted and suspended in guanidinium-based solution and are nonviable.

  Study phs004276

• Genomic Sequencing of Pediatric Rhaboid Cancers

  In this study, we sequenced the exomes of 35 rhabdoid tumors, highly aggressive cancers of early childhood. This study is part of a larger effort to characterize pediatric cancers as part of the Slim Initiative for Genomic Medicine (SIGMA) project.

  Study phs000508

• Advanced Genomic Techniques in Sequencing of Colorectal Cancer

  We developed a method that uses allelic imbalance information in combination with phased genomic sequencing to generate mega-haplotypes that can encompass entire chromosome arms. We applied this technique to characterize aneuploidy and chromosomal alterations in colorectal cancers.

  Study phs001400

• Large Cancer Fingerprint Screening for Detection of Minimal Residual Disease.

  We describe an approach for large cancer fingerprint screening and its application to cell-free DNA from patients with cancer. Our approach involves tracking somatic mutations identified from patients' tumor biopsies, in the cell-free DNA from a blood draw.

  Study phs001977

• NCI's Collection of Datasets for Health, Medical, and Biomedical Research Purposes

  This collection provides access to NCI's collections of datasets for the purpose of performing health, medical, or biomedical (HMB) research. This collection would not support ancestry lineage research not related to a specific medical or health conditions.

  Study phs003044

• Chromosome Errors in Human Eggs and Natural Fertility

  The overall aim of this project is to investigate chromosome errors in human oocytes as a function of age. We aimed to identify molecular mechanisms underpinning these errors and how they may shape the curve of natural fertility in humans.

  Study phs001922

• Genomic Characterization of Brain Metastases from Lung Cancer

  Metastatic disease to the brain is associated with a poor prognosis. Our understanding of the genetic drivers of metastasis remain limited. Whole-exome sequencing was performed from brain metastases from lung adenocarcinoma to identify putative drivers of metastatic progression.

  Study phs001920

• Germline Genetic Variants in Cancer-Susceptibility Genes in Patients with Osteosarcoma

  We conducted whole-exome sequencing of germline DNA from patients with osteosarcoma to estimate the frequency of pathogenic/likely pathogenic germline genetic variants in known cancer-susceptibility genes in a large population of osteosarcoma patients unselected for family history.

  Study phs002444

• Kids First: Genetics of Kidney and Urinary Tract Malformations

  Congenital defects of the kidney and urinary tract are a common cause of kidney failure in children and adults and elucidation of the genetics of these disorders will provide new opportunities for diagnosis, risk stratification and prevention of complications.

  Study phs002162

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma samples (99 FFPE tumor tissue derived DNA and 9 circulating tumor DNA) and corresponding germline DNA of 38 controls. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dac EGAC50000000261

• Target bisulfite sequencing of uterine cervical cancer

  We performed targeted bisulfite sequencing of the HLA-A promoter region in cervical tissue samples to investigate DNA methylation patterns that regulate immune recognition and antigen presentation, which may influence viral immune surveillance and malignant transformation in cervical pathology.

  Study JGAS000825

• Comprehensive sequencing analyses of uterine and ovarian carcinosarcoma

  We collected 109 primary tumor and mached normal samples of uterine and ovarian carcinosarcoma. The purpose of this study is to find novel therapeutic options for carcinosarcoma as well as a clue to understand the molecular histogenic mechanism.

  Study JGAS000172

• Comprehensive analyses of genetic aberrations in gastroenterological tumors

  Intestinal metaplasia (IM) is a risk factor of gastric cancer in gastric mucosa with Helicobacter pylori infection. To explore the susceptibility to the cancer development in pure gastric IM, we investigated landscape of genetic alterations in gastric single-glands with IM.

  Study JGAS000269

• Comprehensive molecular and clinicopathological profiling of desmoid tumors

  Previous studies have not clearly identified a prognostic factor for desmoid tumors (DT). Whole-exome sequencing and/or RNA sequencing were performed in 64 cases of DT to investigate the molecular profiles in combination with the clinicopathological characteristics.

