Search Results - EGA European Genome-Phenome Archive

Avelumab or M7824 for People with Recurrent Respiratory Papillomatosis

This submission includes genomic data derived from the study of clinical samples from two different phase II trials. These trials evaluated the clinical efficacy and safety of avelumab or M7824 in the treatment of adults with recurrent respiratory papillomatosis (RRP). Subjects with aggressive RRP were treated with three to six doses of avelumab or M7824. Pre-treatment or post-treatment snap frozen papilloma and normal mucosa samples were subjected to whole exome sequencing and bulk RNA-seq. A total of twenty subjects were enrolled and treated. 

Study phs002373

Genetic and Environmental Risk Factors for Hemorrhagic Stroke (GERFHS)

GERFHS is a population-based, case-control study of hemorrhagic stroke in the Greater Cincinnati/Northern Kentucky region. Cases are recruited from within 50 miles of the University of Cincinnati and population-based controls are matched to cases by age (+/- 5 years), race and gender from the same population as cases. All study participants are of self-reported non-Hispanic Caucasian ethnicity and the data show consistency with the principal component projections. The current submission includes genome wide genotyping on a subset of these cases and controls.

Study phs000874

Precise reconstruction of the tumor microenvironment using bulk RNA-seq and a unique machine learning-based algorithm trained on artificial transcriptomes

Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. Here, we present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of > 9,400 tissue and blood sorted cell RNA profiles to accurately reconstruct the tumor microenvironment (TME). Bioinformatic correction for technical and biological variability, aberrant cancer cell expression inclusion, and the accurate quantification and normalization of transcript expression increased the stability and robustness of Kassandra. Performance was validated on over 4,000 H&E tissue slides and more than 1,000 normal and tumor tissues by comparison with cytometric, immunohistochemical or single-cell RNA-seq measurements. Kassandra accurately deconvolved stromal and immune elements of blood and tumors, revealing the role of the TME in tumor pathogenesis. Digital TME reconstruction revealed that the presence of PD1-positive CD8+ T cells strongly correlated with immunotherapy response and increased the predictive potential of established biomarkers, indicating that Kassandra could potentially be utilized in future clinical applications.

Dataset EGAD00001008776

Genomics of acral lentiginous melanoma

Melanoma is the most aggressive type of skin cancer, causing about 75% of dermatological cancer deaths. Acral lentiginous melanoma (ALM) is the most common subtype of melanoma in admixed Latin American populations, but very few tumour genomes and exomes, all from European-descent individuals, have been analysed across several studies. Because of this, the genomic landscape of ALM is mostly unknown. Our aim in this project is to define this landscape and identify driver somatic alterations by whole-exome sequencing a collection of ALM germline/tumour paired FFPE samples from the National Cancer Institute of Mexico. . This dataset contains all the data available for this study on 2023-03-09.

Dataset EGAD00001010126

RNA sequencing in primary inflammatory (TPP) macrophages following deletion of a disease-associated gene desert at chr21q22, disruption of ETS2, or treatment of ETS2-edited macrophages with a HIF1α stabiliser.

This dataset comprises raw RNA sequencing data (FASTQs) from primary inflammatory (TPP) macrophages that were unedited (non-targeting control, NTC), edited to delete the disease-associated chr21q22 enhancer region (n=5), or edited to disrupt ETS2 with 1 of 2 independent gRNAs (n=9). We also performed RNA-sequencing in NTC or ETS2-edited TPP macrophages that were treated for 12 hours with vehicle (DMSO) or roxadustat (30 uM, n=3). Macrophages were detached using Accutase and lysed. RNA was extracted from cell lysates using an AllPrep DNA/RNA Mini Kit (Qiagen). Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NextSeq500. Raw data are provided as 50 bp paired-end Illumina reads.

Dataset EGAD00001011338

Safety and Efficacy of Intravenous Norepinephrine for Orthostatic Hypotension

Patients with chronic autonomic failure (CAF) often have disabling orthostatic hypotension (OH). OH in CAF patients is often associated with supine hypertension (hypertension while lying down), which can be severe. Drugs to treat OH worsen supine hypertension. Therefore, the combination of OH with supine hypertension poses a difficult therapeutic challenge. This protocol is a first step toward development of a way to maintain blood pressure during standing without worsening hypertension while lying down. The research question is will a drug (norepinephrine) given intravenously (IV) prevent blood pressure from falling in patients with orthostatic hypotension. This is a placebo controlled, blinded study of 15 patients with neurogenic orthostatic hypotension. The study consists of two experimental days per participant. On a day before the day of norepinephrine (NE) infusion, the patient undergoes head-up tilting while blood pressure is monitored. Tilt angles are increased until the patient has orthostatic symptoms, systolic pressure decreases to less than 90 mm Hg, or systolic pressure decreases by more than 80 mm Hg. On the day of NE infusion patients, receive NE and placebo with the sequence of treatments randomized. If the patient has severe supine hypertension (more than 200 mm Hg systolic), then NE is infused beginning with the patient at whatever tilt angle is required for baseline pressure to be less than 200 mm Hg. NE is infused at doses titrated to keep directly recorded systolic blood pressure at or above the baseline value during exposure to higher tilt angles. When placebo is given, angles of tilt are increased until the patient has orthostatic symptoms, systolic pressure decreases to less than 90 mm Hg, or systolic pressure decreases by more than 80 mm Hg.

