14465 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001001356

• MS Risk Gene Data Access Committee

  Dac EGAC00001001416

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001001459

• Pediatric Low-Grade Glioma Sequencing Data Access Committee

  Dac EGAC00001001498

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001001542

• BIH COVID-19 airway single-cell data access committee.

  Dac EGAC00001001627

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001001716

• Data Access Commitee of Nanjing Medical University Affiliated Jiangsu Cancer Hospital

  Dac EGAC00001001774

• Long-read isoform in breast cancer - Data Access Commitee

  Dac EGAC00001001821

• Data Access Commitee for Translational Neurodegeneration Group - Technical University of Munich

  Dac EGAC00001001831

• RiMod-FTD Data Access Commitee

  Dac EGAC00001001879

• Data Access Commitee for Translational Neurodegeneration Group Technical University of Munich

  Dac EGAC00001001916

• University of Helsinki Systems Biology and Turku University Hospital Data Access Committee

  Dac EGAC00001001937

• 4C_Breast Data Access Committee

  Dac EGAC00001001968

• Department of Pathology and Tumor Biology, Kyoto University, Data Access Commitee

  Dac EGAC00001001992

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002014

• Data Access Commitee of Nanjing Medical University Affiliated Jiangsu Cancer Hospital

  Dac EGAC00001002086

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002207

• Data Access Committee for LUAD m6A profiling

  Dac EGAC00001002257

• Human and rat skeletal muscle multiomic profiling data access committee

  Dac EGAC00001002380

• ​Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002417

• University of Melbourne Centre for Cancer Research (UMCCR) Data Access Committee

  Dac EGAC00001002442

• Brain Tumour Research Program Telethon Kids Institute Data Access Committee

  Dac EGAC00001002507

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001002975

• High hyperdiploid acute lymphoblastic leukemia SNP array data Data Access Committee

  Dac EGAC00001003124

• CloneTracer manuscript Data Access Commitee

  Dac EGAC00001003143

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002159

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002781

• SEP Mobidic DAC

  Data access committee for U1236 SEP datasets

  Dac EGAC50000000216

• DAC ICARUS LUNG 01

  Data access comittee for ICARUS LUNG 01

  Dac EGAC50000000459

• Data access committee for MS cervical lymph node scRNAseq dataset

  Dac EGAC50000000524

• MOSAIC Window DAC

  Data Access Committee for the MOSAIC Window initiative.

  Dac EGAC50000000398

• Data access committee (DAC) for EPI-clone manuscript

  Dac EGAC00001003526

• DAC_ADARIO

  Data access committee for ADARIO / Targeting ADAR1 in Immuno-Oncology

  Dac EGAC50000000343

• A proof-of-concept study of sequential treatment with the HDAC inhibitor vorinostat following BRAF and MEK inhibitors in BRAFV600 mutated melanoma

  "Purpose: Development of resistance limits the clinical benefit of BRAF and MEK inhibitors (BRAFi/MEKi) in BRAFV600 mutated melanoma. It has been shown that short-term treatment (14 days) with vorinostat was able to initiate apoptosis of the resistant tumor cells. We aimed to assess the anti-tumor activity of sequential treatment with vorinostat following BRAFi/MEKi in patients with BRAFV600 melanoma who progressed after initial response to BRAFi/MEKi. Patients and Methods: Patients with BRAFi/MEKi resistant BRAFV600 melanoma were treated with vorinostat 360 mg QD for 14 days followed by BRAFi/MEKi. The primary endpoint was an objective response rate of progressive lesions of at least 30% according to RECIST 1.1. Secondary endpoints included progression-free survival (PFS), overall survival (OS), safety, pharmacokinetics of vorinostat and translational molecular analyses using ctDNA and tumor biopsies. Results: Twenty-six patients with progressive BRAFi/MEKi resistant BRAFV600 mutated melanoma received treatment with vorinostat. Twenty-two patients were evaluable for response. The ORR was 9% (one complete response for 31.2 months and one partial response for 14.9 months. Median PFS and OS were 1.4 and 5.4 months, respectively. Common adverse events were fatigue (23%) and nausea (19%). ctDNA analysis showed emerging secondary mutations in NRAS and MEK in eight patients at time of BRAFi/MEKi resistance. Elimination of these mutations by vorinostat treatment was observed in three patients. Conclusions: Intermittent treatment with vorinostat in patients with resistant BRAFV600 mutated melanoma is well tolerated. Although the primary endpoint of this study was not met, durable anti-tumor responses were observed in a minority of patients (9%). "

  Study EGAS00001007709

• Mutational Landscape and Tumor Burden Assessed by Cell-Free DNA in Diffuse Large B-Cell Lymphoma: a Population-based Study

