14663 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor infiltrating T cells.

  Study EGAS00001006141

• Genomic profiling of metastatic basal cell carcinoma reveals candidate drivers of disease and therapeutic targets

  Study EGAS00001006148

• Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA

  Study EGAS00001006759

• NPY methylated ctDNA is a promising biomarker for treatment response monitoring in metastatic colorectal cancer

  Study EGAS00001006820

• JAK/STAT signaling promotes the emergence of regenerative cell states in ulcerative colitis

  Study EGAS00001007098

• Transcriptome analyses of a large cohort of adult B cell acute lymphoblastic leukemia samples

  Study EGAS00001007217

• Mechanism of action and resistance to Trastuzumab Deruxtecan in patients with metastatic breast cancer

  Study EGAS00001007372

• CUPiD, a cfDNA methylation-based tissue-of-origin classifier for Cancers of Unknown Primary

  Study EGAS00001007445

• RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity

  Study EGAS00001007529

• Low-coverage whole-genome sequencing of cancer and healthy plasma circulating DNA

  Study EGAS00001007593

• scRNA-seq analysis Identifies Hepatic IL-13-Producing ILC3-Like Cells Potentially Linked to Liver Fibrosis

  Study EGAS00001007207

• The WID-EC test for the detection and risk prediction of endometrial cancer

  Study EGAS00001005033

• The DNA methylome of cervical cells and risk of ovarian cancer

  Study EGAS00001005045

• Genomic profiling of subcutaneous patient derived xenograft models of solid childhood cancer

  Study EGAS00001006710

• DEREGULATION OF PRE-mRNA SPLICING IN MISMATCH REPAIR DEFICIENT COLORECTAL CANCER

  Study EGAS00001004863

• Medulloblastoma WES

  WES for tumor and normal samples

  Study EGAS50000000261

• Single Cell Transcriptomics of peripheral immune cells pre- and post-Immune Checkpoint Blockade

  Study EGAS00001005507

• Characterization of UV DNA damage in B-cell precursor acute lymphoblastic leukemia

  Study EGAS00001008128

• An Integrated Approach to Patient Stratification and Therapy Selection in Acute Myeloid Leukemia

  Study EGAS00001004655

• Single cell RNA sequencing of relapsed/refractory multiple myeloma

  Study EGAS00001004805

• Whole Genome Methylation in CLL

  Study EGAS00001000272

• Genetic landscape of non-Down syndrome acute megkaryoblastic leukemia

  Study EGAS00001000379

• GEenetic landscape of hypodiploid acute lymphoblastic leukemia

  Study EGAS00001000380

• A renal cell carcinoma tumorgraft platform to advance precision medicine

  Study EGAS00001005516

• Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia (HIPO, H005)

  Study EGAS00001006361

• FFPE_whole_genome_pilot

  To assess feasibility of whole genome sequencing

  Study EGAS00001001967

• Deep_sequencing_of_melanoma_for_driver_mutations

  Deep sequencing of melanoma for driver mutations

  Study EGAS00001000857

• Angiosarcoma targeted pulldown cancer gene panel

  Extension of angiosarcoma whole genome sequencing study

  Dataset EGAD00001001064

• 20200819_EGA_Qld_Melanoma.biomarkers

  A study looking at Germline and Somatic biomarkers using WES data only

  Dataset EGAD00001006374

• CB

  CB: Aligned sequences used in the error modeling study

  Dataset EGAD00001005261

• RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes

  Study EGAS00001006273

• Characterization of a novel MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line RNA-Seq derived

  Study EGAS00001006803

• HCA_Heart_Adult_Wellcome_spatial

  Spatial transcriptome analysis of the human heart

  Study EGAS00001007848

• Mutations in SKI in Shprintzen-Goldberg syndrome lead to attenuated TGFB responses through SKI stabilization

  Study EGAS00001004908

• Plasma DNA end analysis (mouse)

  Plasma DNA end analysis (mouse)

  Study EGAS00001006700

• Genome-wide sequencing of (cell-free) DNA from Nipple aspirate fluid of Breast cancer patients

  Study EGAS00001007214

• Cell-free DNA sequencing data of healthy control, atrophic gastritis, and gastric cancer patients’ blood

