UK_ReplicationChip
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002118 | EGA |
REPOSITORIES: EGA
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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 exomechip 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
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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