  Study JGAS000270

• Whole genome bisulfite sequencing of hepatitis B virus-associated hepatocellular carcinoma tumor and non-cancerous samples

  To understand comprehensive epigenetic alterations in hepatitis B virus-associated HCC, we have conducted a whole genome bisulfite sequencing of 5 tumor samples and 3 non-cancerous samples (3 pairs and 2 tumors).

  Study EGAS00001002230

• Whole exome sequencing of virus-associated HCC

  To understand comprehensive combinations of molecular alterations and seek for potential therapeutic targets/pathways in virus-associated HCC, we have conducted a whole exome sequencing (in-solution capturing all human coding exons) of 150 pairs of HCC cases.

  Study EGAS00001000389

• Single-cell profiling maps the spectrum of crosstalk between glioma cells and tumor associated macrophages

  Tumor associated macrophages (TAMs) are a heterogeneous glioma infiltrate, implicated in cancer progression. We performed single-cell RNA-sequencing, to survey TAM response-patterns in glioma.

  Study EGAS00001002185

• Clinical Utility of Breast cancer Research by Inocras, Catholic university hospital and Samsung medical center

  Breast cancer remains a major global challenge. To comprehensively characterize its genomic landscape and clinical significance, we analyzed whole genome sequences from 1,364 clinically annotated breast cancers, integrating transcriptome data from most of the tumors.

  Study EGAS50000001062

• Innate immune cell subsets are enriched in synovial fluid of ACPA-negative rheumatoid arthritis and characterised by distinct type I IFN gene signatures

  This study provides a detailed comparison of the myeloid cell landscape in the SF of patients with ACPA+ and ACPA− RA, highlighting the unique involvement of type I IFN responses in ACPA− RA.

  Study EGAS50000001260

• Liquid biopsy to identify taxane resistance in castration-resistant prostate cancer patients

  Taxanes are life-prolonging treatments for patients with advanced prostate cancer. However, treatment resistance and lethal disease invariably develops. We here used liquid biopsies to identify and characterize resistance to cabazitaxel using a targeted sequencing panel (PCF-SELECT).

  Study EGAS50000001292

• smallRNA-seq of isolated pancreatic islets

  In this study we performed smallRNA-sequencing, a sequencing method designed for small noncoding RNAs, to investigate the miRNA expression profile of human islets isolated from pancreata of donors without diabetes mellitus (n=3) and donors with type 2 diabetes (n=3).

  Study EGAS50000000865

• Whole exome sequencing of FFPE material from 41 pediatric BCP-LBL patients.

  This study contain the results of whole exome sequencing analyses of FFPE material from 41 pediatric B-cell precursor lymphoblastic lymphoma patients. Samples were sequenced with a target coverage of 200x. Data are provided as Fastq files.

  Study EGAS50000000290

• Clinical Utility of Breast cancer Research by Inocras, Catholic university hospital and Samsung medical center

  Breast cancer remains a major global challenge. To comprehensively characterize its genomic landscape and clinical significance, we analyzed whole genome sequences from 1,364 clinically annotated breast cancers, integrating transcriptome data from most of the tumors.

  Study EGAS50000001377

• HER2_positive_Breast_Cancer_

  We propose to definitively characterise the somatic genetics of HER2+ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000042

• Matched_Pair_Cell_Line_Tumour_RNAseq

  In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Study EGAS00001000434

• Genetic_factors_underlying_premature_MI_in_Greek_families_without_vessel_disease

  The study will analyse by exome sequencing 8 Greek family members with an excess of potentially damaging mutations relating to premature MI and no vessel disease, to identify genetic factors underlying this condition. This is a follow on from project GPMI-NVD

  Study EGAS00001000478

• Multiomic cell-free DNA profiling to inform molecular classification and immunotherapy outcomes in endometrial cancer

  This study involved a cell-free DNA (cfDNA) framework integrating genomic, transcriptomic and epigenomic profiling to investigate patient response to immune checkpoint inhibitors in advanced endometrial cancer (EC) with mismatch repair deficiency (dMMR).

  Study EGAS50000001582

• Paroxysmal_Neurological_Disorders___rare_epilepsies

  We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.

  Study EGAS00001000421

• The Asian Diversity Project: genotyping of 37 Asian populations and ethnic groups

  The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection.

