14676 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Jagged ends of plasma DNA (human)

  Jagged ends of plasma DNA (human)

  Study EGAS00001005562

• ATAC-seq/ChIP part

  Epigenetics: ATAC-seq and ChIP-seq data

  Study EGAS00001006520

• The genomic landscape of GCs

  whole-genome sequencing of 168 paired GCs.

  Study EGAS00001007355

• The cell free DNA methylome of primary and metastatic prostate tumors

  Study EGAS00001005522

• Collaborative Study of Genes, Nutrients and Metabolites (CSGNM)

  While many genetic and metabolic studies focus on understanding disease states, this genome wide association study (GWAS) was designed to understand the influence of genetic variants on circulating metabolites and factors in normal, healthy individuals. Over 2500 healthy, ethnically Irish college students attending Trinity College Dublin completed a health and diet questionnaire and provided a non-fasting blood sample to be used for genetic and metabolic analysis. The questionnaire was designed to collect information on age, sex, height, weight, medical conditions, smoking, dietary habits, and consumption of alcohol, fortified foods, and supplements. Extracted DNA was genotyped using the Illumina HumanOmni1-Quad Beadchip. Metabolites were measured using a number of methods and focused on those relevant to the folate/vitamin B12 pathway.

  Study phs000789

• Genomic Regions Associated with Susceptibility to Barrett's Esophagus and Esophageal Adenocarcinoma in African Americans: The Cross BETRNet Admixture Study

  Differences in rates of diseases between different populations with similar environments are presumed to be secondary to variability in population frequencies of disease causing alleles. Recently admixed populations such as African Americans (AAs) provide a natural opportunity to identify disease-causing variants by examining the ancestry of long chromosomal haplotypes. Admixture mapping approach can be successful in locating genes for diseases such as EAC whose rates varies markedly between the ancestral populations. This is a case only study with 54 African American cases and also on a subset of 28 cases with high genotyping quality. We seek to identify chromosome regions that have excess European ancestry and contrasting it to excess African ancestry.

  Study phs001454

• Episodic Ataxia Syndrome: Longitudinal Study

  Individuals with episodic ataxia experience recurrent attacks of dizziness and incoordination; between attacks patients are typically normal. The majority of cases are likely caused by an inherited genetic mutation. However, in some patients we are unable to identify the mutation. So far, 2 genes have been identified which cause different types of episodic ataxia. Ultimately, when the actual mutation is identified the protein product of the gene can be studied and specific medications can be designed. During this study, we will clinically evaluate patients with EA and follow them over time to help us better characterize the disease. We will also obtain blood samples to test for the known genetic mutations. In the future, we plan to coordinate trials of medications for the treatment of these disorders.

  Study phs000521

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): COVID-19 Experience Study (C19EX) Survey

  This was conducted virtually through the Achievement studies platform during the current COVID-19 pandemic. Participants were asked to complete a survey every day to capture information about whether they had experienced symptoms corresponding to respiratory, ILI, and COVID-19 infections within the previous 24 hour period, their experiences with the healthcare system, treatments, diagnostic testing, and their behaviors and potential risk factors. Participants were also asked to share their wearable activity tracker data. The purpose of this study was to better understand the geographic spread of diseases, impacts on daily life, and behavioral and physiological functioning in relation to recent self-reported respiratory disease, influenza-like-illness (ILI), and coronavirus disease (COVID-19) events.DOI: https://rapids.ll.mit.edu/10.57895/6m5z-je42

  Study phs002537

• Dana-Farber Cancer Institute (DFCI) Wu Lab/Avicenne CLL RNA-Seq Study

  Chronic Lymphocytic Leukemia (CLL) is a hematological malignancy characterized by accumulation of CD5+ B cells in peripheral lymphoid organs, bone marrow and blood. Recently, the advent of large-scale whole-exome sequencing of hundreds of CLL samples has led to gain a comprehensive understanding of the mutational landscape of this clonal B cell malignancy, but the functional effects of the putative driver mutations thus discovered are largely unknown. In this study, we analyze RNA-seq data from CLL patients to characterize dysregulated biological pathways regarding the presence of recurrent mutations. Source of tumor is patients' PBMC isolated from peripheral blood using the Ficoll method. Purity was confirmed using flow cytometry flow (>80% in all cases).

