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HUGO Mutation Database InitiativeNewsletter No. 16 |
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Incyte Genomics and MDI will no longer be working together to fund the Central Depository in the immediate future.
We have submitted a grant application to the NIH, U.S.A. for funding of the Central depository and its coordination. In summary, an international team of MDI members has submitted one grant together with subcontracts for different parts. The named investigators in the proposal are as follows:
BiSC, Toronto, Canada: J. Cuticchia, C. Porter, C. Talbot, S. Teebi
KI, Stockholm, Sweden: A. Brookes
EBI, Cambridge, UK: H. Lehväslaiho
EMBL, Heidelberg, Germany: P. Bork
MDI, Melbourne, Australia: RGH. Cotton , R. Horaitis
Rockefeller University, New York, USA: A. Auerbach
McGill University, Montreal, Canada: C. Scriver
St. James' University Hospital, Leeds, UK: G. Taylor
The Specific aims in the application are as follows: The objective of this proposal is to establish a public domain system for the capture of human gene-related variations, and phenotype altering mutations in particular, plus a database system to present these meaningfully. Specifically:
1. To create a system that enables and encourages researchers, clinicians, diagnostic laboratories, and companies to submit unpublished mutations and correlated phenotypes for incorporation into the public system. The enabling technical implementation of this is the "WayStation". Means of encouragement for researchers to submit to the WayStation will include: a) a system of capturing mutations from diagnostic and research laboratories, b) the publication of citations in Human Mutation, the proposed-society journal, and c) the issuance of PubMed IDs.
2. To support the HUGO Mutation Database Initiative (MDI) editorial office, the "Office", in its efforts to: a) promote widespread community involvement and enlist locus curators, b) encourage data submission and sharing, and c) establish an editorial review system, independent of institution and database.
3. To create a centralized public resource, the "Warehouse" for the robust storage and presentation of core data summaries and source-links for gathered mutations, other known sequence variations, and related clinical phenotypes, in both gene and genomic contexts. (This will be a development of the existing public HGBASE database.)
4. To capture mutations from extant Locus Specific Mutation Databases (LSDBs), published literature, and generic databases (GenBank/EMBL/DDBJ, OMIM) for import into the system and distribution to interested parties. (A joint task of WayStation and Warehouse.)
5. To create a flexible standard for mutation/polymorphism and phenotype description based on UML / XML. This will facilitate both the capture of target information and its wide distribution. (A task common to all three principal project nodes plus a number of external collaborators.)
6. To support existing and new LSDBs by providing computer services, simple off-the-shelf software, and the WayStation interface, to enable the easy establishment of such databases and provide the route through which they can receive data submissions. (A task largely of the WayStation plus the Office.)
Opinions on adapted bylaws are underway, you will be advised of any developments soon. We anticipate the Society will be formed in San Diego at our Oct. 12 meeting and an agreement between the HUGO MDI and Wiley-Liss will be signed shortly making "Human Mutation" the society journal.
None this issue.
The following databases have recently been released:
1. Database on inherited cardiac arrhythmias (TTR- OMIM 176300) http://PC4.FSM.it:81/cardmoc/
Curators: The working group on arrhythmias and the study group of molecular basis of arrhythmias of the European society of Cardiology
2. The Tissue Non-specific Alkaline phosphatase Gene Mutations Database (ALPL ; MIM 171760) http://www.sesep.uvsq.fr/Database.html
Curators: Etienne Mornet, SESEP Laboratory at the University of Versailles-Saint Quentin en Yvelines (France)
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Coordinator Rania Horaitis horaitis@mail.medstv.unimelb.edu.au |