14506 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Brain_Disease_Wellcome_Leap_Delta_Tissue_Spatial

  Utilising Spatial Transcriptomics to investigate how the tumour microenvironment regulates glioblastoma cell states.

  Study EGAS00001005801

• IACS treatment on breast cancer bone metastases

  Off-target effect of IACS on breast cancer bone metastases.

  Study EGAS00001006908

• HSP90 inhibitor resistant cell line

  Genetic analysis of K562 cell which are resistant against HSP90 inhibitors.

  Study EGAS00001006381

• Reference epigenome IPS-NPC02 h3k4me3 ChIP-Seq data generated from KEP study

  IPS-NPC02 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007288

• Reference epigenome IPS01_N_Fibroblast_WGBS data generated from KEP study

  A IPS01_N_Fibroblast_WGBS paired end data for iPSC(Oct4)

  Dataset EGAD00001003473

• Reference epigenome ADMSC05 WGBS data generated from KEP study

  ADMSC05 WGBS paired end data

  Dataset EGAD00001007136

• Reference epigenome ADMSC07 WGBS data generated from KEP study

  ADMSC07 WGBS paired end data

  Dataset EGAD00001007138

• Reference epigenome ADMSC06 WGBS data generated from KEP study

  ADMSC06 WGBS paired end data

  Dataset EGAD00001007137

• Reference epigenome ADMSC08 WGBS data generated from KEP study

  ADMSC08 WGBS paired end data

  Dataset EGAD00001007139

• Reference epigenome IPS04_X_Fibroblast_WGBS data generated from KEP study

  A IPS04_X_Fibroblast_WGBS paired end data for iPSC(Oct4)

  Dataset EGAD00001003476

• MPB_Bonn

  1000Genomes imputed data set of 581 cases and 417 controls for male-pattern baldness

  Dataset EGAD00001001456

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (28 tumor/control pairs)

  Dataset EGAD00001003207

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (cell_line)

  Dataset EGAD00001003210

• The_GENCODE_exome___sequencing_the_complete_human_exome

  We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an addition 5,594 genes and 10.3 Mb compared to current sets which mainly target the CCDS database. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed covers 47.9Mb and performed well in sequence capture experiments with HapMap and clinical samples. Samples within this study are prepared with either the CCDS or GENCODE exome products.

  Study EGAS00001000016

• Primary Cytotoxic T Cell Lymphomas Harbor Recurrent Targetable Alterations in the JAK-STAT Pathway

  Cytotoxic cutaneous T cell lymphomas (CTCLs) are uncommon but highly aggressive cancers of skin-homing cytotoxic T cells. These include the established World Health Organization (WHO) entity primary cutaneous gamma delta T cell lymphomas (PCGDTLs), the provisional WHO entity primary cutaneous CD8+ aggressive epidermotropic T cell lymphoma (PCAETCL), and samples that do not currently fit into a WHO category, referred to as cytotoxic CTCL-NOS (not otherwise specified). In this study, 35 CTCL cases were examined, and 9 PCAETCL cases were confirmed by CD8 expression and full-thickness epidermotropism. Whole genome sequencing (WGS) and bulk RNA sequencing were performed on these samples.  

  Study phs002499

• Effects of tobacco smoking on the tumor immune microenvironment in head and neck squamous cell carcinoma

  This study was designed to measure immune cell differences between HNSCC patients according to smoking history. We measured CD3, CD8, FoxP3, PD-1 and PD-L1 for immune markers and Pancytokeratin to distinguish between tumor and surrounding tissue. We observed that current smokers have significantly lower numbers of immune cells surrounding the tumor than former or never smokers. GSEA analysis of RNAseq data from this cohort suggests that smoking is associated with reduced Interferon (IFN) Alpha and Gamma levels, and also with reduced levels of IFN-response cytokines CXCL9, 10 and 11. These results emphasize the hypothetical benefits of smoking cessation during treatment for HNSCC.

  Study phs001994

• PGRN/PAT: The genomic basis for susceptibility to drug-induced long QT syndrome (diLQTS)

  The goal of this study was to search for genetic variants that could be responsible for modifying the risk of drug-induced long QT syndrome (diLQTS). diLQTS is a relatively common adverse drug event and has been a leading cause for drug relabeling and withdrawal from the market. Our hypothesis, that variants in genes which regulate electrical properties in the heart modify the risk of diLQTS, was tested by sequencing approximately 225 patients of European descent using next-generation targeted captured or whole exome sequencing. Data from cases and controls (1:2) were analyzed to identify both rare and common genetic variation.

  Study phs000808

• Genomic and Transcriptomic Profiling of Patients with Malignant Pleural and Peritoneal Mesothelioma: The NCI Cohort

  Malignant mesothelioma is an aggressive cancer with limited treatment options and poor prognosis. Better understanding of mesothelioma genomics and transcriptomics could advance novel therapies. We performed whole-exome sequencing (WXS) of germline and tumors of 122 patients, and RNA-sequencing (RNA-Seq) of tumor samples of 100 patients with pleural, peritoneal, and tunica-vaginalis mesothelioma.The biospecimens used in this study were collected as a part of the Mesothelioma Natural History Protocol (https://clinicaltrials.gov/ct2/show/NCT01950572), wherein, samples were collected from subjects with malignant mesothelioma as listed in the eligibility criteria below and written consent from each participant was obtained before sample acquisition.