  Purpose: We analyzed the utility of cfDNA in a prospective population-based cohort to determine the mutational profile, assess tumor burden, and estimate its impact in response rate and outcome in patients with DLBCL. Experimental Design: One-hundred patients were diagnosed with DLBCL during the study period. Mutational status of 112 genes was studied in cfDNA by targeted next-generation sequencing. Paired formalin-fixed paraffin-embedded samples and volumetric PET/CT were assessed when available. Results: Appropriate cfDNA to perform the analyses was obtained in 79/100 cases. At least one mutation could be detected in 69/79 cases (87%). The sensitivity of cfDNA to detect the mutations was 68% (95% CI: 56.2-78.7). The mutational landscape found in cfDNA samples was highly consistent with that shown in the tissue and allowed genetic classification in 43% of the cases. A higher amount of ctDNA significantly correlated with clinical parameters related to tumor burden (elevated LDH and β2-microglobulin serum levels, advanced stage, and high-risk IPI) and total metabolic tumor volume assessed by PET/CT. In patients treated with curative intent, high ctDNA levels (>2.5 log hGE/mL) were associated with lower complete response (65% vs. 96%, P<0.004), shorter progression-free survival (65% vs. 85%, P=0.038) and overall survival (73% vs. 100%, P=0.007) at 2 years, although it did not maintain prognostic value in multivariate analyses. Conclusions: In a population-based prospective DLBCL series, cfDNA resulted an alternative source to estimate tumor burden and to determine the tumor mutational profile and genetic classification, which have prognostic implications and may contribute to a future tailored

  Study EGAS00001004733

• Genome wide association study on coronary heart disease in patients with familial hypercholesterolemia

  Mutations in the low-density lipoprotein receptor (LDLR) gene cause familial hypercholesterolemia (FH), a disorder characterized by coronary heart disease (CHD) at young age. We aimed to apply an extreme sampling method to enhance the statistical power to identify novel genetic risk variants for CHD in individuals with FH. We selected cases and controls with an extreme contrast in CHD risk from 17 000 FH patients from the Netherlands, whose functional LDLR mutation was unequivocally established. The genome-wide association (GWA) study was performed on 249 very young FH cases with CHD and 217 old FH controls without CHD (above 65 years for males and 70 years of age for females) using the Illumina HumanHap 550K chip. In the next stage, two independent samples (one from the Netherlands and one from Italy, Norway, Spain, and the United Kingdom) of FH patients were used as replication samples. In the initial GWA analysis we identified 29 independent single nucleotide polymorphisms (SNPs) with suggestive associations with premature CHD (p<1×10-4). We examined the association of these SNPs with CHD risk in the replication samples. After Bonferroni correction, none of the SNPs either replicated or reached genome-wide significance after combining the discovery and replication samples. Therefore, we conclude that the genetics of CHD risk in FH is complex and even applying an ‘extreme genetics’ approach we did not identify new genetic risk variants. Most likely, this method is not as effective in leveraging effect size as anticipated, and may therefore not lead to significant gains in statistical power. (NB submitten and conditionally accepted at European Journal of Human Genetics-please use abstract only for internal review until submission complete)

  Study EGAS00001000734

• Intra-tumor heterogeneity and clonal evolution of papillary renal cell carcinoma

  Limited knowledge of intratumor heterogeneity (ITH), and clonal evolution of papillary renal cell carcinoma (pRCC) and rare kidney tumor subtypes hinders understanding of tumorigenesis and therapeutic efficacy. We conducted an integrative genomic and epigenomic ITH analysis and studied clonal evolutionary history of pRCC and rare kidney tumor subtypes. We dissected multiple consecutive samples from the center of the tumor towards the tumor's periphery, a normal sample ~5 cm distant from the tumor, and, where feasible, metastatic regions in the adrenal gland. Specifically, we performed 60X multi-region whole-genome sequencing (mWGS), both genome-wide methylation and SNP array profiling, and deep targeted sequencing (average 500X coverage) of 254 cancer driver genes (PMID:24390350). The study population comprises 39 patients with kidney cancers, including 23 with papillary type 1 (pRCC1), 12 with papillary type 2 (pRCC2), one of which also had areas of clear cell, and one each with collecting duct tumor (cdRCC), renal fibrosarcoma rSRC, mixed pRCC1/pRCC2, and an unclassified renal cancer with mixed features of pRCC2 and cdRCC. Based on DNA sample availability, we conducted whole genome sequencing (WGS) on 124 samples from 29 subjects, deep targeted sequencing on 139 samples from 38 subjects, SNP array genotyping on 101 samples from 38 subjects, and genome-wide methylation profiling on 139 samples from 28 subjects. All assays were performed on tumor, metastasis and normal tissue samples, with the exception of the SNP array genotyping, which was conducted only on tumor samples.