  Study EGAS00001007308

• Neural Systems, Inhibitory Control, and Methamphetamine Dependence

  The Neural Systems, Inhibitory Control, and Methamphetamine Dependence study started in 2011 and is currently finishing data collection for its last participants. The study included methamphetamine abusing individuals and healthy control participants aged 18-55 years. Participants who qualified over the telephone were scheduled to visit the London Laboratory at the UCLA Semel Institute for Neuroscience and Human Behavior for the In-Person Screening Phase. The screening procedures, usually scheduled over two visits, determined if participants were eligible to complete the subsequent study visits. Both groups completed identical screening procedures, with the exception of more in-depth drug use questions for the methamphetamine users. After providing written consent, participants completed questionnaires about their mood, medical, psychiatric and drug use history, personality and life experiences. They also provided a urine sample to determine what drugs they recently used and a breath sample to determine the carbon monoxide levels in their system. The drug screen tested for recent methamphetamine, cocaine, opiates/opioids, benzodiazepines, THC and other amphetamines. Methamphetamine participants needed to test positive for methamphetamine at admission. If methamphetamine participants tested positive for any drugs other than methamphetamine or marijuana, and if healthy control participants tested positive for any drugs other than marijuana, they were excluded from the study. Additionally, the urine samples of female participants were tested for pregnancy; pregnant females were also excluded. If no exclusionary criteria were met during the first screening visit, participants completed a second screening visit to ensure they were mentally and physically healthy enough to participate. The second screening visit included a psychiatric diagnostic interview (DSM-IV (SCID-I) for first 500 participants and the MINI International Neuropsychiatric Interview M.I.N.I for the last 50 participants). Additionally, laboratory tests and procedures were completed by the UCLA General Clinical Research Center and interpreted by a study physician. Laboratory tests included vital signs (heart rate--BPM, blood pressure, and respirations), an electrocardiogram (ECG) to record the electrical activity of the heart, and an 18-cc blood sample to perform laboratory tests which included a complete chemistry and metabolic panel, hepatic panel, Hepatitis-C tests, and HIV test. The laboratory tests from this blood sample ensured that participants' liver and kidneys were functioning normally, and that their standard blood counts (red cell, white cell, and salts) were also normal. If a Hepatitis-C (HCV) or HIV test was positive, participants were not allowed to continue in the study and their results were reported to the California State Health Department. Participants deemed eligible to continue in the methamphetamine group participated on an outpatient basis or were admitted to the UCLA Medical Center to participate on an inpatient basis for up to 10 days. Typically, detectable levels of methamphetamine in urinalysis remain for 2-3 days, therefore inpatient days 0-3 served as a "washout period" and the methamphetamine abusing inpatient participants provided daily urine samples to test for recent drug use and pregnancy (female participants only). Outpatient participants were also required to remain abstinent from all drugs except nicotine and marijuana for at least 4 days prior to study sessions. Self-reported abstinence for outpatients was verified by urine toxicology and saliva screening at every visit to UCLA before completion of study procedures. Neurocognitive assessments, about three hours each, typically took place on two separate days. The purpose of the neurocognitive sessions were to assess participants' intellectual and neurocognitive functioning. On either the same day as the neurocognitive testing or on separate days, both methamphetamine abusers and healthy controls were administered a structural MRI to collect information on brain structure.

  Study phs001197

• Population Architecture using Genomics and Epidemiology (PAGE): Multiethnic Cohort (MEC)

  The Multiethnic Cohort (MEC) has established a large biorepository of blood and urine (N=67,000) and cryopreserved lymphocytes (N=15,000) linked to extensive, prospectively collected risk factors (e.g., diet, smoking, physical activity), biomarkers and clinical data for five racial/ethnic groups. This cohort study of over 215,000 men and women in Hawaii and California is unique in that it is population-based and includes large representations of older adults (45-75 yrs at baseline) for five US racial/ethnic groups (Japanese Americans, African Americans, European Americans, Latinos and Native Hawaiians) at varying risks of chronic diseases. Within the PAGE investigation, the MEC proposes to study: 1) diseases for which we have DNA available for large numbers of cases and controls (breast, prostate, and colorectal cancer, diabetes, and obesity); 2) important cancers that are less common (e.g., lung, pancreas, endometrial cancers, NHL) but for which we propose to pool our data with other funded groups; 3) common traits that are risk factors for these diseases (e.g., body mass index/weight, waist-to-hip ratio, height) and 4) relevant disease-associated biomarkers (e.g., fasting insulin and lipids, steroid hormones). The specific aims are: 1) To determine the population-based epidemiologic profile (allele frequency, main effect, heterogeneity by disease characteristics) of putative causal variants in the five racial/ethnic groups in the MEC; 2) for variants displaying effect heterogeneity across ethnic/racial groups, we will utilize differences in LD to identify a more complete spectrum of associated variants at these loci; 3) investigate gene x gene and gene x environment interactions to identify modifiers; 4) examine the associations of putative causal variants with already measured intermediate phenotypes (e.g., plasma insulin, lipids, steroid hormones); and 5) for variants that do not fall within known genes, start to investigate their relationships with gene expression and epigenetic patterns in small genomic studies. This study is part of the Population Architecture using Genomics and Epidemiology (PAGE) study phs000356.