  Study EGAS00001002100

• Balanced_Brain_Tumour_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000360

• 560 whole-genome sequenced breast cancers

  A comprehensive characterisation and analysis of 560 human breast cancers through genome-wide approaches including genomics, transcriptomics and epigenomics.

  Study EGAS00001001178

• Whole genome amplification and whole genome sequencing of human single cells

  Human single fibroblasts and T-lymphocytes were amplified using multiple annealing and looping-based amplification and multiple displacement amplification. Amplified products were next subjected to whole genome sequencing with the goal of performing a genetic variant analysis.

  Study EGAS00001003108

• IBDCA_Edinburgh

  In this experiment we have sequenced tumour normal pairs from patients presenting with CRC who have a prior history of inflammatory bowel disease. The idea is to identify driver mutations, new genes and novel pathways associated with the development of these malignancies.

  Study EGAS00001001129

• Predictor_RIO_TNBC

  In this study, samples fom a window study of the PARP inhibitor rucaparib in patients with primary triple negative or BRCA1/2 related breast cancer (RIO trial) will be investigated. Samples will undergo whole genome sequence and analysis, including use of HR Predict.

  Study EGAS00001002805

• Triple_Negative_Breast_Cancer_sequencing

  We propose to definitively characterise the somatic genetics of triple-ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000161

• Genomic landscape of IG-MYC positive Burkitt lymphoma with precursor B-cell immunophenotype.

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing of a rare Burkitt lymphoma subtype with precursor B-cell immunophenotype. Analysis were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002968

• Whole exome sequencing of Ewing and CIC-DUX4 sarcoma tumoroid models

  Tumoroid models from Ewing sarcoma and CIC-DUX4 sarcoma models were generated from patient tumor biopsies. Tumoroids were established in 3D matrigel domes and then propagated on a matrige layer. Whole exome sequencing was performed with established tumoroid models.

  Study EGAS50000000379

• RNA sequencing of Ewing and CIC-DUX4 sarcoma tumoroid models

  Tumoroid models from Ewing sarcoma and CIC-DUX4 sarcoma models were generated from patient tumor biopsies. Tumoroids were established in 3D matrigel domes and then propagated on a matrige layer. RNA sequencing was performed with established tumoroid models.

  Study EGAS50000000380

• Lifelines NEXT

  The Lifelines-NEXT is a cohort of newborns followed up from birth up to the age of 1 year and later. The cohort includes approximately 1,500 newborns and their mothers from the 3 provinces of the Northern Netherlands.

  Study EGAS50000000133

• Colorectal cancer functional annotation - MPRA

  We performed a Massively Parallel Reporter Assay (MPRA) in colorectal cancer (CRC) cell lines HT29 and SW403 and normal colon cell line HCEC-1CT. We specifically targeted the regions around the CRC GWAS loci to identify which variants alter transcription.

  Study EGAS50000000406

• Single-cell transcriptomics of neuroblastoma tumors

  Single-cell RNA-sequencing (CITE-seq) and single-nucleus RNA-sequencing data were generated from neuroblastoma patient tumors to uncover transcriptional heterogeneity at a single-cell resolution. In addition, we used the data to validate our findings of the NBAtlas.

  Study EGAS50000000223

• Chromatin run-on and RNA sequencing of fibrolamellar carcinoma

  Fibrolamellar carcinoma (FLC) is a rare, therapeutically intractable liver cancer that disproportionately affects youth. Here we used chromatin run-on sequencing to characterize the enhancer landscape in FLC and RNA sequencing to identify dysregulated genes in FLC.

  Study EGAS00001004169

• Whole Exome Sequencing of healthy Spanish individuals

  The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population.

  Study EGAS00001000938

• Transposome_Bisulfite_Sequencing

  DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

  Study EGAS00001000751

• Uterine leiomyoma: DNA methylation, chromatin activity and gene expression

  In this study, we observed the effects of different uterine leiomyoma driver mutations to tumor DNA methylation, chromatin activity and gene expression, to form a comprehensive view on the epigenetic consequences of the mutations.

