-Allele Variant Entry Form
-Quick Summary of Working groups
-San Francisco Meeting
-LSDB for X-linked adrenoleukodystrophy
-ALFRED-Allele FREquency Database
-European School of Medical Genetics Autumn Courses
-Alzheimer Disease database
-Tuberous Sclerosis, TSC1 & 2 database
-HC FORUM
- HUGO MDI Meeting, San Francisco 19 October '99 (in association with ASHG '99)***
Quick Summary of Working groups:
Ethnic & National databases-
Turkish database is now available, others are under construction. Finnish, Jewish, Chinese, Arab and India mutation databases. Australian database which hopefully will act as a model is now in the discussion stage.
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Patient Aspects of databases-
No tangible material has come from this group yet, hopefully an article being written by the Co-Chair of this group will stimulate some discussion after it is published.
Copyright & Intellecutual Property of databases-
1. An invited speaker Prof. Jerome Reichman (Prof. of Law, Vanderbilt Univ. School of Law) will be addressing this important topic at the San Francisco meeting.
2. An article was solicited from Mr Stephen Maurer (attorney at law) specializing in this area and has been submitted.
3. Dr Heikki Lehvaslaiho (EBI) to talk about the alternative of "copylefting" at the San Francisco meeting.
Quality Control & Peer Review of databases-
1. The allele variant Entry form is almost done. It will be finalized in San Francisco.
2. An article discussing the definition of a mutation and polymorphism and defining the characteristics needed to decide if a mutation found in a patient is disease cuasing or not has been published: Cotton and Scriver (1998) Proof of disease cuasing mutation, Hum Mut 12:1-3.
3. A paper has been submitted which looks at the quality of data as published in journals and suggested methods of attaining high quality by Cotton and Horaitis.
Polymorhisms-
The massive interest in polymorphisms or SNPs has resulted in a database for SNPs at NCBI (http://www.ncbi.nlm.nih.gov/SNP/) (which also takes harmful mutations) to receive SNPs discovered through NCBIs funding of a search for SNPs and an industry collaboration to set up a database for SNPs (HGBASE-http://hgbase.interactiva.de). This exercise is thus at a stage where we cannot influence events to a large extent but perhaps we could use the resources of one or other system.
Nomenclature-
Drs J.T. Den Dunnen and S. Antonarakis are now updating the Antonarakis et al 1998 nomenclature article to include more complex mutations. These new proposed suggestions should stimulate much discussion once published.
Software & Content-
Scriver et al (1999) Guidelines and Recommendations for Content, Structure and Deployment of Mutation Databases. Hum Mut 13:344-350 referred to as the "guidelines document" has been updated and submitted for publication.
Central databases-
GDB has now redefined its role in its move to Toronto and has expanded a wish to move with HUGO MDI to set up a global system. The other central (general) databases continue to act independently with EBI the only one working directly with the MDI by way of loading locus-specific databases onto its server. The others only have links.
San Francisco Meeting
As you know, the next MDI meeting will be held in San Francisco Oct. 19th. Registration is still open and posters are still able to be presented. Closing date for all those who have not sent their abstracts yet is Sept. 27th WITH NO EXCEPTIONS. If you wish to present a poster, please let me know immediatley, do not show up wisthout having informed me first, as I need to hire the poster boards and our funds are limited.
We hope discussion will be promoted on various issues and have invited speakers this year to cover issues such as copyright & intellectual property of databases, patient aspects of databases and the ethics of Databases. The Preliminary Program and other details are included below. The meeting website is: http://ariel.ucs.unimelb.edu.au:80/~cotton/announ.htm
***
CORRESPONDENCE
-LSDB for X-linked adrenoleukodystrophy available in September.
A collaboration between the Department of Neurogenetics at the
Kennedy Krieger Institute / Johns Hopkins University (Baltimore, MD,
USA) and the laboratory of Genetic Metabolic Diseases at the Academic
Medical Center (Amsterdam, the Netherlands) has resulted in the
initiation of a LSDB for mutations identified in
the gene for X-linked adrenoleukodystrophy (X-ALD). X-ALD, the most
common peroxisomal disorder, is a progressive neurodegenerative
disease with an estimated incidence of 1:50.000. No effective
therapies for X-ALD are available. Clinical manifestations range from
the extremely progressive childhood cerebral form which leads to
severe disability and death before ten years of age, to slowly
progressive less severe adult forms that involve mainly the spinal
cord, and occasionally to milder forms that are compatible with
survival to old age. This extreme phenotypic variability in X-ALD
can not be explained by mutations in the defective gene, identical
mutations are associated with all clinical phenotypes. Currently,
there are over 275 mutations in this gene known to us. An extreme
high percentage of these mutations are non-recurrent (65%).
