Human Genome Variation Society(formerly HUGO-Mutation Database Initiative)Newsletter No. 1 |
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(Previous HUGO-MDI newsletters may be found on our website at: www.genomic.unimelb.edu.au/hgvs/newsletters.html, these may be helpful for new members to familiarize themselves with our projects).
This is the first of the new series of Newsletters since the society was formed (See below). There are some points to be made.
First, welcome to the paid up members and we hope you benefit from being members and contribute towards our aims of collecting and distributing all mutations.
Second, our large MDI mailing group is encouraged to join our Society to make it strong to be able to make an impact.
Third, this newsletter will be sent to all the original MDI mailing list until the year's end or we achieve 150 members that is ever soon. At that time we will review further mailings to that group.
Finally, the conditions of membership mention a monthly newsletter, we are not clear how this slipped through but until now a bimonthly newsletter was fine and we are likely to stick to this format otherwise content may be too thin.
Prof. Richard G.H. Cotton, President
. Depository of mutations
. Diagnostic Mutation database
. Nomenclature of mutations
. "LSDB in a box"
As you all know this Society was inaugurated 12th October last year. We were incorporated in New York State (USA) on 8 November 2001 as a not-for-profit organization. We now have 56 members and the number is steadily increasing. Breakdown of memberships is as follows: 33 from Europe, 18 from Nth America (USA & Canada), and 5 from the rest of the world. Those of you receiving this who are not yet members and would like to join see form at: www.genomic.unimelb.edu.au/hgvs/join.html. A full print and online subscription to Human Mutation is part of the membership.
A few members have expressed concern regarding the start date of their journal subscription. We are only able to send subscriptions to Wiley in monthly batches. Once the Wiley subscriptions department receives the listing and payment they begin processing which may take 4-6 weeks. Members are then emailed or mailed a registration form directly from the subscriptions department, once registered, they will be able to access the online version of Human Mutation immediately. The print version should follow shortly thereafter.
We are still looking for a HGVS logo. There are 4 entries at present. If you wish to enter please see www.genomic.unimelb.edu.au/mdi/logocomp.html for instructions. The winner receives a free 1-year subscription to the Society. Note that ONLY 2 colours may be used (not including white).
A revised version of the grant for the proposed WayStation/Office/WareHouse variation depository has been submitted to NIH (USA) on March 1 for their consideration. We await the outcome.
It is known that it is becoming more difficult to publish single mutations in genes. It is also assumed that collection of all variation in genes is a necessary foundation for the promoting of human health. Diagnostic laboratories produce highly quality-controlled mutations for diagnostic purposes, but rarely have the time or inclination to attempt to publish them. An initiative has begun to attempt to capture variation defined in diagnostic and other relevant laboratories.
Graham Taylor (Leeds, UK) is leading this high priority activity and is trying to procure funds. Graeme Suthers (Adelaide, Australia) and Richard Cotton are also discussing how to get funding for this project to begin a diagnostic mutation database in Australia as a pilot version. You should all think about this as well if it is of relevance and interest to you. As soon as we have a country up and running it will set a great precedent.
There has been quite a lot of discussion amongst the Nomenclature Working Group regarding mutation nomenclature in the recent months. The main problem seems to be start point in incompletely sequenced genes rather than the nomenclature itself. Several regimes were suggested to deal with this. It has been decided to discuss these issues in full at our Baltimore meeting on Tuesday October 15 (satellite to ASHG, see below). If you wish to have your ideas heard please try to attend this meeting or at least indicate your interest and/or ideas to Rania so you may be included in this group.
It has long been discussed that there should be some easy-to-use off-the-shelf software tailored for mutation databases available for locus specific database curators if they so require it. There is, however, some debate as to whether this software is really necessary. There are clearly two schools/approaches (a) Use software packages already developed by MDI members UMD/MUTbase/MuStar by Beroud/Vihinen/Brown respectively that are clearly up and running and (b) the centralist approach whereby databasing by remote curators occurs but on a central server. To get this project underway we need to attract funding.
All members who wish to make an announcement of interest to members in these newsletters please send a short paragraph to Rania at (horaitis@medstv.unimelb.edu.au) to be included in the next issue.
Communicated by Anthony Brookes PhD, Karolinska Institute, Sweden
Reflecting a continued growth in project size, scope and relevance, the HGBASE database has recently changed its name to HGVbase (Human Genome Variation database).
The overall projects' goals remain unchanged: creation of a meaningful summary of all known sequence variation in the human genome, plus the biological consequences of this variation, in order to facilitate research into questions of human history and how a person's genome affects common disease risk, drug responses, and other complex phenotypes. Non-redundant records are created from data that may be gathered from any and all public sources. New and emerging dimensions to the project include functional predictions for amino-acid variations, various assay suggestions, coordinate-based (regional) search options, and systems for handling haplotype, genotype, and phenotype data. Disease-causing mutations are a particular new area of focus, wherein we will provide the central storage and distribution functions for a global collection of such data being undertaken by a network of teams in allegiance with the recently inaugurated Human Genome Variation Society (HGVS - www.hgvs.org).