  Study phs001573

• Non-viral precision T cell receptor replacement for personalized cell therapy

  The T cell receptor (TCR) provides the fine specificity of T cells to recognize mutations in cancer cells 1-3. We developed a clinical-grade approach based on CRISPR/Cas9 non-viral precision genome editing to simultaneously knock-out the two endogenous TCR genes, TCRα (TRAC) and TCRβ (TRBC), and insert in the TRAC locus the two chains of a neoantigen-specific TCR (neoTCR), isolated from the patient’s own circulating T cells using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with refractory solid cancers received up to three distinct neoTCR-transgenic cell products, each expressing a patient-specific neoTCR, in a cell dose-escalation, first-in-human phase 1 clinical trial (NCT03970382). One patient had grade 1 cytokine release syndrome, and one grade 3 encephalitis. All had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease, and the other 11 had disease progression as best response on therapy. NeoTCR-transgenic T cells were detected in tumour biopsies post-infusion at frequencies higher than the native TCRs pre-infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs recognizing mutational neoantigens, the simultaneous knock-out of the endogenous TCR and knock-in of the neoTCRs using single-step, non-viral precision genome editing, the manufacturing of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene edited neoTCR T cell products, and the ability of the transgenic T cells to traffic to the patients’ tumours.

  Study EGAS00001006898

• National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) Consortium Glaucoma Genome-Wide Association Study

  This is a case-control study of primary open angle glaucoma (POAG). POAG is an intraocular pressure (IOP) related progressive optic neuropathy that ultimately leads to blindness. For this study we have formed a collaborative consortium contributing 2170 POAG cases and 2347 controls with a unified definition of POAG (the NEIGHBOR consortium: NEI Glaucoma Human genetic collaBORation). The case definition has also been harmonized with an additional 976 cases and 1140 controls from the NHGRI supported GENEVA (gene-environment) study of glaucoma (GLAUGEN) (NIH/NHGRI U01HG004728, Pasquale PI). Cases and controls were recruited from ophthalmology clinics and were examined by ophthalmologists. For cases, the clinical exam included intraocular pressure measurements, optic nerve assessment and visual field evaluation. Controls had no family history of glaucoma, normal intraocular pressure and normal optic nerves. Cases and controls were also drawn from two clinical trial populations: Advanced Glaucoma Intervention Study (AGIS, NEI U10EY006827, D. Gaasterland PI) and Collaborative Initial Glaucoma Treatment Study (CIGTS, NEI U10 EY009149, P. Lichter PI). The NEIGHBOR consortium has two Co-Principal Investigators: J. Wiggs (Harvard, MEEI), and M. Hauser (Duke). The consortium includes eleven different centers where data collection and analysis take place. The eleven sites and investigators are: Harvard Medical School (Massachusetts Eye and Ear Infirmary) (J. Wiggs, L. Pasquale); Duke University Medical Center (M. Hauser, E. Hauser, R. Allingham, S. Schmidt); University of Michigan (J. Richards, S. Moroi, P. Lichter); University of Miami (M. Pericak-Vance, R. Lee, D. Budenz); Vanderbilt University (J. Haines); University of California San Diego (K. Zhang, R. Weinreb; T. Gaasterland); University of Pittsburgh (J. Schuman, G. Wollstein); University of West Virginia (A. Realini, J. Charlton, S. Zareparsi); Johns Hopkins University (D. Friedman, D. Zack); Stanford University (D. Vollrath, K. Singh), Eye Doctors of Washington (D. Gaasterland). Hemin Chin serves as the NEI Staff Collaborator. This national collaborative study is supported by multiple NIH grants: NEI R01 EY015543 (Allingham); NEI U10 EY006827 (D. Gaasterland); NHLBI R01 HL073389 (E. Hauser); NEI R01 EY13315 (M. Hauser); NEI U10 EY009149 (Lichter); NEI R01 EY015473 (Pasquale); NEI U10 EY012118 (Pericak-Vance); NEI R03 EY015682 (Realini); NEI R01 EY011671 (Richards); NEI R01 EY09580 (Richards); NEI R01 EY013178 (Schuman); NEI R01 EY015872 (Wiggs); NEI R01 EY009847 (Wiggs); NEI R01 EY010886 (Wiggs); NEI R01 EY144428 (Zhang); NEI R01 EY144448 (Zhang); NEI R01 EY18660 (Zhang). Funding support for genotyping, which was performed at the Johns Hopkins University Center for Inherited Disease Research, was provided by the National Eye Institute (X01HG005259).

  Study phs000238

• Walter and Eliza Hall Institute Research Data Access Committee

  Dac EGAC00001002877

• Genetics of gene expression in primary human immune cells Data Access Committee

  Dac EGAC00001003318

• Bolleboom-Gao peri-tumoral snRNA-seq glioblastoma dataset 2022/A - Data Access Committee

  Dac EGAC00001003049

• Genetics of gene expression in primary human immune cells Data Access Committee

  Dac EGAC00001003327

• Data Access Commitee for the project : Methylome profiling of human mesenchymal chondrosarcoma

  Dac EGAC00001003217

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001003220

• Data Access Commitee for single-cell analysis of multiple myeloma and precursors

  Dac EGAC00001002920

• VIB_VRC Data Access Committee

  Dac EGAC00001000042

• Department of Pediatrics, The University of Tokyo, PPB Data Access Committee

  Dac EGAC00001000163

• SA Pathology Data Access Committee

  Dac EGAC00001000220