14504 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• L1 Retrotransposon sequencing in Cocaine Use Disorder - Study 1

  Cocaine Use Disorder (CUD) is a global public health problem, with no effective pharmacotherapies. While CUD is marked by high heritability, discovery of variants associated with risk for CUD has proven difficult. We used Restriction Enzyme Based Enriched L1 sequencing (REBELseq) to amplify L1 retrotransposons in gDNA isolated from medial prefrontal cortex NeuN+ neuronal nuclei from 25 CUD cases and 26 controls. Amplified libraries were sequenced on the Illumina HiSeq 4000 platform, and sequencing data was analyzed with the REBELseq bioinformatics pipeline.

  Study phs001966

• RNA-Seq data_MM study cohort (n=73) and human myeloma cell lines

  Multiple myeloma (MM) represents approximately 10 % of all hematological malignancies and patients present with a variety of clinical manifestations and diverse cytogenetic backgrounds While MM patient survival has greatly improved due to novel treatments in the last years, the disease is generally considered incurable with a median survival of approximately 6 years. Therapy resistance remains as a major obstacle, causing almost all patients to eventually relapse, underlining the persisting need to identify novel therapeutic targets and biomarkers associated with disease progression.

  Study EGAS50000000392

• Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer

  The analysis of e2QTL allows for the identification of context-specific eQTL effects (Kim-Hellmuth et al. (2017), PMID: 28814792). To evaluate how inter-individual genetic variability influences the regulation of DNA damage-induced apoptosis, we performed e2QTL analysis of CD8+ T cells from 461 healthy European participants stimulated with high doses of 5 different carcinogens. These include Methyl-methanesulfonate (MMS), tert-butyl-hydroperoxide (TBOOH), benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), 4-hydroxycyclophosphamide (HC) and UVC radiation.

  Study EGAS50000000666

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

  We investigated cell type specific changes of gene expression and chromatin accessibility in the caudate nucleus of N=6 individuals with and N=8 individuals without cocaine use disorder using postmortem human brain samples. We performed single-nuclei RNA-sequencing and single-nuclei ATAC sequencing in the same cells using the 10xMultiome platform. The N=14 tissue donors were of African-American ancestry. The cohort consists of N=5 female and N=9 male individuals.

  Study EGAS50000000480

• Boson HCV infected liver bulk RNASeq study

  ACE2 is a receptor for the SARS-CoV-2 and differences in its expression may affect susceptibility to infection. In a genome-wide eQTL analysis using hepatitis C virus-infected liver tissue, we discovered that polymorphism in a type III interferon gene (IFNL4), which eliminates IFN-lambda-4 production, is associated with a two-fold increase in ACE2 RNA expression. Conversely, among genes negatively correlated with ACE2 expression, IFN-signalling pathways were highly enriched and ACE2 was downregulated after IFN-alpha treatment.

  Study EGAS00001004996

• 46 CLL Whole Genome Sequencing Study

  Chronic lymphocytic leukaemia (CLL) consists of two biologically and clinically distinct subtypes defined by the abundance of somatic hypermutation (SHM) affecting the Ig variable heavy-chain locus (IgHV). The molecular mechanisms underlying these subtypes are incompletely understood. Here, we present a comprehensive whole-genome sequencing analysis of somatically acquired genetic events from 46 CLL patients, including a systematic comparison of coding and non-coding single nucleotide variants, copy number variants and structural variants, regions of kataegis and mutation signatures between IgHVmut and IgHVunmut subtypes.

  Study EGAS00001003254

• RNAseq of 704 patients with soft tissue tumors

  The dataset contains transcriptome sequencing (RNA-seq) data of 704 soft tissue tumors (STT) from 704 patients. The sequencing data comes in FASTQ format and contains 1408 files. A total of 56 different STT types were included in the present study and each tumor type was represented by >2 samples. The vast majority of the patients had been diagnosed and treated at the sarcoma centers in Lund (Sweden) or Stockholm (Sweden) during the period 1988-2020, but also a few samples from other centers, obtained through previous collaborative projects, were included. RNA was extracted from fresh frozen tumor material and samples were primary lesions unless otherwise indicated. The sequencing was performed using 2x150 bp paired-end chemistry on a series of Illumina instruments at various facilities during the period 2013-2023.Samples were obtained after informed consent from the patients and the study was approved by the regional ethics committee (Etikprövningsmyndigheten, Uppsala, dnr 2023-01550-01, dnr 2025-02997-02).

  Dataset EGAD50000002120

• RNA-seq of high-grade serous ovarian cancer in long-term survivors (MOCOG study)

  RNA-seq dataset of high-grade serous ovarian cancer (HGSC) tumours from long-term survivors performed as part of the Multidisciplinary Ovarian Cancer Outcomes Group (MOCOG) study. The dataset includes fastq files from 56 HGSC tumours (53 primary tumours and 3 recurrent tumours) from 53 long-term survivor patients. Libraries were generated using the Illumina Stranded mRNA Prep and 150 bp paired-end sequencing was performed to a minimum of 100 million reads on Illumina NovaSeq 6000 instruments.

  Dataset EGAD00001008537

• Autozygosity pilot - British-Pakistani from Birmingham

  The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 50-80%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples.