  Study phs000220

• Identifying novel DNA damage response genes in radiosensitive individuals

  Ionizing radiation is an effective therapeutic agent for cancer treatment as well as a potent carcinogen. Sensitivity to the cell-killing effects of radiation can vary across human population with a subset of individuals displaying extreme hypersensitivity. It is usually attributable to inherited defects in DNA damage response pathways. The present study was designed to elucidate the genetic basis of variation in hypersensitivity to radiation exposure through exome sequencing of radiosensitive individuals, with the ultimate goal of identifying genes with the most significant effects on cellular DNA damage responses. The study participants included subjects referred for clinical testing for Ataxia-telangiectasia (A-T), Nijmegen Breakage Syndrome (NBS) or Ligase IV Syndrome. These are rare, recessive genetic disorders and hypersensitivity to radiation exposure is a common phenotype among individuals affected by all the three disorders. The study participants exhibited phenotypic characteristics similar to individuals with A-T, NBS or Ligase IV Syndrome, but lacked the causative mutations in ATM (GeneID:472) or NBN (GeneID:4683) genes. For further validation of the radiation sensitivity phenotype among the enrolled subjects, B-lymphoblastoid cells lines were established for each subject from peripheral blood lymphocytes. Each cell line was evaluated for displaying impaired survival rates relative to normal controls after exposure to ionizing radiation. 53 subjects with validated phenotype were finally included in the study and DNA extracted from their B-lymphoblastoid cell lines was used for exome sequencing. This sequencing data for radiation sensitive subjects is being made available in the dbGaP. It is hoped that this resource will be beneficial for researchers who wish to further investigate components of human cellular DNA damage response pathways and/or genetic architecture underlying radiation hypersensitivity. This data may also aid in the rational design of new radiosensitizing or radioprotective agents.

  Study phs001911

• The G2 gene expression signature and MYC overexpression are independent poor prognostic factors in childhood high-grade osteosarcoma

  Purpose In high-grade osteosarcoma, prognostic factors at diagnosis are insufficient for stratifying patients into relevant subgroups. Recently, a transcriptomic study developed the G1/G2 gene expression signature, in which the G2 signature was associated with unfavorable survival. An orthogonal study identified MYC amplification as an unfavorable prognostic factor using targeted next-generation sequencing. The purpose of this study was to validate the independent prognostic value and to investigate the combined prognostic value of the G1/G2 signature with, MYC amplification and/or MYC expression for survival prediction. Material and methods This study included pediatric and adolescent patients with high-grade osteosarcoma. RNA sequencing was performed in 48 patients. Whole-exome sequencing was performed in 40 patients. Gene expression signature scores, MYC amplification (defined as > 7 copies) and MYC expression levels were calculated. Multivariable Cox proportional hazards analysis was performed for event-free survival (EFS) (primary endpoint) and overall survival (OS) (secondary endpoint). Results In the full cohort, the 3-year event-free survival rate was 37%. In multivariable Cox regression analysis with metastatic disease stage (n=21, 44%) as covariate, the G2 signature and MYC expression were independently associated with worse outcomes in terms of EFS (Hazard ratio (HR) 3.32, 95% confidence interval (CI) 1.34-8.21 and HR 3.38, 95%-CI 1.71-6.66, respectively) and OS (HR 4.07, 95%-CI 1.19-13.9 and HR 2.88, 95%-CI 1.22-6.76, respectively). MYC amplification was not associated with EFS or OS in univariable analysis (HR 1.88, 95% -CI 0.74-4.77 and HR 0.79, 95%-CI 0.21-3.05, respectively). Conclusion The G2 gene expression signature and MYC expression were independently associated with unfavorable outcomes in a pediatric cohort of patients with high-grade osteosarcoma. The combined prognostic value warrants further prospective validation and could potentially serve as a stratification marker for future osteosarcoma treatment protocols.

