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

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• NIBIT-M4 Data Access Commitee

  Dac EGAC00001002947

• VIB CCB Translational Genetics Data Access Commitee

  Dac EGAC00001002959

• Data Access Commitee for sputum bacterial microbiome data

  Dac EGAC00001003004

• Tampere University Hospital Leukemia Research Data Access Committee

  Dac EGAC00001003156

• NOWAC blood-breast cancer Data Access Committee

  Dac EGAC01000000024

• Molecular Pathology of Lymphoid Neoplasms Data Access Commitee

  Dac EGAC00001003346

• VIB CCB Translational Genetics Data Access Committee

  Dac EGAC00001003415

• IRIBHM computational biology data access committee

  Dac EGAC00001003436

• Data Access Committee for data from EGAS00001007708

  Dac EGAC00001003486

• Singapore Gastric Cancer Consortium Data Access Committee

  Dac EGAC00001002251

• DAC_ICARUS_BREAST01

  Data access committee for ICARUS BREAST 01

  Dac EGAC50000000344

• Genome Asia 100K Consortium

  Dac EGAC00001001439

• Department of Gastroenterology and Hepatology Data Access Committee

  Dac EGAC00001003021

• HaikaLab Immuno-Oncology research group Data Access Committee

  Dac EGAC50000000387

• Data Access Committee for data from EGAS00001007484

  Dac EGAC00001003459

• Walter and Eliza Hall Institute Research Data Access Committee

  Dac EGAC00001003583

• NHLBI TOPMed - NHGRI CCDG: The Vanderbilt University BioVU Atrial Fibrillation Genetics Study

  Atrial fibrillation (also called AFib or AF) is a quivering or irregular heartbeat (arrhythmia) that can lead to blood clots, stroke, heart failure and other heart-related complications. At least 2.7 million Americans are living with AFib. Individuals with early onset atrial fibrillation (AF) are included in this study of cases from the BioVU sample repository. BioVU is Vanderbilt's biobank of DNA extracted from leftover and otherwise discarded clinical blood specimens. BioVU operates as a consented biorepository; all individuals must sign the BioVU consent form in order to donate future specimens. BioVU subjects are de-identified and linked to the Synthetic Derivative enabling researchers to access genetic data/DNA material as well as dense, longitudinal electronic medical record (EMR) information.

  Study phs001624

• Whole exome and MiSeq HTT sequencing of Huntington's disease patient samples

  Sequencing of Huntington's disease patient samples. Whole exome sequencing (n = 463) and MiSeq HTT amplicon sequencing (n = 584) BAM/BAI files. Two analyses (one linear and one logistic) with relevant files.

  Dataset EGAD00001009077

• Ultra-deep sequencing of cell-free DNA derived from reference materials and a patient with asymmetric overgrowth

  This dataset contains: Ultra-deep sequencing data using the Duplex sequencing technology of: 1.) SeraSeq cfDNA reference materials with spike-in variants with allele frequencies from 0% to 5% 2.) One cfDNA sample from a CRC patient 3.) One cfDNA sample from a patient with asymmetric overgrowth Paired-end sequencing was performed with 2x151 bp reads on the NextSeq 500 system. Data is provided as mapped .bam files (aligned to GRCh38/hg38).

  Dataset EGAD00001009784

• Concatenated long-read single-cell RNA sequencing of momentum biopsies of ovarian cancer patients

  Concatenated long-read single-cell RNA sequencing samples prepared using 10X and the HIT-scIsoSeq protocol. The sequencing was performed on Sequel II Pacbio machine. 3 ovarian cancer patients, 5 omentum biopsies samples: 3 metastasis samples (one per patient), 2 healthy samples (one per patient except Patient2). 4 bam files per metastasis sample, 2 bam files per healthy sample.

  Dataset EGAD00001009814

• Reference exome data for Australian Aboriginal populations from Western Australia and the Northern Territory

  Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. The data is provided as 2 VCF files, one for the WA population and one for the NT population.

