14478 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• The dataset for Genomic landscapes of endometrioid and mucinous ovarian cancers and morphologically similar tumor types

  The dataset for “Genomic landscapes of endometrioid and mucinous ovarian cancers and morphologically similar tumor types” includes 288 bam files from whole genome, whole exome and targeted next-generation sequencing on the Illumina HiSeq2500 and MiSeq. The samples analyzed include tumor and normal tissue samples from patients with cancer.

  Dataset EGAD50000000744

• Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing in Familial amyotrophic lateral sclerosis (ALS)

  To identify the genetic cause and modifiers of Familial amyotrophic lateral sclerosis (ALS), we performed Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing of Familial amyotrophic lateral sclerosis (ALS) patients.

  Study JGAS000358

• NFE2 and PF4 as Translational Biomarkers for BET Inhibition-Induced Thrombocytopenia in Preclinical and Clinical Studies

  Blood samples from patients treated with BMS-986158 were investigated for association with thrombocytopenia following BET inhibition. Hypotheses of translational biomarkers for early prediction of thrombocytopenia associated with BET inhibition were explored.

  Study EGAS50000001162

• Single nucleus and spatial transcriptomic characterization of prostate cancer versus normal controls

  10x Genomics Visium and Chromium platforms were used for spatial and single-nuclei RNA-sequencing, respectively. Cohort consisted of 8 prostate cancer patients (8 prostate cancer + 8 paired non-malignant control samples, fresh-frozen)

  Study EGAS50000001143

• Whole transcriptome sequencing of pediatric T-cell acute lymphoblastic leukemia

  Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is rare and its pathogenesis is poorly understood. To investigate molecular basis of pediatric T-ALL, we performed whole transcriptome sequencing in 123 cases of pediatric T-ALL.

  Study JGAS000090

• Whole-exome sequencing of pediatric solid tumors

  Pediatric solid tumors are rare, whose pathogenesis is poorly understood. To investigate the genetic basis of pediatric solid tumors, we performed whole exome sequencing in 16 rhabdmyosarcoma (RMS) cases and 7 pleuropulmonary blastoma (PPB) cases.

  Study JGAS000036

• Comprehensive analyses of genetic aberrations in cholangiolocarcinoma

  The nature of CLC is still unclear and its pathological classification still remains controversial. To clarify the positioning of CLC among primary liver cancers, and to find characteristics that could distinguish CLC from other liver cancers.

  Study JGAS000597

• Bisulfite sequencing of cell-free DNA in NMOSD patients

  Cell-free DNA was extracted from plasma and analyzed by bisulfite sequencing in Neuromyelitis Optica Spectrum Disorders(NMOSD) patients and healthy controls(HC). we aimed to investigate the primary source of cell-free DNA production.

  Study JGAS000515

• Genomic Profiling Reveals Heterogeneous Populations of Ductal Carcinoma In Situ

  Whole Exome Sequencing(WES) and copy number variation(CNV) analysis were performed using breast samples collected from non-invasive breast cancer patients in order to analysis of somatic mutations related to breast tumor phenotypes.

  Study JGAS000202

• Metastatic_Breast_Cancer_Whole_Genome

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

  Study EGAS00001000902

• Deciphering RBP - alternative splicing networks in ALS iPSC-MN: TDP-43, NOVA1, NOVA2 and RBFOX2 eCLIP-seq

  We produced enhanced cross-linking immunoprecipitation (eCLIP) sequencing data of the RNA binding proteins (RBP) TDP-43, NOVA1, NOVA2 and RBFOX2 in iPSC motor neurons of two healthy control individuals, respectively.

  Study EGAS00001005880

• Whole exome and whole genome sequencing of juvenile myelomonocytic leukemia (JMML)

  To obtain a complete registry of gene mutations in JMML, whole-exome sequencing was performed for paired tumor-normal DNA from 13 JMML cases, of which 2 cases were also analyzed by whole genome sequencing.