  Study phs002335

• A study of resistance to novel coronavirus infection in health care workers

  There have been cases of what appear to be nosocomial infections among healthcare workers at several hospitals. The infected healthcare workers were assumed to have contracted the disease through close contact with infected patients. However, we confirmed at each medical institution that there were many healthcare workers who had apparently had closer contact with infected patients than with infected patients, but had not contracted the disease. Thus, the purpose of this study was to clarify the internal factors that make individuals less susceptible to novel coronavirus infection and their stress tolerance, and to establish a system that contributes to the appropriate allocation of healthcare workers and the creation of a system that can more safely deal with this disease in the future.

  Study JGAS000562

• Exome sequencing of UK Birth Cohorts - Millennium Cohort Study

  Birth cohort studies involve repeated surveys of large numbers of individuals from birth and throughout their lives. They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technologies. This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights from population genetics to rare disease associations. Avon Longitudinal Study of Parents and Children (ALSPAC)recruited 14,775 babies of predominantly White ethnicity in the Avon county of south-west England between 1991 and 1992. Born in Bradford (BiB) is similarly focused on a particular local area, the city of Bradford in the north of England, and recruited 13,858 babies between 2007 and 2011, of whom ~41% self-report as white British and ~59% as other ethnicities, predominantly Pakistani. Millennium Cohort Study (MCS) is a national cohort that recruited 18,827 children born between 2000 and 2002, intentionally over-sampling areas with high child poverty, large ethnic minority populations, and smaller UK nations (Wales, Scotland and Northern Ireland) Available here is a subset of exome-sequenced parents and children from these studies (CRAMS and post-QC VCFs) as detailed in https://doi.org/10.12688/wellcomeopenres.22697 [doi.org]. Phenotypic data is also available by submitting an application to the corresponding cohort: https://cls.ucl.ac.uk/cls-studies/millennium-cohort-study/ [cls.ucl.ac.uk]

  Dataset EGAD00001015372

• Clinical validity of post-surgery circulating tumor DNA (ctDNA) in stage III colon cancer patients treated with adjuvant chemotherapy: the PROVENC3 study

  The PROVENC3 study aimed to determine the clinical validity of post-surgery ctDNA testing in patients with stage III colon cancer treated with adjuvant chemotherapy (ACT). Blood was collected pre-surgery, post-surgery and post-adjuvant chemotherapy. Tumor-informed plasma ctDNA detection was performed through integrated whole genome sequencing (WGS) analyses of formalin-fixed paraffin-embedded tumor tissue DNA (80x), white blood cell germline DNA (40x) and plasma cell-free DNA (30x). These raw WGS data for 209 patients are shared in .cram format in this EGA submission. For 196/209 of these patients there is overlapping FFPE tumor RNA sequencing data available, shared in .fastq format in this EGA submission.

  Study EGAS50000000804

• The Pioneer 100 Wellness Project (P100)

  108 individuals (age 21-89+ years; 59% males, 41% females; 89% Caucasian; not recruited based on any specific phenotype) participated in an IRB-approved study from April 2014 to January 2015. Each individual had the genome sequenced in full. Blood was collected in clinics every three months. Additionally, participants completed at-home collections of saliva, stool, and first morning void urine every three months. Stool and saliva samples were shipped directly to the vendor by the participant, while urine was given back to the study coordinators for distribution to the proper sample vendor. For each successful participant in each round we carried out 218 clinical laboratory tests, measured up to 643 metabolites and 262 proteins, and measured the abundance of 4616 operational taxonomic units (OTUs) in the gut microbiome using 16S rRNA sequencing. The P100 study had four objectives: 1) Establish cost-efficient procedures for generating, storing and analyzing multiple sources of health data obtained over time from participants and analyzed in combination with genomic data; 2) Develop and deploy analytic tools for integrating these diverse datasets and deriving actionable information from their observed interrelationships; 3) Identify novel patterns within the streams of health data that indicate either wellness, or transitions between wellness and disease; 4) Learn how to best interface with and present longitudinal health information to individuals by studying the reactions and feedback from participants as they are presented actionable information.