  Dataset EGAD00001005189

• GeneScreen, a Population Based, Targeted Genomic Screening Study

  The GeneScreen research study was based at the University of North Carolina (UNC) at Chapel Hill. It brought together researchers from different disciplines, including genetics, clinical medicine, bioethics, sociology, anthropology, psychology, and public health, to study the best ways to offer targeted genetic screening to the general adult population. DNA samples were collected from people who joined GeneScreen to look at a targeted panel of 17 genes. It tested for genetic differences (called mutations) that can cause one of 11 rare, but preventable or treatable conditions, including certain types of cancer and heart disease. Each condition has specific medical advice people can follow with their doctors to prevent or treat a serious health problem. The GeneScreen study was approved by the UNC Institutional Review Board and by the Kaiser Permanente Center for Health Research Institutional Review Board. GeneScreen is funded by the National Human Genome Research Institute of the National Institutes of Health.

  Study phs001817

• dbGaP Collection: NIH Autism -omics Studies

  Autism Spectrum Disorders (ASD) are early onset neurodevelopmental syndromes characterized by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. ASDs afflict ~1% of the human population, and represent a major public health burden. Evidence for the etiology of ASD has consistently pointed to a strong genetic component, though the genetic architecture is indisputably complex. This dbGaP Collection consists of studies that include GWAS, sequencing (targeted, exome, whole genome), transcriptomics, etc, across many different cohorts. Many of the datasets have been curated and harmonized with NDAR prior to submission to dbGaP. Researchers who request and are approved to access this collection will be granted access to all related substudies in dbGaP as well as all NDAR data. Individual level genomics data will only be available for download through dbGaP along with minimal phenotype and pedigree information. Detailed phenotype and available imaging data related to these same research subjects are available for query and download within NDAR. The NDAR GUID will allow individual genomic data to be associated with all NDAR data collected for those subjects.

  Study phs000764

• Open Targets 020 Epigenomes of Cell Lines (2018-10-23)

  There is currently a drive to establish cell based assay systems of greater human biological and disease relevance through the use of well characterised transformed cell lines, primary cells and complex cellular models (e.g. co-culture, 3D models). However, although the field is gaining valuable experience in running more non-standard & complex cell assays for target validation and compound pharmacology studies, there is the lack of a systematic approach to determine if this expansion in cell assay models is reflected in increased human biological and disease relevance. The increasing wealth of publically available transcriptomic, and epigenome (ENCODE and Epigenome Roadmap) data represents an ideal reference mechanism for determining the relationship between cell types used for target & compound studies to primary human cells and tissues from both healthy volunteers & patients. The CTTV020 epigenomes of cell line project aims to generate epigenetic and transcriptomic profiles of cell lines and compare these with existing and newly generated reference data sets from human tissue and cell types. The aim is to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients. Multiple cell types commonly used within research have been grouped according to biology. Examples include erythroid, lung epithelial, hepatocyte cell types and immortalised models of monocyte / macrophage biology. 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 please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-10-23.

