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(Previous HGVS & 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).
The long awaited WayStation to receive and review unpublished mutations is now open for business and was officially announced at the recent International Congress of Genetics in Melbourne. First time visitors to the site who wish to submit information must first register and submit their credentials. After submission of their mutation(s) the data is sent to an expert "Gene Editor" for review. If accepted the submission, called a Genome Variation Report (GVR) is issued a Human Mutation reference and may be eligible for a PubMed ID. The data will then be stored until the Central Database (being constructed) is up and running. The early opening of the WayStation should alleviate some of the problems with reporting newly discovered mutations as they most often never appear in the literature. As the Waystation is new, there may be some teething problems in the beginning that need to be sorted out, and your submission may take longer to be reviewed than is planned however at least it will be available to the public eventually and you will receive a citeable reference. This announcement was also reported in Science Vol.301, 1 Aug. 2003 p573.
To submit your mutations visit: http://www.centralmutations.org
The Society journal Human Mutation has increased impact factor once again rising from 6.31 to 6.89. The journal is receiving an ever increasing number of high quality manuscripts.
A very successful meeting was held in Palm Cove, QLD, Australia in early July in association with the International Congress of Genetics in Melbourne. The meeting attracted over 170 registrants and many new technologies were reported. The next meeting will be held in 2005. The post meeting website including a printable PDF copy of the programme may be found here. Human Mutation will feature a Special Issue of invited manuscripts arising from this conference. A small HGVS meeting was held during the ICG meeting also.
The mutation nomenclature pages on the HGVS Website are continuously updated and maintained by Dr. Johan T. den Dunnen. A recent addition is the "mutation checklist" to assist people writing publications by pointing out the most problematic issues. The checklist should assist those preparing a publication to describe sequence variants following the current recommendations.
HGVS Scientific & Annual General Meeting Los Angeles, 4th November; Abstracts & registrations now being accepted, closing date for abstracts Oct. 10 -see details below. If you wish to present an oral presentation you better register and send your abstract in ASAP! However, you do not need to present an abstract to attend the meeting.
HGVS Board Meeting Los Angeles, 3rd November 6:00PM - 10:00PM. All board members have received details, if you have not yet indicated if you will attend please contact Rania.
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.
PhenoFocus is an open collection of researchers interested in developing optimal public-domain solutions for computational handling of phenotype data. Informatics management of phenotypes and genotype-phenotype relationships represents an important scientific goal of the post-genomic era. Progress will require widespread adoption of standardized, powerful data models for phenotype information, and consensus exchange formats for phenotype data distribution. These solutions do not yet exist, and their development will be non-trivial given the almost boundless range of phenotypes that may need to be dealt with. The PhenoFocus network is seeking to create effective guidelines for modelling phenotype data, with a special emphasis upon human disease states. Key objectives include; - ensuring broad community input to the challenge - synergizing ongoing efforts to quickly create effective solutions The project website provides a notice-board that; - tracks ongoing efforts and approaches being explored in the field - summarizes contact details and research interests of PhenoFocus members - posts texts and links to ideas from individuals seeking community comment The PhenoFocus group requests and welcomes general input on its activity, contributions, and new member contacts. These communications, current project discussions, and any other matters, are processed in open forum via the groups email address which is: phenofocus_at_ebi.ac.uk
Contributed by: Professor Anthony J Brookes, Vice-Chairman, Clinical Genomics Unit, Coordinator Center for Genomics and Bioinformatics Karolinska Institute, Berzelius väg 35 S-171 77 Stockholm, Sweden
ALFRED - The ALelle FREquency Database ALFRED (the ALelle FREquency Database) is designed to store and disseminate frequencies of alleles at human polymorphic sites for multiple populations, primarily for the population genetics and molecular anthropology communities. The emphasis remains on populations typed for multiple polymorphisms and polymorphisms typed on multiple populations. Allele frequencies at each site are linked to the specific populations and specific samples of those populations with descriptions. When available, haplotype frequencies are also included. Currently, ALFRED has data on 815 polymorphisms, 357 populations and 15180 frequency tables (one population typed for one site). ALFRED is accessible from http://alfred.med.yale.edu . Data in ALFRED come from two sources: they are extracted from the literature or they are submitted by researchers. Currently, ALFRED contains considerable unpublished gene frequency data from the Kidd Lab.
All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching.
Flexible methods of searching ALFRED are available. Selecting locus, population or polymorphic site from the entry page and following the links available will lead to information on the locus, population or site you selected and eventually allele frequency data. All frequency data are linked to their source, either a publication or the laboratory contributing the data. Data can also be retrieved from specific publications, if they have been entered, by searching on the name of an author. Links to other web sites such as Ethnologue, dbSNP, LocusLink, PubMed are also provided from the relevant page.
Data for individual polymorphisms can be displayed in graphic, table, and semi-colon delimited (for downloading) formats. In addition, the entire database can now be downloaded in XML format by following the link provided in the web site (http://alfred.med.yale.edu/alfred/xmldatadump.asp ). The DTD (Data Type Definition) developed is also provided for download and use for the validation of the XML files. Twice a month the XML files are updated. Depending on requirements, a researcher can download the entire database with or without the descriptions or have the tables separately downloaded in XML format.
A web page has been prepared for the purpose of providing guidelines to users for submitting data to ALFRED (http://alfred.med.yale.edu/alfred/AboutALFRED.asp#datasubmission). We are requesting that researchers help us by submitting their data using the excel spreadsheet provided at this page.
Graphical overviews of the database contents can be viewed at the page http://alfred.med.yale.edu/alfred/alfredsummary.asp . A 'sites per population' web page (http://alfred.med.yale.edu/alfred/sitesperpop_graph.asp) shows graphically (and numerically) the number of allele frequency tables for each population. A 'populations per site' web page (http://alfred.med.yale.edu/alfred/popspersite_graph.asp) similarly represents the number of allele frequency tables for each polymorphic site.
ALFRED now has a page dedicated for user registration (http://alfred.med.yale.edu/alfred/registration.asp ). The primary benefit of registering is to receive the ALFRED Newsletter. The newsletter provides hints on how to efficiently use ALFRED for various purposes and will provide highlights and recent additions to ALFRED on a regular basis.
ALFRED is supported by the US National Science Foundation.
Contributed by: Haseena Rajeevan, Systems Programmer - ALFRED, Yale University
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Date:
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Tuesday 4th November 2003 The biggest HGVS event of the year! TIME TO REGISTER NOW! |
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ASHG Conference Hotel: Roman Room, Millenium Biltmore Los Angeles, Los Angeles, CA, U.S.A. |
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Time:
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Registration:
8:00AM |
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Fee includes administrative costs, conference materials, coffee breaks, a buffet luncheon and mixer. HGVS member: US$80 (HGVS members receive a 25% reduction in meeting registrations. To join HGVS click here). |
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Abstracts: |
Closing date is 10th October 2003. Registrations without presentations are also accepted. |
| Associated with: |
An ancillary meeting of the American Society of Human Genetics Annual Meeting |
Send HUGO your up-to-date contact details to register your interest in attending HGM2004. Full participant registration and/or exhibitor registration will be sent to you as soon as they are available Meeting web site: http://hgm2004.hgu.mrc.ac.uk
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Coordinator Rania Horaitis horaitis@mail.medstv.unimelb.edu.au |
