ArcOGEN_Illumina610k_subset_2 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010000744 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-1 with consent for osteoarthritis studies only.
| EGAD00010000924 | EGA
Project description:Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-24v1-0 with consent for osteoarthritis studies only.
| EGAD00010000927 | EGA
Project description:Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-0 with consent for osteoarthritis studies only.
| EGAD00010000923 | EGA
Project description:Subset 1 of osteoarthritis cases genotyped on Illumina610k from the arcOGEN Consortium (http://www.arcogen.org.uk/) with broader consent.
| EGAD00010000742 | EGA
Project description:Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-0 with broader consent.
| EGAD00010000925 | EGA
Project description:Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-1 with broader consent.
| EGAD00010000926 | EGA
Project description:Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-24v1-0 with broader consent.
| EGAD00010000922 | EGA
Project description:Osteoarthritis cases genotyped on Illumina HumanOmniExpress from the arcOGEN Consortium (http://www.arcogen.org.uk/) with broader consent.
| EGAD00010000740 | EGA
Project description:The arcOGEN study is a UK-wide collaboration effort by the Arthritis Research UK Osteoarthritis Genetics (arcOGEN) Consortium (http://www.arcogen.org.uk/) aimed at the identification of the genetic determinants of osteoarthritis (OA). Unrelated samples were collected in 2 stages from 10 United Kingdom locations (London, Nottingham, Oxford, Sheffield, Southampton, Edinburgh, Newcastle-Upon-Tyne, Sheffield, Wansbeck, and Worcester). The majority of cases had primary OA requiring joint replacement of the hip or knee while a smaller number were ascertained by radiographic evidence of disease (Kellgren-Lawrence (KL) grade ≥2). The exclusion criteria included the need for joint replacement due to fracture, secondary OA of any cause, and developmental, vascular, or infective causes of joint disease. The full genotype data generated from the arcOGEN genome-wide association scan (GWAS) is contained in separate datasets because of differences in patient consent between the different collection sites.
| EGAS00001001017 | EGA
Project description:<b>Project Description:</b><br/>The Malaria Host-Pathogen Interaction Center (MaHPIC) is a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (HHSN272201200031C, 2012-2017; see <a href='http://www.systemsbiology.emory.edu' target='_blank'>http://www.systemsbiology.emory.edu</a>). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (<i>e.g.</i>, clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC.<br/><br/><b>MaHPIC Experiment Description:</b><br/>Sixteen healthy volunteers, 7 malaria naïve and 9 semi-immune, aged 18-45 years, were enrolled in this study during October 2012 to November 2013. Malaria-naive volunteers were recruited in Cali, Colombia, a non-endemic city; those with previous malaria experience were recruited in Buenaventura, a malaria-endemic area on the Colombian Pacific Coast. The study was approved by Institutional Review Boards (IRB) of the Malaria Vaccine and Drug Development Center–MVDC (CECIV, Cali) and Centro Médico Imbanaco (Cali). All protocols and documentation were reviewed and samples shipments approved by the Emory IRB. Male and female patients were eligible for inclusion, which included two steps: 1) age between 15-60 years, hemoglobin levels > 9g/dL, presence of current <i>Plasmodium vivax</i> infection, absence of other <i>Plasmodium</i> species determined by thick blood smear and PCR, blood parasite count of 0.1% or more, absence of other acute or chronic diseases, being able to sign an informed consent form; 2) healthy 18 to 45 years old man or non-pregnant women, capacity to sign an informed consent in a free and voluntary way, acceptable understanding of the clinical trial through the approval of a questionnaire regarding the information given in the consent process, obligatory use of adequate contraceptive method from beginning of recruitment and screening time up to three months after last immunization, do not have chronic or acute diseases, accept not traveling to malaria endemic areas during the clinical trial, have telephone at home or mobile phone that permit permanent contact for follow up, being willing to participated during both steps of the clinical trial. Exclusion criteria included pregnancy, abnormal laboratory test values, hemoglobin pathology, glucose-6-phosphate dehydrogenase (G6PDH) deficiency, positive for blood bank infectious diseases (syphilis, HIV, Chagas disease, HTLV 1–2, and hepatitis B and hepatitis C), or have any condition that would increase the risk of an adverse outcome. Volunteers were infected with <i>P. vivax</i> via sporozoite challenge by exposing volunteers to bites of 2–4 mosquitoes (<i>Anopheles albimanus</i>) of the same infected batch. Plasma samples were collected at 4 time points: Baseline, 1 month pre-inoculation; Diagnosis; 3 weeks post-treatment; 4 months post-treatment. As soon as parasites were detected by thick blood smears, participants were treated orally with curative doses of chloroquine (1500 mg chloroquine provided in three doses: 600 mg initially then 450 mg doses at 24 and 48 hours) and primaquine (30 mg dose given once per day for 14 days). Clinical trial registration: NCT01585077. Samples were analyzed with liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS), evaluated in a time course and between naïve and semi-immune volunteers. Within the MaHPIC, this project is known as ‘Experiment HuC’. Samples were obtained in collaboration with Socrates Herrera from the Malaria Vaccine and Drug Development Center, Colombia. Metabolomics results were produced by Dean Jones at Emory University. To access other publicly available results from HuC and other MaHPIC Experiments visit <a href='http://plasmodb.org/plasmo/mahpic.jsp' target='_blank'>http://plasmodb.org/plasmo/mahpic.jsp</a> . This page will be updated as datasets are released to the public.<br><br>The following contributed to the creation of this dataset: The MaHPIC Consortium, Jeremy D. DeBarry, Mary R. Galinski, Luiz G. Gardinassi, Socrates Herrera, Myriam Arévalo-Herrera, Dean P. Jones, Jessica C. Kissinger, Shuzhao Li, Regina Joice Cordy, Esmeralda VS Meyer, Mustafa V. Nural, Suman B. Pakala, ViLinh Tran, Karan Uppal<br><br> Linked Studies: <a href='/metabolights/search?freeTextQuery=MaHPIC' target='_blank'><span class='label label-success'>Malaria Host-Pathogen Interaction Center (MaHPIC)</span></a>
2018-06-19 | MTBLS665 | MetaboLights