  Study phs002207

• Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

  In this study, we describe a systematic analysis of pseudogene 'transcription' from an RNA-Seq resource of 293 samples, from 13 cancer and normal tissue types. We observed a highly prevalent, genome-wide expression of pseudogenes that could be categorized as universally expressed or lineage- and/or cancer-specific. We also explored disease subtype specificity and functions of selected expressed pseudogenes. We provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.

  Study phs000525

• Gene Expression Signatures in CATHGEN

  Case control cohort: The details have been previously published: American Heart Journal. 2010;160:371-379 e372. Briefly, a nested case:control cohort of CATHGEN participants who had experienced death or MI (n = 250) after their index catheterization and age-, sex-, and race-matched controls (n = 250) who were free of death/MI > 2 years after cardiac catheterization was identified as part of the MURDOCK Horizon 1 Cardiovascular Disease Study.21 Sufficient RNA for microarray analysis was available in 447 members of this cohort. Observational cohort: 224 sequential CATHGEN samples were selected for whole blood RNA analysis, of which, 191 had sufficient RNA for microarray analysis.

  Study phs000551

• Genetic Basis of Cryptorchidism

  Non-syndromic cryptorchidism is a common malformation, but the genetic loci that increase susceptibility to cryptorchidism remain unknown. A genome-wide association study (GWAS) was completed to determine whether common allelic variants are associated with susceptibility to cryptorchidism. Two sets of discovery groups were genotyped. Group 1 (559 cases and 1772 controls) was genotyped with HumanHap550v1.0, HumanHap550v3.0 or Human610-quad v1.0. Group 2 (353 cases and 1149 controls) was genotyped with HumanOmniExpress-12v1 or HumanOmniExpress-12v1-1. The sample and marker QCs were performed separately using PLINK (v1.07; http://pngu.mgh.harvard.edu/purcell/plink/) and logistic regression analyses were performed with first and second multidimensional scaling (MDS) components as covariates.

  Study phs000986

• Whole Genome Comparisons of Breast Cancers and their Xenotransplants

  Early passage breast cancer xenografts have been proposed as alternatives to cell lines as model systems for studying the basic biology of tumors and for advancing therapy development. This study explores the relatedness of primary disease genomes to their matched xenotransplants. Using paired-end massively parallel sequencing 17 matched progenitor tumor, xenograft and normal trios were sequenced to at least 30-fold coverage with diploid coverage of at least 95% of the genome as determined by SNP array concordance. RNA sequence was generated from the xenograft tumors. The xenografts were derived from a spectrum of tumor samples from patients with both early and advanced breast cancer.

  Study phs000611

• Genomics of Blastic Plasmacytoid Dendritic Cell Neoplasm

  The goal of this study was to understand the genetic evolution and tumor phylogeny of blastic plasmacytoid dendritic cell neoplasm (BPDCN). BPDCN can present in patients with skin tumors of leukemia cells and no bone marrow or blood involvement, or alternatively, with both skin tumors and blood/bone marrow leukemia cells at the time of diagnosis. Here, we performed longitudinal sampling of tissues from patients with BPDCN, including both skin tumors and bone marrow, and in some cases serially at different time points through the course of diagnosis and treatment. These were studied by whole exome or whole genome DNA sequencing, comparing tumor samples to matched normal samples.

  Study phs003228

• Supraphysiologic MDM2 Expression Impacts P53-Independent Chromatin Networks and Therapeutic Responses in Sarcoma

  We collected multiple liposarcoma samples from different patients, including different subtypes (DD, WD) and normal adipose tissue as control. This study provides the biggest liposarcoma cohort to date, and examined the molecular regulatory circuits associated with MDM2 overexpression. To this end, we obtained not only RNA-seq data, but also ChIP-seq from Jun, RUNX, MDM2, P53 and H3K27ac, as well as hiChIP from tumor samples and cell lines. We found that MDM2 binds to thousands of genes involved in cellular growth and stress response in a P53-independent manner. Furthermore, we described these active genes engaged in multi-way topological interactions that resemble transcriptional hubs.

  Study phs003272

• Integrated Clinical and Transcriptomic Profiling to Characterize Disease Phenotype

  Personalized medicine requires that we first address the challenge of genetic heterogeneity, prominent in rare cancers to common disease. While current clinical DNA sequence data successfully identify novel genetic variants, the genomic data alone are insufficient biomarkers of clinical phenotype. There is an unmet need for systematic integration of specific functional genomic data with patient genetic data, in order to bridge the knowledge gap between genetic variation and clinical phenotype. This specific study is focused on functional genomic data from platelets as disease-specific cells that are also ideal for proof-of-principle transcriptomic investigation (being anucleate), and highly-relevant to multiple disease processes.

  Study phs002121