  Study EGAS00001004499

• Genome-wide study of resistance to severe malaria in eleven worldwide populations

  A genome-wide study of resistance to severe malaria in 18,000 samples from eleven worldwide populations, including eight populations sub-Saharan Africa.

  Study EGAS00001001311

• HCA_Heart_Disease_BHF_DZHK_RNA_

  Cell Atlas of the diseased human heart. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001004566

• All available datasets of DEEP

  All available datasets of DEEP. There are several Reference Epigenomes available. For metadata check out www.deep.dkfz.de One reference epigenome represents a set of 6 ChIP-Seqs, WGBS, RNA-Seq, smallRNA-Seq and sometimes DNase1 and/or NOME-Seq.

  Study EGAS00001001608

• SPECTA__NGS_Screening_Program_for_Efficient_Clinical_Trial_Access

  SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer.

  Study EGAS00001000728

• Isotype_resolved_sequencing_of_B_cell_receptor_in_measles_virus_infection

  Isotype-resolved sequencing of B cell receptor in measles virus infection 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002635

• RNAseq_of_Human_Organoid_Lines

  The study will use RNAseq to aid in benchmarking different culture conditions in a set of genetically annotated human organoid lines. The data will be used to assess whether there is any clonal differences introduced when culturing these lines in different conditions.

  Study EGAS00001003888

• Transcriptome_analysis_of_LCM_samples_

  We aim to set up a RNA pipeline for LCM samples to study transcriptome landscape of tumor and normal tissues. RNA was extracted from Lazer capture micro-dissection tissues and cDNA libraries were prepared with SMARTseq2 protocol. Libraries are pooled to be sequenced.

  Study EGAS00001003862

• Gene_epression_regulation_in_cytokine_induced_immune_cell_states

  We isolated T cells and monocotyes from healthy platelet donors and cultured them in resting and stimulated conditions with addition of a range of cytokines. We performed RNA sequencing to assess impact of different disease-relevant cytokines upon immune cell responses.

  Study EGAS00001003823

• STRATAA_RNAseq

  Transcriptome signatures of acute typhoid infection This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001003967

• Whole_Genome_Sequencing_of_Human_Organoid_Lines

  The study will use WGS to aid in benchmarking different culture conditions in a set of genetically annotated human organoid lines. The data will be used to assess whether there is any clonal differences introduced when culturing these lines in different conditions.

  Study EGAS00001003538

• Subtype specific studies of breast cancer progression. Milan cohort.

  The aim of this study is to compare DCIS and IBC in a subtype stratified manner in several genomic levels (gene expression, copy number, methylation).The data in this archive is supplementary to previously published data.

  Study EGAS00001004390

• COVID-19 Postmortem Lung snRNA-seq

  A deeper understanding of the pathological mechanisms of SARS-CoV-2 infection is required to combat COVID-19. Through this dataset, we analyze postmortem lung cells from patients that are infected/uninfected with SARS-CoV-2 with snRNA-seq.

  Study EGAS00001004689

• Overactivation of the IGF signalling pathway in osteosarcoma

  Tumour samples (low coverage WGS) from 35 patients with osteosarcoma were included. All samples were re-evaluated by an experienced bone pathologist who confirmed the diagnosis and a tumour content >50% per sample. All tumours represented conventional high-grade osteosarcomas.

  Study EGAS00001004767

• Targeted sequencing of brain AVM tissues

  We previously identified somatic activating KRAS mutations in a majority of human arteriovenous malformations (AVMs), using whole exome sequencing. We have now performed targeted sequencing on AVMS, investigating genes in the RAS-MAPK pathway, angiogenesis and brain vascular disorders among others.

  Study EGAS00001006729

• Cellular Analysis of Resistance and Evolution in IDH-mutant glioma

  We profiled a total of 75 IDH-mutant gliomas to study tumor evolution in this tumor type, among which 51 samples are presented here. These data reflect a combination of whole genome sequencing, whole exome sequencing, 10x single nucleus RNA sequencing, and 10x simultaneous single nucleus RNA and ATAC sequencing.