  Study EGAS00001000521

• ChIP-seq data of Hodgkin lymphoma cell line L-428

  ChIP-seq data (H3K4Me3, H3K27Ac histone modifications) of Hodgkin lymphoma cell line L-428. Samples were processed as previously described (Sud et al., 2018). The files are in bam format, aligned to build 37.

  Study EGAS00001003033

• Whole genome DNA sequencing for two long-lived humans.

  Two long-lived human samples were sequenced to a mean 20x coverage genome wide. Sequencing was done using the Illumina hi-seq platform, alignment to GRCh37/hg19 reference genome was done using the BWA alignment tool.

  Study EGAS00001000877

• Celiac disease case-control North Indian Immunochip dataset

  Illumina Immunochip genotype data for coeliac disease and control samples of North Indian samples origin. Data is in PLINK binary format. Calling algorithm for genotypes is based on GenomeStudio (GenTrain), with manual clustering of selected variants.

  Study EGAS00001000849

• Breast Cancer PDTX Encyclopaedia

  Molecular data from the collection of PDTX breast cancer models described in Bruna et al, 2016. Cell. It includes whole exome sequencing, shallow whole genome sequencing, expression arrays and reduced bisulfite representation sequencing (RRBS).

  Study EGAS00001001913

• Shwachman_Diamond_syndrome__SDS___Exome_sequencing

  Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive disorder characterized by exocrine pancreatic insufficiency, bone marrow dysfunction, leukemia predisposition, and skeletal abnormalities. We aim to characterise the structural effects of SDS in patients with this disorder by exome sequencing.

  Study EGAS00001000264

• BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia

  Hijacking of primitive hematopoietic enhancers, or generation of a neo-enhancer by genomic amplification, results in deregulation of BCL11B as the defining feature of a subset of T/myeloid leukemia

  Study EGAS00001004810

• BLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples

  BLLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001001596

• The Druze analysis group

  To comprehensively characterize the genetic structure of the Druze population, we recruited and genotyped 40 parent-offspring trios from the Upper Galilee in Israel and the Golan Heights, attempting to capture different extended families (clans) across various geographical locations.

  Study EGAS00001000963

• BASIS_RNAseq

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000707

• Edinburgh_Naevi_Cohort

  In this project we have sequenced the exome of skin moles (melanocytic naevi) and also normal skin from young and old people. We are interested in looking at the clonality of these lesions and the burden of UV mutations

  Study EGAS00001002347

• Microbial signatures and innate immune gene expression in lamina propria phagocytes of inflammatory bowel diseases patients

  The microbial populations associated with the lamina propria phagocyte population in CD and UC patients was examined. Specifically, the differences between phagocyte-associated microbiota (PAM) and mucosa-associated microbiota were determined.

  Study EGAS00001003105

• Balanced_Ependymoma

  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 EGAS00001000174

• Monotherapy_Breast_Cancer

  These samples are from locally advanced breast cancers that have been treated with epirubicin monotherapy before surgery. We will sequence some samples from patients with good response to the therapy and some with poor response to the therapy.

  Study EGAS00001000165

• Genetics_of_gene_expression_in_human_macrophage_response_to_Salmonella

  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 EGAS00001002236

• 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

• Breast_Cancer_FRT_RNA_seq

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

  Study EGAS00001000420

• GWAS and Meta-analysis on Frontal Fibrosing Alopecia in two European Populations

  Summary statistics of a GWAS meta-analysis for frontal fibrosing alopecia (FFA). A total of 7,039,930 genotyped and imputed variants were used for 1,044 European severe FFA cases and 4,145 matched population controls.

  Study EGAS00001003460

• Lung_Multi_site_Targeted_Sequence_Capture

  DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Study EGAS00001000436

• (h)MeDIP-Seq of high-risk prostate cancer

  Immunoprecipitation of methylated and hydroxymethylated DNA was performed on DNA isolated from tumoral and non-tumoral prostate tissue of patients with high-risk disease. Samples were sequenced on the Illumina HiSeq as 50 bp single end.

  Study EGAS00001001019

• InsPIRE islets

  We explored the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using RNA-Seq and genotyping data from 420 islet donors and 26 FAC sorted beta-cells.