  Study phs001363

• Rare Cancer Tumors Project

  A large proportion of common cancers affecting patients around the world have been selected for comprehensive cancer genome studies. Further efforts will be needed to tackle the remaining tumor types, including the rare forms of cancers. Although rare, these cancers tend to be more aggressive and fast growing with an early recurrence following initial chemotherapy and poor prognosis. Besides, patients diagnosed with rare cancers may have difficulty finding a physician knowledgeable in treating their type of cancer. While sample collection is a major challenge, the integrated genomic analyses would identify novel causative genes in these rare cancers, shed new light on the biology of the rare cancers, as well as guide novel targeted cancer therapies. Through efficient collaboration, the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine (BCM) has collected/is expected to collect 20 different types of rare cancers, 15-30 cases each. Whole-exome sequencing and high-resolution SNP array analysis were/will be performed for all cases and whole-genome sequencing was designed for a selected subset of the cases. The Rare Cancer Tumors Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in this sub-study, please click on the following sub-study below or in the "Sub-studies" section of this top-level study page phs000725 Rare Cancer Tumors Cohort. phs000754 Intracranial Germ Cell Tumors phs000861 Craniopharyngioma Tumors phs000859 Sezary Syndrome Genomic Analysis

  Study phs000725

• Oral Immunotherapy for Induction of Tolerance and Desensitization in Peanut-Allergic Children (IMPACT)

  Brief Summary:This is a randomized, double-blind, placebo-controlled, multi-center study comparing peanut oral immunotherapy (OIT) to placebo in the induction of tolerance and desensitization in peanut-allergic children. Eligible participants with peanut allergy will be randomly assigned to receive either peanut OIT or placebo for 134 weeks followed by peanut avoidance for 26 weeks.Detailed Description:An initial oral food challenge (OFC) to 1 g of peanut flour (500 mg peanut protein) will be conducted. Participants must have a clinical reaction during this OFC to initiate study dosing. After the initial OFC, the study design includes four phases:Initial dose escalation (1 day): Peanut or placebo dosing will be given incrementally and increase every 20 minutes until a dose of 12 mg peanut flour (6 mg peanut protein) or placebo flour is given. Build-up (30 weeks): Initial observed dose administration of highest tolerated dose, followed by daily OIT at home with return visit every 2 weeks for dose escalation. Maintenance (104 weeks):The participant will continue on daily OIT with return visits every 13 weeks. At the end of this phase the participant will undergo a blinded OFC to 10 g peanut flour (5 g peanut protein). Avoidance (26 weeks): In this final phase participants will be seen every 13 weeks. At the completion of this phase participants will have a final blinded OFC to 10g peanut flour (5 g peanut protein)

  Study phs003109

• Phenotype Risk Scores Identify Patients with Unrecognized Mendelian Disease Patterns

  This study was designed to assess the phenotypic effects of rare variants. Rare variants are difficult to study in a high-throughput manner because most cohorts are underpowered to detect associations. In order to gain power to test rare variants, we use Phenotype Risk Scores (PheRS) based on features of Mendelian diseases. PheRS is calculated using claims data from an EHR that is mapped to clinical features from OMIM's clinical descriptions of Mendelian disease. We calculated PheRS for 1,204 Mendelians diseases in a cohort of 21,701 individuals genotyped on the HumanExome BeadChip. We then tested for association between these diseases and rare variants in causal genes. A phenotype risk score is calculated as the weighted sum of features for a given disease. The features are defined as a set of phecodes (consolidated ICD codes) associated with a particular Mendelian disease as described in OMIM. The weights for each phecode are calculated as the log inverse prevalence of the phecode in our cohort. For an individual, their score equals the sum of the weights for each phecode that is present in their medical record. Our study was based on a cohort of individuals with genotype data linked to de-identified electronic health records (EHR) from Vanderbilt's BioVU resource. We hope that this method will help generate phenotype-genotype correlation data on rare variants which in turn may inform rare variant interpretations use for diagnostics.