  Dataset EGAD00001004415

• Sickle Cell Disease Implementation Consortium Registry (SCDIC Registry-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To understand the barriers to care and other factors related to reduced healthcare utilization after the transition from pediatric to adult SCD care which may contribute to increased morbidity and mortality.Background: Fifty years ago, it was rare for individuals with SCD to live beyond childhood. Advances in care delivery and treatment have more than doubled the life expectancy of individuals with sickle cell disease (SCD) since 1972. Beginning in the 1970s, measures such as newborn screening, prophylactic administration of penicillin, and immunization against bacterial infections decreased complications and morbidity, increasing the length and quality of life of children with SCD. Blood transfusions are currently the only proven way to prevent some of the major complications of SCD, especially recurrent stroke. They are also used frequently to help manage some of the acute complications of SCD. More recently, the use of hydroxyurea (HU) as a therapeutic agent to increase fetal hemoglobin has been shown to further reduce the debilitating symptoms of and improve survival in SCD. L-glutamine and crizanlizumab are additional treatments to reduce pain crises and voxelotor is approved to lower the risk of anemia and improve blood flow. In the absence of a widely accessible cure, treatment for SCD is usually aimed at avoiding crises, relieving symptoms, and preventing complications. Many of the advances in treatment have not translated into an increase in longevity or quality of life for adolescents and adults because of disparities in access to routine primary health care.Individuals with SCD experience a markedly increased mortality beginning in the second decade of life. The third and later decades of life are frequently associated with severe chronic pain progressive organ damage and frequent hospitalizations. The provision of evidence-based and expert opinion-based care in SCD is complicated by the difficulties that many patients experience in obtaining access to the health care system and in receiving long-term care from knowledgeable providers. A registry of 2,400 people with SCD was established to provide a rich resource to study the natural history of SCD and to understand barriers to care during the transition from pediatric to adult care. Participants: 2,438 participants with a confirmed diagnosis of SCD were enrolled into the registry over an 18-month period. At the time of enrollment, all participants were 15-45 years of age, English speaking, and without a bone marrow transplant.Design: The SCDIC Registry is a longitudinal observational cohort study. At enrollment, data collection included a medical record abstraction of clinical history, the most recent lab results, and a participant survey which included several patient reported outcomes from PROMIS, ASCQ-Me and NeuroQoL. Similar surveys were administered at annual follow-up. Four to five years after enrollment, a second record abstraction was completed with all clinical events that occurred since enrollment and another set of recent labs. There were many research questions proposed to be answered with the study data thus there was no primary outcome.Conclusions: As noted previously, there were no primary outcomes determined at the start of the study. Research questions included examination of co-morbidities, healthcare utilization, and patient reported outcomes. Key findings from the Registry include:Executive dysfunction, learning difficulties, and poor comprehension significantly associated with poor activities of daily living skills. Executive dysfunction also associated with HU non-adherence. Continuing HU after conception increased odds of miscarriage or stillbirth compared to women who were not using HU. Continuing HU after conception increased odds of low birth weight in infants. Compared to adolescents, young adults had significantly more severe pain, organ dysfunction, mental health disorders, sleep problems, and barriers to medical care. Young adults were significantly less likely to see a sickle cell specialist in the past 2 years. Females had higher pain frequency and severity, more pain episodes, anxiety, depression, hospitalizations, and higher fetal hemoglobin levels. Males had more respiratory, musculoskeletal, genitourinary, and cardiovascular complications, more skin ulcers, and more use of HU. Among 128 subjects that died during the study period, iron overload, pulmonary hypertension, and depression, were significant predictors of the risk of death in multivariate analyses.

  Study phs004203

• Recurrent CLTC::SYK fusions and CSF1R mutations in juvenile xanthogranuloma of soft tissue

  In this study, the genomic landscape of extracutaneous juvenile xanthogranuloma (JXG) was analyzed. By leveraging the Dutch Nationwide Pathology Databank (Palga), tumor samples were obtained from different academic medical centers in the Netherlands. The study was approved by the Palga Scientific Council and Privacy Committee (LZV-2016-183) and the Institutional Review Board of Leiden University Medical Center (B19.074). In addition, the study was approved by the Biobank and Data Access Committee of the Princess Máxima Center for Pediatric Oncology (PMCLAB2024.0512). Provided are whole transcriptome sequencing (WTS) data of 3 histiocytic tumors with CLTC::SYK fusions. WTS was performed in the routine workflow of the Princess Máxima Center for Pediatric Oncology (as described in Hehir-Kwa, et al. JCO Precis Oncol 2022). RNA was derived from formalin-fixed paraffin-embedded tumor tissue (n=1) or from frozen tumor tissue (n=2).

  Study EGAS50000000584

• LUD2015-005 Trial Data Access Committee

  Dac EGAC00001002863

• THE NOWAC BLOOD-BREAST CANCER COMMITEE DATA ACCESS AGREEMENT

  Dac EGAC00001000743

• Board considering access to van Hijfte snRNA-seq GBM dataset

  Dac EGAC00001003044

• Genomics of MPNST (GeM) Consortium Data Access Committee

  Dac EGAC00001002563

• Thirant et al Nature Communications 2023 Data Access Commitee

  Dac EGAC00001003192

• European Network of Genomic and Genetic Epidemiology Data Access Committee

  Dac EGAC00000000008

• "Data Access Center Cancer Genomics Group"

  Dac EGAC00001000030

• Cancer Genome Database Data Access Committee (CGDB_DAC)

  Dac EGAC00001000033

• Signal Transduction Team ICR (2011) Data Access Committee

  Dac EGAC00001000040

• UPF - Evolutionary Population Genetics lab Data Access Committee

  Dac EGAC00001000244

• MS-Twin Data Access Committee

  Dac EGAC00001000331

• Coagulation Factor XI GWAS meta-analyses Data Access Committee

  Dac EGAC00001000567

• Data access committee for BAMS exome sequencing data.