  Study EGAS00001008073

• Common Variant GWAS, Genetics & Epidemiology of Colorectal Cancer Consortium (GECCO)

  Genetics & Epidemiology of Colorectal Cancer Consortium (GECCO) is a collaborative effort which aims to accelerate the discovery of colorectal cancer-related variants by discovering, replicating and fine-mapping Genome Wide Association Study (GWAS) findings, conducting a meta-analysis of GWAS data, and investigating how genetic variants are modified by environmental risk factors. The coordinating center for this consortium is based at the Fred Hutchinson Cancer Research Center (Principal investigator: Ulrike Peters). The GECCO Consortium is utilized in the following dbGaP individual studies. To view genotypes, and derived variables collected in these individual studies, please click on the following individual studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs001078 GECCO Consortium. phs000965 VITAL phs001056 DALS phs001077 WHI Colorectal Cancer phs001092 PMH CCFR phs001094 PLCO phs001104 ASTERISK phs001113 DACHS phs001114 HPFS phs001128 PHS phs001129 NHS phs001170 Colo2and3 phs001171MEC Colorectal Cancer

  Study phs001078

• Clonal Evolution of Pre-Leukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia

  Acute myeloid leukemia is an aggressive clonal malignancy of the bone marrow that is the direct result of sequential acquisition of mutations in a single lineage of cells. In this study, we investigate a model in which this mutational acquisition occurs serially in long-lived self-renewing hematopoietic stem cells eventually resulting in frank acute myeloid leukemia. Coding mutations in multiple AML patients were identified using exome sequencing followed by sanger sequencing validation. The level of these mutations was then assessed in residual hematopoietic stem cells from each patient using targeted deep sequencing. These population-level estimates of mutant allele burden were then validated in single cell assays targeted to the identified mutations. This allowed for determination of the order of acquisition of the mutations that preceded the development of the leukemia. The results of this study identify pre-leukemic hematopoietic stem cell clones that could contribute to patient relapse and outcome.

  Study phs000549

• Comprehensive Omics Analysis of Pediatric Solid Tumors and Establishment of a Repository for Related Biologic Studies (10C0086)

  This study (10-C-0086) collected and analyzed tumor and circulating tumor omics of pediatric and young adult patients with relapsed rhabdomyosarcoma who were co-enrolled in and receiving treatment on the interventional study 17-C-0049. We sought to describe the summary genomic findings of tumors, and report on the detection of circulating tumor DNA (ctDNA) in serial samples. Tumor tissue and blood were collected and analyzed. Tumor samples were subjected to whole exome and/or whole genome sequencing paired with RNA-Seq. Cell free DNA (cfDNA) was extracted from serially collected blood samples and sequenced. Fusion status, mutations, and IGF1R and YES1 expression from tumor samples revealed the presence of a PAX3 fusion in most samples, a number of common mutations, and universal but heterogeneous expression of IGF-1R and YES1. ctDNA was detected above the 3% threshold in a majority of patients and analysis of cfDNA demonstrated an ability to monitor tumor clonal evolution.

  Study phs003243

• NHLBI TOPMed: Walk-PHaSST Sickle Cell Disease (SCD)

  Walk-PHaSST study is a multi-center clinical trial to evaluate the effects of sildenafil on Sickle Cell Disease (SCD) population with low exercise capacity associated with an increased Doppler-estimated pulmonary artery systolic pressure (as assessed by the tricuspid regurgitant velocity (TRV)). It is a double-blind, placebo-controlled trial to assess the safety, tolerability, and efficacy of sildenafil in patients with SCD who had both an elevated TRV and decreased exercise capacity. The screening phase of the study enrolled 720 subjects and 74 of them were randomized for the clinical trial. For the screening cohort, we have collected general demographics and race/ethnicity, hemoglobin genotype, physical examination, laboratory screening, transthoracic Doppler echocardiography, and 6 minute walk test in 9 US and 1 UK site. The walk-PHaSST biorepository have banked samples from 610 of the screening subjects. A total of 592 subjects from the screening phase are included in the TOPMed program for WGS.

  Study phs001514

• Circulating Tumor DNA as a Biomarker in Patients with Stage III and IV Wilms Tumor: Analysis from a Children's Oncology Group Trial, AREN0533

  We evaluated the utility of circulating tumor DNA (ctDNA) as a biomarker in the serum and urine of 50 patients with Stage III or Stage IV Wilms tumor (WT) that were enrolled on Children's Oncology Group (COG) trial AREN0533. 49 out of 50 patients had matched tumor samples available for comparison. We profiled samples with ultra-low pass whole genome sequencing (ULP-WGS) and detected ctDNA in 82% of serum samples and 26% of urine samples. We also identified copy-number changes and single-nucleotide variants in the serum and urine samples, and compared them to the tumor data. Our study highlights the advantages of using ctDNA as non-invasive prognostic biomarker with the potential to detect tumor heterogeneity in patients with WT. We believe that prospective validation of ctDNA as a prognostic biomarker in patients with WT is warranted. The ULP-WGS and targeted next-generation sequencing (OncoPanel) data are available in this study.

