Objective
The 22 Network laboratories undertook to screen a total of 81 markers each over the 2 years. At the end of the first year, a total of more than 343 or more markers (weighted value) had been distributed. During the first year 2 batches of markers were sent out, and a third batch of markers was planned for distribution to all Network laboratories. This batch consisted exclusively of polymerase chain reaction (PCR) based markers, which had been selected by continuous screening of literature and the genome database (GDB). A large consignment of high quality markers were sent to all laboratories. These markers are part of the set of microsatellite markers spanning the whole human genome. The information value of these markers was extremely high, with an average heterozygosity of 79%.
Each of the 22 network laboratories was supplied with a Unix workstation. This included a run time version of the Sybase relational database management system, together with a Sybase application called GENBASE and the version 6 CEPH database in Sybase format. In all, data on 576 markers were submitted. These corrected data are available in CRI-MAP format by anonymous file transfer protocol (FTP).
Following the data collection phase, a process of map construction was initiated. Each Network laboratory was assigned 1 or more of the 22 autosomal chromosomes or chromosome X. Map building began in parallel with the elimination of allelic exclusions, with corrections being reported so that the data could be corrected and the CRI-MAP input files regenerated on a continuous basis. Intralocus recombinants were detected and reported back to the contributing laboratories who, in turn, fed corrections back to the central site. When complete, the CRI-MAP output files were uploaded by FTP and transformed into PostScript figures by a set of Unix scripts. The framework maps were juxtaposed with 800-band ideograms and a representative set of cytogenetic data chosen from GDB to map the relationship between the ideograms and the maps.
The European Human Gene Mapping Project (EUROGEM) is funded by the European Commission as a collaborative effort to produce a high density linkage map of the human genome. The project is organized as two centralized facilities supplying the 22 network laboratories with the necessary resources (markers and DNA) for linkage studies.
One of these two resource centres is based at the Centre d'Etude du Polymorphisme Humain (CEPH) in Paris. Its role is to supply the participating laboratories with DNA from 40 three-generation families. The other resource centre is based at the Imperial Cancer Research Fund in South Mimms, UK. This centre prepares and supplies the markers to be typed across the families. Two types of markers are supplied: DNA probes for Southern blotting and primers for analysis by polymerase chain reaction (PCR).
In the initial 24 months of the project, over 1800 markers will be screened by the participating laboratories. Approximately half of the markers will be provided by the probe resource centre; the individual laboratories will supply the rest.
In addition to the preparation and distribution of markers, the probe resource centre is also involved in isolating new markers, and in acquiring informative markers, which have been published in scientific literature, from the originators. In the isolation of new markers two approaches are being used. In the first approach, short repeat sequences have been identified from sequence databases and screened for polymorphic length variation by PCR. The second approach is to screen phage and cosmid libraries, either for polymorphic variation of short nucleotide repeats (as above) or with a synthetic decanucleotide probe which detects areas of high variability. The clones identified with this probe are highly likely to detect variable number tandem repeat (VNTR) polymorphisms in Southern blot analysis.
Both screening programmes have been set up and positive clones have been identified for further analysis. The work is expected to lead to the discovery of a number of new markers when the material has been fully analyzed.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences biological sciences microbiology virology
- natural sciences biological sciences genetics DNA
- natural sciences biological sciences genetics chromosomes
- natural sciences biological sciences genetics genomes
- natural sciences computer and information sciences databases relational databases
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Coordinator
EN6 3LD Potters Bar
United Kingdom
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