  Dac EGAC00001000583

• UK Biobank Access - http://www.ukbiobank.ac.uk/using-the-resource/

  Dac EGAC00001000641

• University Hospital of Basel - Novartis collaboration Data Access Committee

  Dac EGAC00001000747

• JDRF/Wellcome Diabetes and Inflammation Laboratory Data Access Committee

  Dac EGAC00001000756

• GWAS of Childhood acute lymphoblastic leukaemia - Data Access Committee

  Dac EGAC00001000859

• Harbin Medical University Cancer Hospital Data Access Commitee

  Dac EGAC00001000948

• Data Access Committee for Niigata-NIG collaborative work

  Dac EGAC00001000955

• Human LV H3K27ac ChIP-seq Data Access Commitee

  Dac EGAC00001001169

• ASAN Center for Cancer Genome Discovery Data Access Commitee

  Dac EGAC00001001285

• St. Anna Children's Hospital / CCRI Histiocytosis Data Access Committee

  Dac EGAC00001001297

• Singapore National Precision Medicine Programme Data Access Committee

  Dac EGAC00001001322

• ASAN Center for Cancer Genome Discovery Data Access Commitee

  Dac EGAC00001001391

• Data Access Commitee, UCSF Pediatric Bithalamic Glioma Genome Project

  Dac EGAC00001001394

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001001404

• Cancer Sequencing Data Access Committee

  Dac EGAC00001001428

• Melanoma Spatial Heterogeneity Data Access Committee

  Dac EGAC00001001446

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001001505

• Tampere University Hospital Leukemia Reserach Data Access Committee

  Dac EGAC00001001551

• Mapping of mtDNA deletions and duplications Data Access Committe

  Dac EGAC00001001558

• Princess Margaret Head and Neck Cancer Data Access Committee

  Dac EGAC00001001647

• MD Anderson Lymphoma & Myeloma Data Access Committee

  Dac EGAC00001001685

• FIMM AML Single-Cell RNA-seq Data Access Committee

  Dac EGAC00001001709

• Biomedical Epigenomics Data Access Committee

  Dac EGAC00001001720

• Plasma cells in coeliac disease Data Access Committee

  Dac EGAC00001001753

• Low-grade Serous Ovarian Carcinoma Data Access Commitee

  Dac EGAC00001001763

• Breast Cancer Single-Cell Data Access Committee

  Dac EGAC00001001974

• VIB CCB Translational Genetics Data Access Committee

  Dac EGAC00001002006

• Multifocal ileal NETs WGS HFF7VCCXY folder Data Access Committee

  Dac EGAC00001002033

• IDIBAPS - Translational Research in Hepatic Oncology - Data Access Commitee

  Dac EGAC00001002069

• Varn Lab Data Access Committee

  Dac EGAC00001002118

• Molecular Characterization of HCC in Mongolia Data Access Commitee

  Dac EGAC00001002158

• MRC Institute of Genetics and Cancer Data Access Committee

  Dac EGAC00001002163

• Data access committee breast cancer whole genome sequencing HRD

  Dac EGAC00001002286

• Multifocal ileal NETs WGS HF3J5CCXY folder Data Access Committee

  Dac EGAC00001002321

• Multifocal ileal NETs WGS HF3FKCCXY folder Data Access Committee

  Dac EGAC00001002323

• Multifocal ileal NETs WGS HFG3FCCXY folder Data Access Committee

  Dac EGAC00001002324

• Multifocal ileal NETs WGS HF3NYCCXY folder Data Access Committee

  Dac EGAC00001002325

• Multifocal ileal NETs WGS HFFWLCCXY folder Data Access Committee

  Dac EGAC00001002326

• Data access Commitee for anti-PD1 in HCC data

  Dac EGAC00001002404

• Data Access Committee for Niigata-NIG collaborative work

  Dac EGAC00001002429

• Hematology Research Unit Helsinki Data Access Committee

  Dac EGAC00001002444

• Data Access Committee for Niigata-NIG collaborative work

  Dac EGAC00001002469

• B cells in Multiple Sclerosis Data Access Committee

  Dac EGAC00001002476

• TNBC (COH_TNBC_RNAseq) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002518

• TNBC (UW_OvCa_RNASeq) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002524