Study phs001769

Human Dorsal Root Ganglion RNA Landscape Profiling for Neuropathic and Chronic Pain

Bulk and spatial RNA sequencing were performed on human Dorsal Root Ganglia (DRGs), peripheral sensory nerves and nodose ganglia and relative gene abundances were calculated. Various analyses were performed: Human DRG gene expression profiles were contrasted with a panel of gene expression profiles of relevant tissues in human and mouse (integrating, among other sources, datasets from ENCODE and GTex) in order to identify. DRG-enriched gene expression, co-expression modules of DRG-expressed genes, and key transcriptional regulators in humans. Contrasting the human and mouse DRG transcriptomes to identify DRG-enriched gene expression patterns that were conserved between human and mouse, identifying putative cell types of expression of these genes, and potential known drugs that might target the corresponding gene products. Characterization of non-coding RNA profile of human and mouse DRGs. Characterization of DRG-enriched alternative splicing and alternative transcription start site usage based transcript variants in humans and mouse, and the overlap between these two species. Contrasting of human DRG and GTex human tibial nerve samples to identify putative axonally transported mRNAs in sensory neurons. Human DRG and peripheral nerves transcriptomes from donors suffering from neuropathic and/or chronic pain were contrasted with controls to identify. Differentially expressed genes, pathways and regulators path play a potential role in neuronal plasticity, electrophysiological activity, immune signaling and response. Predictive models (Random Forests) were built to jointly predict the sex and pain state of samples based on information contained solely in autosomal gene expression profile. Gene co-expression modules were identified and gene set enrichment analysis performed.to identify sample - pathway associations, and to broadly characterize plasticity in human DRG cell types. Spatial transcriptomics was performed on human DRGs and nodose ganglia to obtain near single-neuron resolution. We identified distinct clusters of human DRG sensory neurons. We characterized the expression of different gene families (e.g., GPCRs, sodium channels, potassium channels, etc.). We investigated differences between male and female neurons.

Study phs001158

Genetic Basis of Developmental Disabilities

Developmental disabilities are birth defects that cause lifelong problems with how a body part or system works. Developmental disabilities include nervous system insults affecting how the brain, spinal cord and nervous system function; they cause intellectual disability, including Down syndrome and fragile X syndrome; and they also cause learning and behavioral disorders, such as autism spectrum disorders. At the Kennedy Krieger Institute, approximately 450 inpatients and 13,000 outpatients are seen per year (involving 114,000 visits). For most of these disorders, the underlying molecular cause has not been identified. Some, such as chromosomal disorders, have a strongly genetic basis while others, such as traumatic brain injury, are caused by environmental insults but are nonetheless influenced by the genetic background. The purpose of the present study is to identify chromosomal abnormalities underlying a variety of developmental disabilities. The approach is to obtain blood and saliva from children, and from one or both biological parents (and in some cases from siblings and/or additional relatives). Genomic DNA is purified and assayed on single nucleotide polymorphism (SNP) microarrays and/or by sequencing, including whole genome sequencing. These technologies provide high resolution information about chromosomal changes, and the information provided by the parental (and other relatives') DNA allows an interpretation of whether changes in a child are inherited or occur de novo. The study design includes multiple data analysis procedures to interpret the biological significance of findings of chromosomal changes relative to a child's parents, relative to children with similar diagnoses, relative to children with other chromosomal anomalies, and (in some cases) relative to the chromosomal status of siblings. We will further interpret the significance of the findings relative to the general (apparently normal) population by obtaining publicly available data from apparently normal individuals.

Study phs000337

Fixed single-cell transcriptomic characterization of human radial glial diversity

The human neocortex is created from diverse intermixed progenitors in the prenatal germinal zones. These progenitors have been difficult to characterize since progenitors - particularly radial glia (RG) - are rare, and are defined by a combination of intracellular markers, position and morphology. To circumvent these problems we developed a method called FRISCR (Fixed and Recovered Intact Single Cell RNA) for transcriptome profiling of individual fixed, stained and sorted cells. We developed and validated FRISCR on human embryonic stem cells. We then profiled primary human RG (96 - 132 days post conception) that constitute only 1% of the mid-gestation cortex. These RG could be classified into ventricular zone-enriched RG (vRG) that express ANXA1 and CRYAB, and outer subventricular zone-localized RG (oRG) that express HOPX. Our study identifies the first markers and molecular profiles of vRG and oRG cells, and provides an essential step for understanding molecular networks driving the lineage of human neocortical progenitors. Reprinted from Thomsen et. al. Nature Methods (2015), with permission from Nature Publishing. Human embryonic stem cell data may be obtained through NCBI's GEO database, using accession number GSE71858. Raw data from one human sample that was not consented to be released to dbGaP may be obtained directly from the authors of Thomsen et. al., 2015.