  Study phs001516

• Comprehensive Genomic Characterization of Translocation Renal Cell Carcinoma

  Xp11 translocation renal cell carcinoma (tRCC) is a rare, female-predominant cancer driven by a fusion between the TFE3 gene on chromosome Xp11.2 and a partner gene on either chrX or an autosome. It remains unknown what types of rearrangements underlie TFE3 fusions, whether fusions can arise from both the active (chrXa) and inactive X (chrXi) chromosomes, and whether TFE3 fusions from chrXi translocations account for the female predominance of tRCC. To address these questions, we performed haplotype-specific analyses of chrX rearrangements in tRCC whole genomes. We show that TFE3 fusions universally arise as reciprocal translocations and that oncogenic TFE3 fusions can arise from chrXi:autosomal translocations. Female-specific chrXi:autosomal translocations result in a 2:1 female-to-male ratio of TFE3 fusions involving autosomal partner genes and account for the female predominance of tRCC. Our results highlight how X chromosome genetics uniquely constrains somatic chrX alterations and underlies cancer sex differences.This version of the dbGaP study provides a comprehensive set of whole genome data and tables with clinical information collected for the 16 patients (15 pateints as tRCC and 1 patient as ccRCC) in the study cohort. The data also contains 12 RNA-seq samples used in the study and analyses. We anticipate that this data will considerably advance our molecular and genetic understanding of oncogenic translocations in TFE3-tRCC involving inactive chromosome X and its role in cancer sex bias.

  Study phs003008

• Diagnostic Genomic Analysis is Prognostic in AYA ALL Patients Treated on a MRD-Stratified Paediatric Protocol

  Background: Over the last decade, next generation sequencing has enabled classification of multiple new recurrent genomic drivers of acute lymphoblastic leukemia (ALL). We provide a comprehensive genomic survey of adolescent and young adult (AYA) patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL06 study. ALL06 clinical trial described the efficacy and tolerability of AYA ALL patients aged 15-39 years treated on a single minimal residual disease (MRD)-stratified platform. In this study we have taken the ALL06 cohort and retrospectively performed comprehensive genomic analyses assessing response of AYA patients with various genomic subtypes treated with a paediatric approach. Methods: Genomic risk classification of B- and T-ALL patients (n=57) enrolled to the study was based on mRNA-Sequencing, MLPA, immunophenotyping and cytogenetics. Results: Using this approach, 36/40 (90%) B- and 13/17 (76.5%) T-ALL patients were classified according to genomic risk. We have linked outcome data with each patient’s genomic risk and found a strong correlation between adverse genomic risk and MRD at the end of consolidation, translating to inferior overall and relapse free survival. Patients with adverse risk genomics who achieved negative MRD status had improved responses compared to those with persistent MRD. Patients with standard risk genomics had excellent responses regardless of their MRD status. Conclusion: Our data argue strongly for incorporation of a genomic risk classification into future ALL treatment paradigms at the time of diagnosis.

  Study EGAS50000000752

• Predictive value of chromosome 18q11.2-q12.1 loss for benefit from bevacizumab in metastatic colorectal cancer; a post-hoc analysis of the randomized controlled trial AGITG-MAX

  Patients and methods: We analyzed tumor samples of 256 patients enrolled in the AGITG-MAX 3-arm randomized controlled trial (RCT) who were randomly assigned to receive either capecitabine, or capecitabine and bevacizumab with- or without mitomycin. Chromosome 18q11.2-q12.1 copy number status was measured and correlated with PFS according to a predefined analysis plan with marker-treatment interaction as the primary end-point.Results: Chromosome 18q11.2-q12.1 losses were detected in 71% of patients (181/256) characteristic for mCRC. Consistent with the non-randomized study, significant PFS benefit of bevacizumab was observed in chromosome 18q11.2-q12.1 loss patients (P=0.009), and not in 18q no-loss patients (P=0.67). Although significance for marker-treatment interaction was not reached (Pinteraction = 0.28), hazard ratio and 95% confidence interval (HRinteraction 0.72, CI 0.39 - 1.32) show striking overlap with the non-randomized study cohorts (HRinteraction 0.41, CI 0.32 - 0.8) supported by a non-significant Cochrane chi-squared (P=0.11) for heterogeneity. Conclusions: PFS characteristics for marker positive- and negative patients randomized for treatment with- or without bevacizumab were consistent with those of the non-randomized discovery study, though the number of AGITG-MAX samples fell short to reach significance for marker-treatment interaction. Post-hoc analysis of the AGITG-MAX RCT provides supportive evidence for chromosome 18q11.2-q12.1 as a clinically relevant predictive marker for mCRC patients.

