UK_exomechip
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002019 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC Replicationchip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper.
| EGAD00010002118 | EGA
Project description:This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC immunochip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper.
| EGAD00010002049 | EGA
Project description:DNA methylation profiling of NeuN+sorted neuronal nuclei from post-mortem brain tissue of Multiple Sclerosis (MS) patients (n=10) (MS) and non-neurological controls (n=7) (non-MS). Genomic DNA was subjected to conventional BS-treatment as well as oxidative BS (oxBS)-conversion using TrueMethylTM 96 kit of CEGXTM (Cambridge Epigenetix Limited) to allow for subsequent detection of hydroxymethylation (5hmC = BS - oxBS).
2019-06-21 | GSE119532 | GEO
Project description:This is a genome wide association study (GWAS) of disease progression in multiple sclerosis (MS). The study involved a total of 12584 cases recruited from multiple centres around the world and tested at 7.8 million common autosomal single nucleotide variants. The data from the European cases (n=4853) are included in this EGA submission in 10 country specific data sub-sets.
| EGAS00001007162 | EGA
Project description:<p>The Bangladesh Risk of Acute Vascular Events (BRAVE) study is a hospital-based case-control study in Bangladesh which was established by the Cardiovascular Epidemiology Unit of Cambridge University in the UK in partnership with the key local cardiology and research centres to examine environmental, genetic, lifestyle and biochemical determinants of myocardial infarction (MI) among this South Asian population. By the end of 2016, this study has recruited ~8000 clinically confirmed first-ever MI cases (with a significant proportion being early-onset MI), and ~8000 healthy controls frequency-matched by age and sex. This site hosts data from ~500 whole genomes and ~1500 whole exomes (50% cases and 50% controls)</p>
| phs001398 | dbGaP
Project description:Long noncoding RNAs (lncRNAs) play a key role in regulating immunological functions. Their impact on the chronic inflammatory disease multiple sclerosis (MS), however, remains unknown. We investigated the expression of lncRNAs in peripheral blood mononuclear cells (PBMCs) of patients with MS and try to explain their possible role in the process of MS. we recruited 26 MS patients according to the revised McDonald Criteria. Then we chosen 6 patients for microarray analysis randomly. Microarray assays identified outstanding differences in lncRNA expression, which were verified through real-time PCR. LncRNA functions were annotated for target genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and regulatory relationships between lncRNAs and target genes were analyzed using the “cis” and “trans” model.
2017-12-08 | E-MTAB-6193 | biostudies-arrayexpress
Project description:Clinical-grade human embryonic stem cells (hESCs) from 4 centres in the UK were cultured in self-renewal conditions Genomic DNA was isolated from low passage hESCs and submitted for SNP analysis using Illumina HumanCytoSNP-12 v2.1 BeadChip arrays
2015-05-05 | GSE68508 | GEO
Project description:Circular RNAs (circRNAs) are recently found to be promising kind of biomarkers for tumors. However, plasma exosomal circRNAs in the diagnosis of hepatocellular carcinoma (HCC) is largely unknown. In this study, we report the application of next-generation sequencing technology for high-throughput profiling of plasma exosome general transcriptome between 3 cases of hepatocellular carcinoma patients and 3 cases of healthy control. We obtained exosomes through ultrahigh-speed centrifugation techniques and verified exosomes through immunoblotting, NanoSight NS300(Malvern Panalytical, Malvern, UK) and JEM-1230 transmission electron microscope (TEM) (JEOL, Tokyo, Japan). And then, we find that there are 41 circRNAs that have differential expression. This study discovered the differences between hepatocellular carcinoma and healthy people preliminarily.
2023-09-30 | GSE174179 | GEO
Project description:Trypanosoma vivax is a vector-borne blood parasite of cattle throughout sub-saharan Africa. For some years the genome sequence of this organism has been in development at the Wellcome Trust Sanger Institute and is shortly to be completed. Analysis of the genome has revealed various putative genes encoding unknown proteins. In an effort to validate these features we will sequence mRNA transcripts from the bloodstream stage of the genome strain Y486. Most of the novel gene families identified from the genome sequence are too diverse to be validated individually, i.e. through RT-PCR, so it is necessary to sequence all cellular transcripts. We hope to confirm the transcription of one or all members of the novel gene families from the resulting transcriptome. While essential for the scientific rigour of the present genome project, this transcriptome will also provide an additional resource for the longer-term benefit of the research community. ArrayExpress Release Date: 2011-02-16 Person Roles: submitter Person Last Name: Quan Person First Name: Lin Person Mid Initials: Person Email: ql3@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Investigator Person Last Name: Jackson Person First Name: Andrew Person Mid Initials: P Person Email: aj4@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Project Coordinator Person Last Name: Sanders Person First Name: Mandy Person Mid Initials: J Person Email: mjs@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30609 | GEO
Project description:<p>This is a multi-centre, case-controlled study to develop a dataset containing 1000 MS cases and 1000 matched controls and to associate DNA sequence (allelic) variations with MS phenotypes.</p> <p>Study subjects were enrolled through a prospective effort initiated in 2003. Three MS clinical centres were involved in subject recruitment and biological specimen collection using identical inclusion/exclusion criteria, two in Europe (Vrije Universiteit Medical Center, Amsterdam; and University Hospital Basel) and one in the US (University of California San Francisco). This study recruited subjects of northern-European ancestry with a diagnosis of MS (<a href="http://www.ncbi.nlm.nih.gov/pubmed/11456302" target="_blank">McDonald et al., 2001</a>), with dissemination in time and space. Patients with Clinically Isolated Syndromes (CIS) were also included if they fulfilled 3 of the 4 Barkhof criteria for dissemination in space as per application of the McDonald criteria (<a href="http://www.ncbi.nlm.nih.gov/pubmed/11456302" target="_blank">McDonald et al., 2001</a>). While recruitment predominantly included subjects with a relapsing onset of MS, individuals with all clinical subtypes of the disease participated, including clinically isolated syndrome (CIS), relapsing remitting MS (RRMS), secondary progressive MS (SPMS), primary progressive MS (PPMS), and progressive relapsing MS (PRMS).</p> <p>The control group consisted of unrelated individuals, primarily spouses/partners, friends, and other volunteers. Control subjects were of northern-European ancestry and matched as a group, proportionally with cases according to age (±5 years) and gender. A familial history or current diagnosis of MS as well as a relation to another case or control subject were considered exclusionary for this group.</p> <p>Protocols were approved by the Committees on Human Research at all Institutions and informed consent was obtained from all participants prior to participation in the study.</p> <p><b>Primary Study Objective:</b><br/>To identify DNA sequence variations (genotype) and flanking sequences that are associated with clinical factors (phenotype) which differ between study subjects with and without MS.</p> <p><b>Secondary Study Objectives:</b> <ol> <li>To develop a clinical dataset including quantitative measures of 1000 well-characterized cases with MS, and 1000 ethnically matched controls.</li> <li>To identify other genotype-phenotype associations in MS study subjects such as magnetic resonance imaging (MRI) measures of disease burden and/or severity.</li> <li>To identify or confirm candidate surrogate markers of neurodegeneration using a variety of techniques including biochemical assays, blood transcriptome analysis, plasma proteomics and MRI*.</li> </ol> </p> <p><b><u>Genotyping</u></b><br/>Genotyping of the complete dataset was performed at the Illumina facilities using the Sentrix® HumanHap550 BeadChip.</p> <p><small><i>*MRI results are not available on dbGaP.</i></small></p>
| phs000171 | dbGaP