Study phs001016

Alzheimer's Disease Genetics Consortium (ADGC) Genome Wide Association Study -NIA Alzheimer's Disease Centers Cohort

The National Institute on Aging (NIA) Alzheimer's Disease Centers (ADCs) cohort includes subjects ascertained and evaluated by the clinical and neuropathology cores of the 29 NIA-funded ADCs. Data collection is coordinated by the National Alzheimer's Coordinating Center (NACC). NACC coordinates collection of phenotype data from the 29 ADCs, cleans all data, coordinates implementation of definitions of AD cases and controls, and coordinates collection of samples. The ADC cohort consists of autopsy-confirmed and clinically-confirmed AD cases, and cognitively normal elders (CNEs) with complete neuropathology data who were older than 60 years at age of death, and living CNEs evaluated using the Uniform dataset (UDS) protocol who were documented to not have mild cognitive impairment (MCI) and were between 60 and 100 years of age at assessment. ADCs sent frozen tissue from autopsied subjects and DNA samples from some autopsied subjects and from living subjects to the National Cell Repository for Alzheimer's Disease (NCRAD). DNA was prepared by NCRAD for genotyping and sent to the genotyping site at Children's Hospital of Philadelphia. ADC samples were genotyped and analyzed in separate batches. [Reprinted from AC Naj et al. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nature Genetics 43, 436-441 (2011). doi:10.1038/ng.801. PMID: 21460841.]

Study phs000372

MSK SPECTRUM - SPatiotemporal Evolution of Cancer Traced Using Multimodalities

MSK SPECTRUM is a multi-modal, interdisciplinary prospective study of spatiotemporal determinants of high-grade serous ovarian cancer (HGSOC) evolution, treatment and response. Accounting for ~80% of ovarian cancers, HGSOC is the most lethal gynecological malignancy and is a cancer of major unmet clinical need. Challenges in disease management relate to several unresolved questions about disease biology and diagnostic modalities. Prospective longitudinal collection of tissues and blood from laparoscopic biopsies and debulking surgeries enable multi-modal molecular measurements. The program brings together formidable expertise at Memorial Sloan Kettering Cancer Center (MSKCC) across the disciplines of high-resolution genomics and computer science, radiology and radiomics, surgery, tissue banking and sample preparation, medical oncology, immuno-oncology and high-resolution tissue profiling to generate a comprehensive and integrative dataset that will allow us to address the following major aims: i) characterize malignant and immune diversity at diagnosis, ii) survey the co-evolution of malignant cells and the immune response, and iii) stratify patients on standard-of-care and investigational compounds based on their genomic and transcriptomic signatures and changes to relevant genes (TP53, CCNE1, BRCA1/2, CDK12). The goal is to create a framework to utilize integrated multi-modal data as a route to advanced diagnostics and to ultimately establish a proof-of-concept for integrated diagnostics.

Study phs002857

Pilot study towards the development of a Companion/Complimentary Diagnosis platform using liquid biopsy with cfDNA for immune checkpoint inhibitor therapy in advanced urothelial cancer

Preliminary analysis was conducted to develop a cfDNA-based platform capable of predicting gene mutation profiles, TMB, gene expression profiles (molecular subtype diagnosis), and immunohistochemical findings (PD-L1 expression) using the primary lesion tissue of bladder cancer and upper urinary tract epithelial cancer, verifying the feasibility of such development.

Study JGAS000714

DFCI Gynecological Oncology Data Access Committee

This Data Access Committee is responsible for reviewing requests to access controlled human genomic data generated as part of the RESOLVE clinical trial at DFCI. The committee ensures that access complies with participant consent, institutional policies, and applicable data protection regulations (e.g., GDPR). Data access decisions are made by a multidisciplinary panel including clinical researchers, bioinformaticians, and data governance officers from Dana-Farber Cancer Institute. The committee reviews each access request to determine whether the proposed research aligns with the study’s consent terms and the data access policy. If approved, access is granted via the European Genome-phenome Archive (EGA) in accordance with EGA’s data use and security guidelines.

