Batch1_Genotypes_Raw
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002126 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Genotypes generated for Puno cohort Batch 2. Case (PRE) and control (PUN) families were recruited in hospital. Raw genotypes no QC. Includes unrelated genotyping controls (HG).
| EGAD00010002124 | EGA
Project description:We performed quantitative proteomic profiling of 786 plasma samples from COVID-19 inpatients, treated at two different hospitals (Charité – Universitätsmedizin Berlin and University Hospital of Innsbruck). Sampling was performed at multiple time points throughout the course of the disease, to create a time-resolved map of COVID-19 progression. Full DIA-NN analysis reports are provided, as well as raw files for the QC runs.
2021-07-19 | PXD025752 | Pride
Project description:While the majority of infants infected with respiratory syncytial virus (RSV) exhibit mild or no symptoms, approximately 3 million children under the age of five are hospitalized every year due to complications from RSV. This research sought to explore the biological processes and related biomarkers responsible for the varied manifestations of RSV disease in young infants. The goal is to pave the way for a more precise categorization of RSV-infected infants based on their medical requirements. Whole blood samples are collected from infant case-control cohort study, the RESCEU case-control cohort is a multinational, multicenter, observational study (clinical trial registration number: NCT03756766). Infants < 12 months old with RSV disease were recruited from the University Medical Center Utrecht (UMCU) in The Netherlands, Hospital Clínico Universitario de Santiago (SERGAS) in Spain, Imperial College (IMPERIAL) National Health Service Trust (NHS) and Oxford University Hospital NHS Trust (OXFORD) in the United Kingdom during the RSV seasons 2017-2018, 2018-2019, and 2019-2020. Healthy controls without underlying comorbidities were recruited outside of the RSV season. Eligibility criteria included hospitalization for less than 48 hours at enrolment or within 96 hours of disease onset, no previous receipt of medications to treat RSV infection, no prior exposure to an investigational RSV vaccine or medication, no previous receipt of immunoglobulins or monoclonal antibodies, and had not used montelukast or oral steroids within seven days before enrolment. Infants with co-morbidities were not evaluated in the manuscript. RSV was detected using RSV point-of-care test (POCT) by either a rapid antigen detection test (Alere I) (Alere Inc, Waltham, Massachusetts) or rapid RSV polymerase chain reaction (PCR) test at the hospital setting, or a RSV PCR test at the laboratory. Convalescence samples were collected 7 ±1 weeks after a positive RSV diagnostic test result. We used microarray to assist us to identify biomarkers for severe RSV disease.
2024-01-03 | GSE246622 | GEO
Project description:In the present study we aimed to investigate the systemic response to a rupture of intracranial aneurysms by an analysis of global gene expression profiles in peripheral blood cells. In addition, we sought to determine whether this approach could provide biomarkers related to clinical status of subarachnoid hemorrhage patients. Patients with subarachnoid hemorrhage from ruptured aneurysm were prospectively recruited from patients consecutively admitted to the Departments of Neurology or Neurosurgery and Neurotraumatology, University Hospital, Krakow, Poland in 2010 and 2011. Control subjects were recruited from patients of the Department of Neurology suffered from headaches.
2014-01-01 | E-GEOD-36791 | biostudies-arrayexpress
Project description:In a study to elucidate the genetic defects in patients with X-linked intellectual disability (XLID) we performed X chromosome-specific BAC-array-CGH and identified 0.33 to 1.0 Mb nonrecurrent copy number gains at Xp11.22 in affected males of unrelated XLID families. All aberrations segregate with the disease in the families and the carrier mothers show a nonrandom X-inactivation. Affected males suffered from mild to moderate ID. Tiling Xp11.22 region-specific oligo-array (ChrX:52.50 - 54.50 Mb) revealed that all aberrations had different start and stop sites. The twofold copy number gain included up to 20 genes but only the HUWE1 gene is located in the minimal common region of overlap in these families. Moreover, expression analysis revealed about twofold increased HUWE1 mRNA levels in affected patients when compared to control individuals. Breakpoint analysis revealed Non-homologous end-joining (4 cases), serial replication slippage (1 case) and non-allelic homologous recmbination (one case) as the potential recombination mechanism.
2012-09-03 | GSE32945 | GEO
Project description:Arginine methylation, Cob1. Wenya Hou et al Jena University Hospital
2018-04-30 | PXD008504 | Pride
Project description:Pseudomyxoma peritonei (PMP) is a subtype of mucinous adenocarcinoma of the appendix, We compared N-linked glycan profiles of PMP tissues to those of normal appendix. N-glycosidase F liberated N-glycan profiles of eight normal appendix samples and eight low-grade and eight high-grade PMP specimens were analyzed by MALDI-TOF mass spectrometry. The most prominent alteration was increased and complex fucosylation in high-grade carcinoma. Authors: Lilli Saarinen, Pirjo Nummela, Hannele Leinonen, Annamari Heiskanen, Alexandra Thiel, Caj Haglund, Anna Lepistö, Tero Satomaa, Sampsa Hautaniemi, and Ari Ristimäki; from Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki; Glykos Finland Ltd, Helsinki; Department of Surgery, University of Helsinki and Helsinki University Hospital; Translational Cancer Biology, Research Programs Unit, University of Helsinki; and Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Hospital, Finland.