  Dataset EGAD50000002485

• TenK10K Phase 1: Whole Genome Sequencing Alignments

  Whole genome sequencing was performed for 1,925 samples from phase 1 of the TenK10K project. Sequencing was done with Illumina 2 x 150bp chemistry on a NovaSeq 6000 instrument to achieve mean 30x coverage. Sequence reads were aligned to the GRCh38 reference assembly with a fork of DRAGMAP v1.3.1. This dataset is comprised of 1,925 alignment files in cram format, and their corresponding index files.

  Dataset EGAD50000002466

• BAM-format HiFi whole genome sequencing reads (PacBio Revio) from stabilized human saliva

  HiFi whole‑genome sequencing data from a single human saliva sample collected and stabilized using an Oragene device. Sequencing was performed on a SMRT® Cell using PacBio Revio™ SPRQ chemistry. Sequencing produced >100 Gb of HiFi reads yielding >30× genome coverage suitable for comprehensive variant and methylation analysis. Dataset includes long‑read HiFi sequences in BAM format, containing both aligned and unaligned reads.

  Dataset EGAD50000002398

• WGS

  A genome-wide approach based on next generation sequencing (NGS) is performed on trios ( Patient+ Father + Mother) with SAID in order to identify known and new gene variants associated with certain forms of the disease. Whole-genome sequencing (WGS) was performed on frozen PBMCs. DNA was extracted using Chemagic Prime ( Perkin Elmer) and quantified with nanodrop. The raw sequencing data is generated on the Novaseq 6000 using an S4 flowcell, with a sequencing depth of ~30X

  Dataset EGAD50000002026

• RNA-Seq for SF3B1 splicing signature

  This dataset includes exome-captured RNA-Seq made with exome v8 (Agilent) - library preparation on a MAGNIS XT-HS2 starting from 100ng of RNA. RNA has been extracted from lymphocytes cultures from 2 probands with SF3B1 mutations and 14 controls. All 16 RNA-Seq were sequenced on a single HighOutput flowcell 2x75bp (NextSeq550). Raw fastq files have between 20 and 30M paired-reads.

  Dataset EGAD50000002121

• single-cell RNA-seq profiling of 2 patient derived colorectal cancer organoids after treatment with a combination of different anticancer drugs

  This dataset consists of single-cell RNA-seq profiling of colorectal cancer organoids derived from two patients. The organoids were profiled both after 4 weeks of treatment and after a drug holiday of two weeks. There are 49 RNA sequence files generated using single cell RNA sequencing technology from 10X genomics.

  Dataset EGAD50000001495

• IgM VDJ repertoire sequencing of 3 healthy donors using 8 different PCR conditions

  Peripheral blood mononuclear cells (PBMCs) were sampled from 3 healthy donors to sequence IgM heavy chain V(D)J repertoire libraries. Libraries were generated by targeting IgM heavy chain V(D)Js with a 5’MTPX primerset and sequenced on an Illumina MiSeq machine. Each donor was sequenced 8 times, varying only PCR amplification conditions, for a total of 24 sequencing libraries and therefore 48 paired-end fastq files.

  Dataset EGAD50000001510

• Whole genome sequencing data from paired tumor and normal tissue in a cohort of NSCLC patients.

  WGS data for paired tumor and normal tissue from 260 patients in the TRACERx ctDNA study. The patient cohort is comprised of NSCLC patients undergoing surgical resection of their tumour. The patients were then followed up for a median of ~5 years after surgery, and serial blood samples were collected. The WGS data here was generated to inform the manufacture of custom ctDNA panels.

  Dataset EGAD50000001693

• Transcriptomic dataset from a phase II study of pembrolizumab and epigenetic modification with azacitidine in platinum-resistant epithelial ovarian cancer

  This dataset includes sequence files from bulk RNA sequencing of tissue biospecimens from a phase II study investigating epigenetic priming followed by immune checkpoint blockade in platinum-resistant epithelial ovarian cancer (NCT02900560). There are 48 bulk RNA sequencing files from 24 specimens included in this dataset.

  Dataset EGAD50000001664

• TIRE-seq_PDN

  TIRE-seq is a novel RNA sequencing method that integrates mRNA purification directly into library preparation, eliminating separate RNA extraction. The technique demonstrated utility across three biological applications, including capturing transcriptional changes in human T cells, identifying genes driving murine dendritic cell differentiation, and analyzing the dose-response effects of temozolomide on patient-derived neurospheres. With its simplified approach and high sequencing efficiency, TIRE-seq offers a cost-effective solution for large-scale gene expression studies.