Dac EGAC50000000712

Bulk RNA and ATACseq of 2 XLP patients and 5-6 HD

The dataset contains five samples from P1, one pre-HSCT and four post-HSCT, one sample from P2 and 5-6 HD. RNAseq reads were processed using the LUMC BIOWDL RNAseq pipeline v5.0.0 (https://github.com/biowdl/RNA-seq). Genes with log2CPM≥1 in at least 10% of all samples were retained for downstream analysis. Differential gene expression analysis was performed using the dgeAnalysis R-Shiny application (https://github.com/LUMC/dgeAnalysis/tree/v1.4.4). ATACseq reads were processed using the LUMC BIOWDL Chipseq pipeline 1.0.0-dev (https://github.com/biowdl/ChIP-seq).

Dataset EGAD50000002072

Identification of cell type differences in FOXN1 mutation carriers by scRNA-seq

scRNA-seq was performed on the BD Rhapsody platform. CD45+ lymphocytes from two FOXN1het patients and one cord blood sample as control were sorted from frozen cryopreserved samples. The samples were split and each sample was stained with 4 Sampletag antibodies before Abseq staining with the BD Immune Discovery panel and 6 additional antibodies was performed to better classify immune cell subsets. The sorted and stained populations were pooled before loading onto the BD Rhapsody cartridge. The manufacturer's protocol was followed for library construction and samples were sequenced on an Illumina NovaSeq 6000.

Dataset EGAD50000001708

10X single cell RNA- and feature barcode sequencing of 38 AML samples

This dataset contains fastq-files from single cell 3' RNA- and feature barcode sequencing of AML samples using 10X technology (Chromium Single Cell 3ʹ Reagent Kit v3). In total, the dataset contains data from 38 AML samples from either bone marrow or peripheral blood, representing the following genetic subtypes: NPM1-mutated, myelodysplasia related, TP53-mutated, CBFB::MYH11, RUNX1::RUNX1T1, AML without class-defining mutations, and AML meeting criteria of two subtypes. The data consists of sequenced gene expression libraries from 38 samples and feature barcoding libraries covering a panel of 10-14 surface proteins for 34 samples.

Dataset EGAD50000001577

Neonatal and adult recent thymic emigrants produce IL-8 and express complement receptors CR1 and CR2

By differential gene expression analysis followed by protein expression and functional studies, we define that the naive T cells having divided the least since thymic emigration express complement receptors (CR1 and CR2) known to bind complement C3b- and C3d-decorated microbial products and, following activation, produce IL-8 (CXCL8), a major chemoattractant for neutrophils in bacterial defense. We also observed an IL-8–producing memory T cell subpopulation coexpressing CR1 and CR2 and with a gene expression signature resembling that of RTEs. JCI Insight. 2017;2(16):e93739. https://doi.org/10.1172/jci.insight.93739

Dataset EGAD00001003793

TMD-AMKL targeted follow-up

Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50 ). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

Dataset EGAD00001000783

Single MII oocyte mRNA expression from women

This dataset contains 14 paired-end FASTQ sequences from mRNA-Seq on single human M-II stage oocytes that were collected from ovarian tissue from unstimulated patients undergoing fertility preservation treatments due to cancer diagnoses, which did not influence ovarian function. Cumulus-oocyte-complexes were matured in vitro according Gruhn et al (Science 365: 1466-1469) and short term flash frozen prior to lysis, RNA extraction, full length cDNA preparation and amplification using the Ultra-low-input SMART-Seq2 v4 kit from Takara Clonetech. Further, these cDNA were used to prepare libraries for sequencing according the Nextera XT DNA library preparation kit from Illumina

Dataset EGAD00001005971

AVENIO Expanded ctDNA panel sequence alignments (BAMs) from plasma DNA of BC, CRC and NSCLC patients

The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.

Dataset EGAD00001006301

Dataset for Ewing_sarcoma_PNET-RNA

Rare cancer sequencing data of 28 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008845

Multi-region RNA-Seq data of 10 neuroblastoma cases

To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region RNA sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

Dataset EGAD00001008133

Single cell RNA-sequencing of tissues from NSCLC patients treated with chemoimmunotherapy

The goal of this study is to characterize immune cell populations by single cell RNA-sequencing (scRNA-seq) in tumor and uninvolved normal tissues from non-small cell lung cancer (NSCLC) patients with resectable non-small cell lung cancer and who received neoadjuvant chemoimmunotherapy. scRNA-seq was performed on seven pairs of tumor and normal tissues as well as one lymph node (LN) sample. Data set includes pair-end fastq files for single cell RNA sequencing of 7 neo-immuno patients. (Total 15 samples and 50 runs).

Dataset EGAD00001009778

WGS data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors - UMCU/NKI

The dataset includes cram files from WGS of 6 NEN tumors or metastases and matched PDTOs. For all tumors, cram files from WGS of either matched normal tissue or matched blood from the corresponding patients are included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.

Dataset EGAD00001009989

CCMA-WGSraw

This dataset has the mapped bam files from WGS for the cancer models in CCMA.

Dataset EGAD00001010035

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