• TNBC (UW_OvCa_WGS) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002544

• NPC genome-wide human SNP array data access commitee

  Dac EGAC00001002560

• Single-cell Multiomics Clonal Hematopoiesis Team Data Access Committee

  Dac EGAC00001002735

• Institute of Pathology LMU Munich Data Access Commitee

  Dac EGAC00001002931

• Institute of Pathology LMU Munich Data Access Commitee

  Dac EGAC00001002932

• Multiple myeloma long-term survivor data access commitee

  Dac EGAC00001003078

• Hospital del Mar Research Insitute Data Access Comitte

  Dac EGAC00001002512

• Kyoto Prefectural University of Medicine Data Access Commitee

  Dac EGAC00001003411

• TNBC (COH_WGS) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002574

• Experimental Therapeutics in Lymphoid Malignancies Data Access Commitee

  Dac EGAC00001003210

• HPV Virome Consortium Data Access Committee

  Dac EGAC00001000141

• Data access commitee at the Molecular Exercise Physiology group

  Dac EGAC00001002606

• APOBEC Breast Data Access Committee

  Sarat Chandarlapaty chandars@mskcc.org

  Dac EGAC50000000554

• UQCCR/QCMG brain metastasis sequence analysis Data Access Committee

  Dac EGAC00001000180

• Data Access Committee for Triple Negative Breast Cancer dataset

  Dac EGAC00001003584

• Combination pembrolizumab and radiotherapy induces systemic anti-tumor immune responses in immunologically-cold non-small cell lung cancer

  The abscopal effects of radiation may sensitize immunologically “cold” tumors to immune checkpoint inhibition (ICI). We investigated the immunostimulatory effects of radiotherapy leveraging multi-omic analyses of serial tissue and blood biospecimens (n=293) from a phase 2 clinical trial of stereotactic body radiation therapy (SBRT) followed by pembrolizumab in metastatic non-small cell lung cancer (NSCLC; NCT02492568). Patients with immunologically-cold tumors (low tumor mutation burden, null PD-L1 expression, WNT-pathway mutated) in the SBRT arm had significantly longer progression-free survival compared to ICI alone (P<0.05). Induction of interferon-gamma, interferon-alpha, and antigen processing and presentation gene sets was significantly enriched post SBRT in non-irradiated tumor sites (FDR adjusted P<0.01). Significant on-therapy expansions of new and pre-existing TCR clones in both the tumor and blood compartments were noted in the SBRT arm (P<0.05). These findings support the systemic anti-tumor effects of immuno-radiotherapy and may open a therapeutic window of opportunity to overcome resistance to ICI.

  Dataset EGAD50000000404

• Genomic Answers for Kids (GA4K)

  Identification of complex genetic variants including defects in gene regulatory circuits and uncharacterized genes present challenges for rare disease diagnosis. In Genomic Answers for Kids program we apply the joint interpretation of patient genome sequence with genomic endophenotypes to expand the clinically actionable genome among pediatric cases of suspected genetic disease. Our objective is to examine the role of novel and under-interpreted sequence variation by combining complete DNA sequences, personal epigenetic variations and massively parallel functional screens. To achieve this we perform augmented whole genome sequence (WGS) interpretation including reanalysis of clinical exomes as well as generating WGS for patients with negative exome results all be subject to family-based semi-automated recall pipeline to discover missed diagnostic variation. We use linked-read and long-read sequencing technologies to focus on putative structural variants missed in short-read genome and exome analysis by the optimized integration of linked and long read technologies that also improve identification of transmission patterns of all variants, as well as resolving genomic regions resistant to standard alignment. We also include tissue DNA sequencing to investigate somatic mosaicism. To further assist with WGS interpretation for uncommon variation we capture snapshots of patient transcriptomes and epigenomes in individual cells using single-cell RNA (scRNA) and sc open chromatin (scATAC) as well as bulk whole genome bisulphite genome sequencing for methylome interpretation. Alternative splicing is functionally assessed in available patient tissues using RNA-seq, including full length cDNA sequences by IsoSeq (PacBio) methodology. Our overarching goal is an increase rate of diagnostic genomic findings up to two-fold among rare disease, resulting in the majority (>50%) of patient cases resolved by the integrated system developed in our program.

  Study phs002206