  Study EGAS00001005453

• T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases

  Colorectal liver metastasis (CLM) is a leading cause of colorectal cancer mortality, and the response to immune checkpoint inhibition (ICI) in microsatellite stable CRC has been disappointing. Administration of cytotoxic chemotherapy may cause increased density of tumour infiltrating T cells, which has been associated with improved response to ICI. This study aimed to quantify and characterize T cell infiltration in CLM using T cell receptor (TCR) repertoire sequencing. Eighty-five resected CLM from patients included in the Oslo CoMet study were subjected to TCR repertoire sequencing. Thirty-five and 15 patients had received neoadjuvant chemotherapy (NACT) within a short or long interval, respectively, prior to resection, while 35 patients had not been exposed to NACT. T cell fractions were calculated, repertoire clonality was analysed based on Hill evenness curves, and TCR sequential convergence was assessed using network analysis. Increased T cell fractions (10.6% vs 6.3%) were detected in CLM exposed to NACT within a short interval prior to resection, while modestly increased clonality was observed in NACT exposed tumours independently of the timing of NACT administration and surgery. While private clones made up >90% of detected clones, network connectivity analysis revealed that public clones contributed the majority of TCR sequence convergence. TCR repertoire sequencing can be used to quantify T cell infiltration and clonality in clinical samples. This study provides evidence to support chemotherapy-driven T cell clonal expansion in CLM in a clinical context.

  Study EGAS00001007136

• Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients

  Background Despite advances in identification of genetic markers associated to severe COVID-19, the full genetic characterisation of the disease remains elusive. Imputation of low-coverage whole genome sequencing (lcWGS) has emerged as a competitive method to study such disease-related genetic markers as they enable genotyping of most common genetic variants used for genome wide association studies. This study aims at exploring the potential use of imputation in lcWGS for a highly selected severe COVID-19 patient cohort. Findings We generated an imputed dataset of 79 variant call format (VCF) patient files using the GLIMPSE1 tool, each containing, on average, 9.5 million single nucleotide variants. The validation assessment of imputation accuracy yielded a squared Pearson correlation of approximately 0.97 across sequencing platforms, showing that GLIMPSE1 can be used to confidently impute variants with minor allele frequency up to approximately 2% in Spanish ancestry individuals. We conducted a comprehensive analysis on the patient cohort, examining hospitalisation and intensive care utilisation, sex and age-based differences, and clinical phenotypes using a standardised set of medical terms specifically developed to characterise severe COVID-19 symptoms for this cohort. Conclusion This dataset highlights the utility and accuracy of lcWGS imputation in the study of COVID-19 severity, setting a precedent for other applications in resource-constrained environments. The methods and findings presented here may be leveraged in future genomic projects, providing vital insights for health challenges like COVID-19.

  Study EGAS00001007573

• Epigenetic age deceleration reflects fitness improvements following a six-month endurance exercise intervention