HGVbase remains a free academic resource, run by a European consortium involving Anthony Brookes et al (Karolinska Institute, Sweden), Heikki Lehväslaiho et al (European Bioinformatics Institute, UK), and Peer Bork et al (European Molecular Biology Laboratory, Germany). Project funding is presently provided by unconditional donations from the KI, EBI, and EMBL institutions, plus industry groups Pharmacia and Celera.
Communicated by Ralf Paschke MD, Istvan-Tibor Nebel, Computer Scientist Leipzig, Germany
We are currently in the process of updating a web database on the TSH receptor (listed in index of Locus Specific Mutation Databases under TSHR 603372 1 ) by means of most up-to-date Internet technology. For instance, we are coding family pedigrees using an algorithm in a computer readable pedigree format. One feature of our database will be the option to transform information on family pedigrees into the database by the publisher using a visual family pedigree computer program.
A uniform data sheet in our database user interface generates a visual family pedigree for each mutation that is listed in the database. To our knowledge, this tool is not yet widely available. Therefore, we would like to promote this visual family pedigree tool for other database owners by the HUGO Mutation Database Initiative.
The program is written in JAVA as an applet to be easily integrated in a web based database. This should facilitate its use for other database owners.
Anyone interested in this tool please contact Dr. Ralf Paschke, pasr@server3.medizin.uni-leipzig.de
Communicated by Aglaia Athanassiadou, PhD, University of Patras, Greece
(ALPHA-SYNUCLEIN, OMIM #163890, also called PARK1 OMIM : #601508; related to PARKINSON DISEASE (PD), OMIM : #168600)
www.med.upatras.gr/medschool/biology/English%20Version/alpha-syn.htm
A new database containing information on the alpha-synuclein locus is presented, containing :
. The alpha-synuclein
locus OMIM numbers.
. A table with the mutations detected so far in the alpha-synuclein locus as
associated with Parkinson's Disease and the corresponding references.
. A list of the references for genotype - phenotype correlations.
. Tables with the negative results of alpha-synuclein mutation search in sporadic,
familial, juvenile, early onset Parkinsonism -all together over 2000 patient
cases and the corresponding references.
All materials appearing can be downloaded as pdf files. New material is very welcome. Please contact A. Athanassiadou: athanass@med.upatras.gr to submit your data (mutations, negative results, references etc).
Communicated by Ernest Beutler, M.D., The Scripps Research Institute, La Jolla, CA, U.S.A.
We are working with two technology companies to develop "genome cards" or "genome trays" with the idea that it may be useful to our community to distribute large numbers of genomic DNA samples identified only by sex, ethnic origin, and age. We expect to have DNA from several thousand persons, and I would appreciate any feedback about the usefulness of this approach, and particularly would like to know who might be interested in beta testing this collection when it becomes available.
Anyone interested in this please contact Prof. Beutler, beutler@scripps.edu
This will be a small meeting, no registration required as HUGO is paying for the room.
| Date: | Sunday 14th April |
| Time: | Meeting at 13.00 - 17:00 |
| Venue: | Room 3F of the SHICC |
If you would like to attend please let Rania know ASAP.
(Formerly HUGO Mutation Database Initiative Meeting)
All are invited and encouraged to attend the annual general meeting of the HGVS in Baltimore. This is our main annual meeting where scientific presentations are usually made in the morning and a business meeting and discussion of problems & plans occurs in the afternoon. Abstracts are invited from all attendees.
The program has not been determined yet, however, apart from scientific presentations from submitted abstracts, we will discuss an update to mutation nomenclature, the planned central variation database plans and progress, plans for collection of variations from diagnostic laboratories, and also discuss the business of the Human Variation Society. The meeting closes with a mixer to give attendees the opportunity to meet and discuss ideas in a casual environment.
Registration fees include room rental, Audio Visual and administrative costs as well as all breaks, a buffet lunch and mixer.
| Date: | Tuesday October 15, 2001 |
| Time: | Registration: 8:00AM, Start: 8:30AM, Finish: 7:00-8:00PM |
| Venue: | Hyatt Regency Baltimore, U.S.A. |
| Registration: | Will be required for this meeting. Details to come soon. You can however register your interest at present. |
| Abstracts: | All HGVS members are invited to send in an abstract. All abstracts MUST be received by 15th September. There is more chance of an oral presentation if you get your abstract in early! (Note you do not need to submit an abstract to attend the meeting.) |
| Organizers: | R. Horaitis,
Executive Secretary HGVS R.G.H. Cotton, President HGVS |
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Coordinator Rania Horaitis horaitis@mail.medstv.unimelb.edu.au |