  Dataset EGAD50000001261

• 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

• Targeted RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoietic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood. Samples were tested in a clinical diagnostic lab to identify relevant SNVs, indels and gene fusions.

  Dataset EGAD50000000980

• A first step towards clinical routine long-read sequencing in Sweden, a national pilot study on chromosomal rearrangements

  PacBio HiFi Revio WGS data from 16 individuals sequenced in the Genomic Medicine Sweden (GMS) Long read project. Each individual was sequenced on one PacBio Revio SMRT cell. The DNA was extracted from blood. The HiFi data was aligned to GRCh38 using minimap2 or the SMRT-link software.

  Dataset EGAD50000000676

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma cases. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dataset EGAD50000000546

• Whole Exome Sequencing Bipolar cases matched controls performed at Broad Inst on cohort from Germany

  This research project was a collaboration between University Hospital Frankfurt and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 823 Bipolar case/control samples from collaborators in Germany. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files.

  Dataset EGAD50000000563

• Whole Exome Sequencing of Bipolar cases, matched controls at Broad Inst on cohort from Cambridge, UK

  This research project was a collaboration between Cambridge University, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 2,873 Bipolar case/control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000627

• RNA-seq dataset

  RNA-seq data from CD20+ sorted cells obtained from peripheral blood and lymph node Follicular Lymphoma patients. These samples were unstimulated after thawing and additionally, peripheral blood samples were stimulated during 7 days in culture as described in Dobaño-López C et al. Stranded RNA-seq libraries were performed using the TruSeq library kit (Illumina, San Diego, CA, USA). Libraries were sequenced on a NextSeq 2000 (Illumina) in a 2x50bp length.

  Dataset EGAD50000000347

• INTEGRATIVE MOLECULAR ANALYSIS OF SKIN TUMORS FROM CYLD CUTANEOUS SYNDROME PATIENTS

  CYLD cutaneous syndrome (CCS) is a rare autosomal dominant disorder characterized by germline CYLD mutations and by multiple benign skin tumors dependent on NF-kB pathway. We assembled a large cohort of CCS rare skin tumors that was profiled with whole exome or genome sequencing, RNA sequencing and methylation arrays to better understand genetic mechanisms of CCS tumorogenesis.

  Dataset EGAD50000000362

• SNP array

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains SNP array data for tumor/normal pairs for a subset of 36 patients from the screening cohort plus an additional relapse tumor of one of those 36 patients. Data was generated on a OmniExpress-24 v1.1 Bead Array (Illumina) and is stored in IDAT file format.

  Dataset EGAD00010002597

• Large deletion predisposes to familial melanoma

  Mutations in CDKN2A and CDK4 account for ~40% of multi-case melanoma families, with another ~10% attributable to BAP1 and genes associated with telomere maintenance. Thus, a substantial proportion of the genetic risk underlying familial melanoma remains unexplained.

  Study EGAS50000001496

• RNA-sequencing of six Pilocytic astrocytoma tumors

  Total stranded TruSeq RNA sequencing by Illumina of six tumor samples from six cases of pediatric Pilocytic astrocytoma. The data is published in the following paper: Tomic TT, Olausson J, Wilzen A, Sabel M, Truve K, Sjogren H, Dosa S, Tisell M, Lannering B, Enlund F, Martinsson T, Aman P, Abel F. A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS One. 2017 Apr 27;12(4):e0175638.

  Dataset EGAD00001003143

• Single-cell Multi-omics Sequencing of Human Early Embryos

  The whole blood of six female volunteers and sperm from one male volunteer were used to extract genomic DNA using a DNeasy Blood & Tissue Kit (QIAGEN). 500 ng gDNA was fragmented into 300 bp by Covaris. Then, the libraries were constructed using a KAPA Hyper Prep Kit (Kapa Biosystems). In total we have 7 samples and the files we uploaded are pair-end fastq files.

  Dataset EGAD00001004108