The database should become available online before October 1st. The URL of the X-ALD mutation database will be made available to you in September.
Stephan Kemp, Dept. Clinical Chemistry & Paediatrics, Amsterdam, The Netherlands
***
ALFRED
ALFRED is the new ALlele FREquency Database from the Kidd Lab
designed to meet the needs of researchers who require easy access to high
quality gene frequency data in a global set of population samples, as well
as educators who can use this information in the classroom. ALFRED can be
accessed through the Kidd Lab home page at
"http://info.med.yale.edu/genetics/kkidd". The primary entryway to data
in ALFRED is through searching for a table of frequencies (see the
"Example Searches" page off the ALFRED home page). Currently (9/99)
ALFRED contains data on 61 populations for up to 141 loci for some
populations. Users can choose which out of a range of fields should be
displayed in the table. The user can also choose to have the output in
easy to read tabular form, or in semicolon delimited form which can then
be copied into the user's spreadsheet for further analysis. From the
tabular form, users can click on the specific names within many of the
fields (such as the polymorphism name or contributor identification
number) to get more detailed information including links to the original
literature. ALFRED also provides a means to directly search for
information on a specific locus or population without going through the
frequency search. New allele frequency data and ancillary information
(population descriptions, references, protocols, etc.) are being entered
as time allows. In addition, the database structure and interface are
still under rapid development; so all comments and suggestions are
welcome.
Michael Osier, Yale University
***
European School of Medical Genetics
La Nunziata Centre, Sestri Levante
Autumn Courses 1999-
-Cancer Genetics, September 29-October 3, 1999
-Genetic Counselling in Practice, October 3-9, 1999
-Developmental Biology and Dismorphology, November 10-13, 1999
-Molecular Cytogenetics, November 14-18, 1999
-Thalassemias and Sickle Cell Anemia in the Mediterranean, November 20-22, 1999
Contact-Prof. Giovanni Romeo, Chief, Genetic Cancer Susceptibility Unit, International Agency for Research on Cancer, 150,Cours A. Thomas,Lyon 69003, Fax : +33-472738388, E-mail: romeo@iarc.fr
Due to the large volume of information, Programmes of the above courses will be sent to you by email on application to Rania or Prof. Romeo.
***
1. Alzheimer Disease Mutation Database
http://molgen-www.uia.ac.be/ADMutations/
Curator: Marc Cruts, Univ. of Antwerp, Dept. of Biochem. Antwerp, Belgium
2. Tuberous Sclerosis, TSC1 & TSC2
http://expmed.bwh.harvard.edu/ts/
Curator: Mary Pat Reeve, Walter & Eliza Hall Institute, Melbourne, Australia
3. -HC FORUM, Human Cytogentics forum
http://HCForum.imag.fr
Curator: Olivier Cohen, Universite Joseph Fourier, Faculte de Medecine de Grenoble, France
This meeting will be held the day before the San Francisco meeting of the American Society of Human Genetics-
TIME: 8.00am-7.00pm
DATE: 19th October 1998
VENUE: The Argent Hotel, San Francisco, U.S.A
REGISTRATION: Academic US$85
Commerical US$130
(Buffet Lunch and mixer included)
http://ariel.ucs.unimelb.edu.au:80/~cotton/sfreg.htm
ORGANISERS: R. Horaitis, R.G.H. Cotton (Australia)
REGISTRATION: Contact R. Horaitis
Email: horaitis@ariel.ucs.unimelb.edu.au
Fax: 61-3-9288-2989
WEBSITE: http://ariel.ucs.unimelb.edu.au:80/~cotton/announ.htmPOSTER ABSTRACTS: (NOT ESSENTIAL TO ATTEND MEETING)
Instructions on registration form.
Deadline-27th September-NO EXCEPTIONS!!
Posted 20th September 1999, questions to Rania Horaitis horaitis@ariel.ucs.unimelb.edu.au