  Study phs002847

• Genome-wide Identification of Variants Affecting Early Human Brain Development

  This is a genome-wide association study (GWAS) of global brain tissue volumes in human infants. The published study for this project includes 561 infants, and 239 parents gave consent for data sharing through dbGaP. An intronic single-nucleotide polymorphism (SNP) in IGFBP7 (rs114518130; GeneID: 3490) met genome-wide significance for gray matter volume (P=4.15x10-10). An intronic SNP in WWOX (rs10514437; GeneID: 51741) neared genome-wide significance for white matter volume (P=1.56x10-8). Additional loci with small P-values include psychiatric GWAS associations and transcription factors expressed in the developing brain. Genetic risk scores for schizophrenia and ASD, and the number of genes affected by rare copy number variants (CNV burden) did not predict global brain tissue volumes. Integrating these results with large-scale GWAS in adolescents [Philadelphia Neurodevelopmental Cohort (PNC)] and adults [Enhancing Neuro Imaging Genetics through Meta-Analysis version 2 (ENIGMA2)] suggested minimal overlap between common variants impacting brain volumes at different ages.

  Study phs001122

• NIDCD Otitis Media Genetic Susceptibility and Middle Ear Microbial Shifts

  The study funded by R01 DC015004 aims to: (1) Identify rare OM susceptibility variants within families and in probands; and (2) Identify differences in the middle ear microbiome due to OM susceptibility variants. This study will also elucidate mechanisms responsible for the formation and growth of cholesteatoma, and bony erosion and complications due to cholesteatoma e.g. intracranial, hearing/vestibular loss, facial nerve palsy. A better understanding of cholesteatoma pathogenesis will potentially reveal novel drug targets, which can lead to new non-surgical therapies for cholesteatomatous OM. Our specific aims for this administrative supplement are: Aim 1 -- Perform RNA-sequencing using cholesteatoma samples collected from Filipino and Colorado patients who will be screened for FUT2, SPINK5 and A2ML1 variants; and Aim 2 -- Using network analysis, identify bone-expressed proteins potentially interacting with FUT2, SPINK5 or A2ML1, then test protein expression in archival human temporal bone in direct contact with cholesteatoma.

  Study phs001941

• The Microbial Ecology of Bacterial Vaginosis: A Fine Scale Resolution Metagenomic Analysis

  Archived self-collected vaginal swabs were utilized from a pilot study of vaginal douching cessation (NIH/NIAID R03-AI061131). Thirty-nine non-pregnant, reproductive-age women who reported the use of vaginal douche products in the two months prior to screening were enrolled. Thirty-three of these successfully completed the 16-week longitudinal study. Participants self-collected vaginal swabs and smears twice weekly. We report sequences based on the analysis of 16S rRNA gene sequences amplified from whole genomic DNA isolated from the swabs. Bacterial vaginosis (BV) is defined by Gram's stain of vaginal fluid (Nugent's score =7). The large body of information generated will facilitate understanding of vaginal microbial community dynamics, the etiology of BV, and drive the development of better diagnostic tools for BV. Furthermore, it is hoped that the information will enable a more personalized treatment of BV and ultimately, prevent adverse sequelae associated with BV.

  Study phs000261

• Dissecting Cell Composition and Drug Sensitivity in Human Adenoid Cystic Carcinomas (ACCs)

  The study reports the results of single-cell RNA sequencing (scRNA-seq), RNA sequencing (RNA-seq), and whole-exome sequencing (WES) experiments performed on malignant cells isolated by flow cytometry from seven patient-derived xenograft (PDX) lines established from human Adenoid Cystic Carcinomas (ACCs). Of these seven lines, five are characterized by well differentiated histology (ACCX5M1, ACCX6, ACCX14, ACCX22, SGTX6) and two by solid histology (ACCX9, ACCX11). Analysis by scRNA-seq of the well-differentiated PDX line ACCX22 led to identification of cell-surface markers (CD49f, KIT) that enabled the differential purification of the two major cellular components contained in well-differentiated ACCs: myoepithelial-like (CD49f-high/KIT-negative) and ductal-like (CD49f-low/KIT-positive) cells. The study reports the analysis by RNA-seq and WES of purified preparations of myoepithelial-like and ductal-like cells from well-differentiated PDX lines (ACCX5M1, ACCX6, ACCX14, ACCX22, SGTX6) and of ductal-like (CD49f-low/KIT-positive) cells from solid PDX lines (ACCX9, ACCX11).

  Study phs002764