  Study EGAS00001003997

• Discovery_of_resistance_mechanisms_to_the_BRAF_inhibitor_vemurafenib_in_metastatic_BRAF_mutant_melanoma

  Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma by massively-parallel sequencing of tumour samples. Comparison of genomic characteristics of pretreatment ‘sensitive’ to recurrence ‘resistant’ tumours to identify the genetics of drug resistance.

  Study EGAS00001000551

• Breast_Cancer_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000210

• Triple_Negative_Breast_Cancer_RNA_Sequencing

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

  Study EGAS00001000377

• BLUEPRINT Epigenetic characterization of megakaryocytes and erythroblasts

  Megakaryocytes and erythroblasts derive from the same progenitor cell type but carry out very different functions. In order to understand how the different functional phenotypes arise we have characterised the epigenetic landscape of these cells.

  Study EGAS00001001641

• Moles

  In this project we have sequenced the exome of skin moles (melanocytic naevi) and also normal skin from young and old people. We are interested in looking at the clonality of these lesions and the burden of UV mutations

  Study EGAS00001000789

• Multisite_Primary_Breast_Cancer

  DNA extracted from multiple biopsies taken from different areas of primary breast tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Study EGAS00001000891

• G3BP2-KIT drives leukemia amenable to kinase inhibition in Ph-like ALL

  We describe a patient with Ph-like ALL, in which leukemic cells harbored an in-frame fusion between the GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2) and the KIT proto-oncogene.

  Study EGAS00001005181

• eccDNA in maternal plasma

  We developed a new bioinformatics method for detecting the eccDNA in plasma. We revealed that the biological properties between eccDNA and linear DNA are different. eccDNA could be potentially provided as a new class of circulating biomarker.

  Study EGAS00001003827

• Molecular programs of melanoma brain metastases (MBM)

  We performed paired-end whole transcriptome sequencing of fresh frozen or intraoperative brain metastases of therapeutically treated stage IV melanoma patients. In addition, we analysed the epigenetic landscape of tumors usind Illumina 850k bead chip technology.

  Study EGAS00001005976

• arrayCGH for copy number profiling on tumor DNA from pediatric cancer tissue samples

  This dataset contains arrayCGH (HumanCytoSNP 850k and HumanCytoSNP v12.1) data from tumor DNA samples of various pediatric cancer entities. Files are provided in IDAT format and as text files processed with GenomeStudio 2.0.

  Study EGAS00001005197

• COIN CRC GWAS data

  Genotype data from the COIN and COIN-B trials of advanced/metastatic colorectal cancer. Data provided in plink format, and has been quality controlled. Control data used was from the WTCCC2 project National Blood Donors (NBS) Cohort (EGAD00000000024).

  Study EGAS00001005421

• NLG-LBC-05 ctDNA

  Correlative analysis of circulating tumor DNA (ctDNA) in aggressive large B-cell lymphoma patients treated in NLG-LBC-05 phase II trial. Whole genome and targeted sequencing was applied to longitudinal plasma cell-free DNA and diagnostic tumor tissues.

  Study EGAS00001005835

• Dedifferentiated_Melanoma

  De- and transdifferentiation of melanoma is a rare histopathological phenomenon that has not be characterised genetically. In this project we plan to sequence the genomes of de and transdifferentiated cases so as to define their genetic make-up.

  Study EGAS00001003471

• RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 10) or with vehicle (N = 10).

  Study EGAS00001006583

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

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

  Study EGAS00001006479

• HCA_Thymus_Paediatric_ThyDesign_RNA_Managed_Access

  T cells are central to adaptive immunity and thus crucial for understanding and treating human disease. While extensively studied in model organisms, translating this knowledge to humans can sometimes be limited by their rapid cross-species evolution and diverse

  Study EGAS00001007687

• Genetic landscape of pediatric ependymoma

  We performed whole-genome sequencing of 42 paired tumor/normal EPD genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000254

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

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

  Dataset EGAD00001008489