  Epigenetic clocks are emerging as promising biomarkers of biological aging, yet their sensitivity to short-term interventions remains unclear. This pilot study investigates whether the GrimAge clock can capture the effects of a six-month cycling-based endurance exercise training intervention, with cardiorespiratory fitness (VO₂ max) and body composition as primary outcomes. We enrolled 42 adults aged 35-65, of whom 38 completed the study and 33 adhered to the protocol (>66% adherence). Participants demonstrated significant improvements in VO₂ max (+20%, P < 0.001) and body composition (P < 0.001). High-quality epigenetic data preprocessing yielded highly reproducible GrimAge estimates (< 2 months measurement error), which strongly correlated with chronological age (R² = 0.86, P < 0.001). On average, GrimAge decreased by 7.44 months relative to the expected trajectory (P = 0.012), reflecting improvements in VO₂ max (R² = 0.27, P = 0.002) but not body composition changes. Notably, GrimAge changes strongly correlated with fluctuations in leukocyte composition, particularly neutrophil fraction (R² = 0.74, P < 0.001). Adjusting for leukocyte composition improved consistency in GrimAge changes, aligning them with additional intervention outcomes and explaining up to 81% of variance. These findings demonstrate that GrimAge is responsive to short-term endurance training, serving as a meaningful biomarker of improved cardiorespiratory fitness, while also capturing immune system variability. This study supports the use of GrimAge in evaluating longevity interventions and highlights the importance of accounting for leukocyte composition in epigenetic aging research.

  Study EGAS00001008221

• Biological Determinants of Peritoneal Dialysis Outcomes

  Peritoneal Dialysis (PD) is a technique for treating kidney failure where fluid is instilled into the body's peritoneal cavity. Fluid and solutes travel across the peritoneum, and this is critical to successful PD. Studies have shown that certain demographic and clinical variables explain a small part of the variability in baseline peritoneal solute transfer rate and water transfer function across the peritoneum. This study sought to identify the common genetic variants associated with the baseline peritoneal function in patients starting treatment with PD and change in function upon treatment with PD. This study has two specific aims: Aim 1: To identify and validate genetic loci that influence the peritoneal solute transfer rate (PSTR) at start of PD. Aim 2: To identify and validate genetic loci in pre-specified biologic pathways with change in peritoneal ultrafiltration capacity. This study incorporates data from participants' peritoneal solute transfer rate in their first ever peritoneal equilibrium test (PET) and changes in the transfer of water across the peritoneal membrane over time in a sub-group of participants, demographic information, and results from laboratory analysis of DNA, blood, and dialysate. This study comprises patient populations from pre-existing biorepositories in Europe, and prospectively enrolled participants in United States, Canada, United Kingdom, and Australia. Clinical data related to the participants' peritoneal solute transfer rate from their first ever Peritoneal Equilibrium Test (PET), demographic information, and change in ultrafiltration capacity over time, are correlated with various genetic markers of interest. For individuals enrolled prospectively, blood and dialysate were collected at the first study visit. Annually, subjects either underwent a PET as standard of care or perform an additional 4-hour dwell as part of the study. These subsequent measures were utilized to determine change in ultrafiltration capacity over time. Inclusion criteria included adults over the age of 20 who are able to provide consent and had a record of a PET within 6 months of starting PD. Subjects with missing outcome data and that did not pass genotyping QC were excluded. Genotyping was performed in two batches using the Illumina InfiniumOmni2-5-8v1-3_A1 array with 2,372,784 single nucleotide variants (SNVs) in the first batch (n=1957). The second genotyping batch (n=1053) was on the InfiniumOmni2-5-8v1-4_A1 array with 2,382,209 SNVs. Imputation was performed using the Michigan Imputation Server and the HRC1.1 genotype reference. The Institutional Review Board of the University of Washington has “dbGaP-certified” the consent forms used to enroll participants in Australia, Canada, and United States and the genotype-phenotype data from the participants (n=827) deposited in the public repository. Furthermore, it has been determined that under the EU-GDPR regulations, depositing data of participants enrolled in UK, Belgium, and Sweden (n=2,023) into dbGaP “serves no lawful purpose” as the consent form used for enrolling participants did not obtain explicit permission for depositing data in a public repository.

  Study phs002996

• The evolutionary dynamics of human colorectal cancer using single-gland spatial multi-omic profiling of DNA, RNA and chromatin.

  Study EGAS00001006088

• The evolutionary dynamics of human colorectal cancer using single-gland spatial multi-omic profiling of DNA, RNA and chromatin.

  Study EGAS00001006122