2018-08-03 | PXD010086 | Pride
Project description:<p>The Sjögren's International Collaborative Clinical Alliance (SICCA) is a multisite observational cohort study that recruited a large cohort of geographically diverse participants. Enrollment of participants began in late 2004 at five (one domestic and four international) sites, in which all groups used the same protocol-directed methods to provide uniform evaluations; collect oral, ocular, and rheumatologic data; and collect specimens. The sites were located at the University of Buenos Aires, Argentina; Peking Union Medical College, Beijing, China; Rigshopitalet (formerly at Glostrup Hospital), Copenhagen, Denmark; Kanazawa Medical University, Ishikawa, Japan; King's College, London, UK (joined in 2007); and the University of California, San Francisco (UCSF). In 2009, Aravind Eye Hospital, Madurai, India; Johns Hopkins University, Baltimore, MD; and University of Pennsylvania, Philadelphia, PA were added as additional SICCA sites. UCSF is the coordinating center for SICCA. All specimens and data collected for SICCA are housed at UCSF.</p> <p>To facilitate the research focused on understanding the genetics of Sjögren'sSjögren's syndrome, high-density SNP genotype data and SICCA clinical information are being made available to the research community. This includes participants recruited from all SICCA research groups (RG). These participants (3,382), blood relatives (439), and unrelated healthy controls (25) had their whole blood or saliva sample (Oragene) extracted for DNA for the GWAS at the UCSF DNA Bank. Eighty eight percent of the participants are women, most are of European or Asian ancestry and the median age is 55.</p> <p>To assess potential batch effects when doing case-control comparisons using planned external controls, 30 DNA samples from each of three studies were genotyped with SICCA DNA samples:</p> <ol> <li>The Genetic Architecture of Smoking and Smoking Cessation - <a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000404.v1.p1">Collaborative Genetic Study of Nicotine Dependence (COGEND)</a> - PI: Laura Bierut.</li> <li>NEI-Age-related disease study (AREDS) - <a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000429.v1.p1">Genetic Variation in Refractive Error Substudy</a> - PI: Dwight Stambolian.</li> <li>Controls from the National Institute of Mental Health's <a href="http://www.nimhgenetics.org/available_data/controls/">(NIMH's)</a> Human Genetics Initiative.</li> </ol> <ul><a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000021.v3.p2">Genome-Wide Association Study of Schizophrenia</a> - PI: Pablo V. Gejman.</ul> <ul><a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000167.v1.p1">Molecular Genetics of Schizophrenia - nonGAIN Sample</a> (MGS_nonGAIN) - PI: Pablo V. Gejman.</ul> <p>Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data quality control, dbGaP preparation and posting, and imputation to 1000 Genomes to increase SNP density was performed by the Center for Biomedical Statistics at the University of Washington. Data analysis was performed at UCSF using software PLINK, EIGENSOFT, and SNPTEST.</p>
| phs000672 | dbGaP
Project description:The study was performed on a subgroup of a larger study including 78 patients with histologically verified HNSCC recruited from Division of Cancer Medicine and Radiotherapy, Norwegian Radium Hospital, Rikshospitalet University Hospital in the period from May 2003 to May 2006. The patients received either post-operative radiotherapy or radiotherapy alone for a period of 5-7 weeks.<br>Ten HNSCC patients, responding to radiotherapy with a high relative increase in plasma DROM and high decrease in FRAP (responder), were compared to ten patients with low increase in DROM and low decrease in FRAP (non responder). Microarray analysis of full blood were performed on pre and post radiotherapy samples.<br>
2010-10-31 | E-MEXP-2460 | biostudies-arrayexpress
Project description:We conducted prospective clinical studies to validate the importance of CD4+ T cells in 13 diseases from the following ICD-10-CM chapters: Neoplasms (breast cancer, chronic lymphocytic leukemia); endocrine, nutritional and metabolic diseases (type I diabetes, obesity); diseases of the circulatory system (atherosclerosis); diseases of the respiratory system (acute tonsillitis, influenza, seasonal allergic rhinitis, asthma); diseases of the digestive system (Crohn’s disease [CD], ulcerative colitis [UC]); and diseases of the skin and subcutaneous tissue (atopic eczema, psoriatic diseases). Study participants were recruited by clinical specialists based on diagnostic criteria defined by organizations representing each specialist’s discipline. Age and gender matched healthy controls (n = 127 and 39, respectively) were recruited in the Southeast region of Sweden from outpatient clinics at the University Hospital, Linköping; Ryhov County Hospital, Jönköping, a primary health care center in Jönköping; and a medical specialist unit for children in Värnamo. Study participants represented both urban and rural populations with an age range of 8–94 years. Patients with type I diabetes and obesity had an age range of 8–18 years. 12 patients had more than one diagnosis.
2021-11-23 | GSE123086 | GEO