  Dataset EGAD00001001025

• Impact of mutational profiles on response of primary oestrogen receptor-positive breast cancers to oestrogen deprivation

  Presurgical studies allow study of the relationship between mutations and response of estrogen receptor positive (ER+) breast cancer to aromatase inhibitors (AIs) but have been limited to small biopsies. Here in Phase I of this study, we perform exome sequencing on baseline, surgical core-cuts and blood from 60 patients (40 AI treated, 20 Controls). In poor responders (based on Ki67 change) we find significantly more somatic mutations than good responders. Subclones exclusive to baseline or surgical cores   occur in approximately 30% of tumours. In Phase II we combine targeted sequencing on another 28 treated patients with Phase I. We find six genes frequently mutated: PIK3CA, TP53, CDH1, MLL3, ABCA13 and FLG with 71% concordance between paired cores. TP53 mutations are associated with poor response. We conclude that multiple biopsies are essential for confident mutational profiling of ER+ breast cancer and TP53 mutations are associated with resistance to oestrogen deprivation therapy.

  Dataset EGAD00001002651

• RNAseq data from the study - Molecular patterns of response and treatment failure after frontline venetoclax combinations in older patients with AML

  This study assessed molecular determinants of response in a cohort of patients with AML that were treated with venetoclax in combination with either DNA methyltransferase inhibitors or low dose cytarabine. RNA sequencing was performed on 31 patients from three different response classes [10 Group A - Durable remission (n=10), Group B - Relapsed (n=10) and Group C - Refractory (n=11)]. Library preparation and sequencing was performed at the Australian Genome Research Facility, using the Truseq Stranded mRNA library kit. Technical and batch replicate samples are included. Gene count data are provided with the original publication. The use of the sequencing data is subject to a data transfer agreement and is restricted to ethically approved research into blood cell malignancies and cannot be used to assess germline variants.

  Dataset EGAD00001005949

• Autozygosity pilot - British-Pakistani from Birmingham 2

  The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples.

  Dataset EGAD00001001026

• Lung cancer organoids addition

  Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term culture conditions of human airway epithelial organoids that contain all major cell populations and allow personalized human disease modelling. We collected macroscopically inconspicuous lung tissue from non-small-cell lung cancer (NSCLC) patients undergoing medically indicated surgery and isolated epithelial cells to engineer 3D organoids. We exploit the potential to derive sub-clones from AOs to demonstrate the feasibility of CRISPR gene editing. Finally, we show that AOs readily allow modelling of viral infections such as RSV and for the first time demonstrate the possibility to study neutrophil-epithelium interaction in an organoid model. Taken together, we anticipate that human AOs will find broad applications in the study of adult human airway epithelium in health and disease.

  Dataset EGAD00001004943

• Single-cell RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015713

• Transcriptomic analysis of peripheral blood dendritic cells and monocytes from patients with familial chilblain lupus and hetereozygous mutations in TREX1

  Study EGAS00001006215

• SNPArray_Thai

  The compressed file contains plink format file for the Affymetrix Human Origins SNP array data of 452 individuals generated and analyzed in Kutanan, Liu et al 2021 study of 33 ethnolinguistic groups in Thailand and Laos.

  Dataset EGAD00010002285

• Redefined indel taxonomy reveals insights into mutational signatures

  Deposited here are whole-genome sequencing bam files from the experimental isogenic cell lines used in the study "Redefined indel taxonomy reveals insights into mutational signatures, Koh, Gene (2023)".

  Dataset EGAD50000000209

• Servicio Hematología_Hospital Universitario de Salamanca_Spain

  Data obtained from Diffuse large B-cell Lymphoma cases from the Haematology Service at the University Hospital of Salamanca. The study was approved by the local Institutional Review Board, and written informed consent, following the Declaration of Helsinki, was obtained from all patients before sample collection.

  Dac EGAC50000000155

• The Pathogenesis and Genetics of Disseminated Coccidioidomycosis

  Whole exome sequencing on patients > 2 years of age with confirmed disseminated coccidioidomycosis, not undergoing active immunosuppressive therapy, negative HIV status. 

  Study phs002881

• Microdissected Pancreatic Cancer Whole Exome Sequencing

  109 micro-dissected pancreatic cancer cases and normal control tissue were subjected to whole-exome sequencing. Microdissection enriches tumor cellularity and enhances mutation calling.

  Study phs000953

• Mutational Landscape Determines Sensitivity to PD-1 Blockade in Non-Small Cell Lung Cancer

  Patients with non-small cell lung cancer were treated with pembrolizumab. Their tumors and matched normal blood were sequenced.

  Study phs000980

• NHLBI TOPMed: Characterizing the Response to a Leukotriene Receptor Antagonist and an Inhaled Corticosteroid (CLIC)

  Within-subject clinical responses to either inhaled corticosteroids or Montelukast were compared in 126 children with mild to moderate asthma.

  Study phs001729

• scRNA-seq of monochorionic dizygotic twin chimera PBMC

  Single cell RNA-seq of PBMC of monochorionic dizygotic twin chimeras. 10x chromium v3.1 was used to generate barcoded scRNA library.

  Study EGAS50000000097

• TOTHER3

  Patritumab deruxtecan in HER2-negative breast cancer: part B results of the window-of-opportunity SOLTI TOT-HER3 trial and biological determinants of early response

  Study EGAS50000000385

• Moroccan Genome Project: Sequencing Data from 109 Whole Genomes of Moroccan Individuals

  This study is the first phase of the Moroccan Genome Project, which included the complete sequencing of 109 genomes from the Kingdom of Morocco. The sequencing was performing using the Illumina NovaSeq6000 platform, with a mean coverage of 30X.

  Dac EGAC50000000353