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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).
Elections
Annual General Meeting of HGVS
Membership Dues to Change in 2006
HGVS Booth at ASHG
Automated Splice Site Analysis Webserver
Exchange standard for genomic polymorphism and related data
WayStation – Now open for its initial submissions
The Leiden Open Source Variation Database (LOVD)
TAZ gene mutation and polymorphism database
Mutation Detection Training Course, Leiden - 2006
6th Australasian Mutation Detection Meeting - 2006
Elections
Four new Board members need to be elected for a three year term. A call for nominations will be made in November 2005 by the Secretary Dr. Bill Oetting. Any member wishing to stand for nomination should put in their proposal to the nominating committee via Rania when the call is made or now but in any event by November 7.
Annual General Meeting of HGVS
Scientific & AGM ; Salt Lake City , Utah , USA . 25 th October 2005 . Registrations are still being accepted. See www.hgvs.org
Membership Dues to Change in 2006
Growth of the Society membership base had seemed to stagnate. Thus a discussion of different options of membership dues was made in the hope that making membership cheaper more members would be attracted to the Society.
The Society dues have been restructured and now include for regular members the options of electronic only access to Human Mutation or access to both the print and electronic versions as before. Cheaper dues (without the journal) for Editors of Human Mutation, students whose supervisiors are regular members and spouses of regular members have also been made available. From 1 st January 2006 the dues will be as follows:
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We remind all members that in order for your subscription to Human Mutation not to be interrupted, to please remember to promptly renew your membership when asked in November.
HGVS Booth at ASHG
The Society will host an exhibitor's booth once again at the American Society of Human Genetics Annual Meeting in Salt Lake City, Utah. The booth allocated is number 1015 located in Publisher's Row. If you are at ASHG please drop by the booth and meet us. Further, feel free to man it for a while to help spread the word.
Anyone wishing 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.
Automated Splice Site Analysis Webserver
HGVS members are invited to evaluate sequence variants that may impact mRNA splicing with the Automated Splice Site Analysis webserver which may be accessed at https://splice.cmh.edu . Upon registration with a valid electronic mail address, sequence changes can be entered either in HGVS-recommended format using HUGO approved gene names or transcript accession numbers, as user-defined sequences, or dbSNP rs identifiers. Sequences are analyzed with information weight matrices that quantify the strengths of either human or mouse con stitutive splice sites, splicing regulatory sequences, or branchpoint recognition sites. The server dynamically produces a set of tables indicating the locations and strengths of affected and pre-existing sites and a sequence figure annotated with binding sites. For a detailed description of the server and its capabilities please see: Nalla VK and Rogan PK. Human Mutation 25:334-342, 2005.
Peter K. Rogan, Ph.D., Laboratory of Human Molecular Genetics, Children's Mercy Hospital and Clinics
2401 Gillham, Kansas City MO 64108 , USA
Exchange standard for genomic polymorphism and related data
We are experiencing a deluge of genome variation, mutation, and related data that con tinues to grow in scale, and this will con tinue for many years to come. Databases and informatics projects are already struggling to store, exchange, and make sense of all this information – much of which will hold key insights into the genetic basis of disease. One way to help this situation is via the development of standard global data models for this kind of information. Therefore, an international con sortium of ~40 academic and commercial groups has come together to create such a standard, and it is called Polymorphism Markup Language (PML).
PML is an XML-based data specification for representing all aspects of sequence variation and genotyping data. It has been designed to unify terminology and structure of information reported by assay instruments, generated by genotyping laboratories, and stored in population allele reports and generic polymorphism databases. It is now an approved Object Management Group ( OMG ) standard supported and successfully trialled by all major SNP databases. Efforts are now underway to develop this further into PML-2, a model that will enable handling of phenotype data and the informative realm of genotype-phenotype relationships.
Anthony J Brookes ( University of Leicester ), on behalf of the PML Development Consortium*
* Funded by the Japan Biological Informatics Consortium (JBIC), the PML initiative involves input from Affymetrix, Bergen Center for Computational Science, Chinese Academy of Sciences, Cold Spring Harbor Laboratory, Effector Cell Institute, European Bioinformatics Institute, Finnish Genome Center Helsinki University, Fujitsu Kyushu System Engineering Limited, Fujitsu Limited, GlaxoSmithKline, Helsinki University, Institute of Genomics & Integrative Biology , INTEC Web and Genome Informatics Corp, International HapMap project, International Rice Research Institute, Japan Biological Informatics Consortium, Japan Biological Information Research Center, Japan Science and Technology Agency, Japan Science and Technology Corporation, Karolinska Institute, Mitsui Knowledge Industry Co., Miyoshi International Patent Office, National Cancer Center Research Institute, National Center for Biotechnology Information , National Institute of Genetics, NCBI, Novus Gene Inc., NTT Data Corp, Point One Systems, LLC, Riken Genomic Science Center, Shanghai Center for Bioinformation Technology, Stanford University, Tokyo Institute of Technology, Tsinghua University, University College London , University of Leicester, Yale University, Yamanouchi Pharmaceutical Co.
WayStation – Now open for its initial submissions
The WayStation website and database will act as a central point for the submission, review and publication of genetic variation data. The WayStation provides a con sistent interface and format to allow the joint submission and correlation of molecular information, defining DNA and/ or RNA changes, together with their associated phenotypic findings.
The ultimate goal is to assemble and share novel variations so that clinicians and diagnosticians will have instant access to accurate, complete, and standardised reports of all mutations and their effects. The rebuilt WayStation is now receiving submission of real investigator- provided information via its online forms, which submissions are being reviewed by WayStation's Gene Editors. These submissions will then be assessed by Wiley and NCBI to ensure that they meet their expectations for Genome Variation Reports (GVR), and to validate their respective submission handling requirements. Submissions are held in strict con fidence at all times prior to publication.
We invite you to submit your novel variations to Human Mutation via the WayStation, and expect your submissions to become GVRs as described above. A member of our group, Conover Talbot Jr in Baltimore USA , will help you personally throughout the submission process, and we welcome your suggestions and comments on any concerns you may have. Further, we solicit your ideas on how we might improve the submission process itself.
http://www.centralmutations.org
Richard Cotton, Co-Editor Human Mutation cotton@unimelb.edu.au
The Leiden Open Source Variation Database (LOVD)
LOVD - http://www.DMD.nl/LOVD/ (Fokkema et al., 2005) - is a database for the collection, display, and curation of DNA variations in genes in accordance with the current HGVS guidelines and recommendations. Since d irect access to up-to-date information on sequence variation is currently provided most efficiently through web-based, gene-centered, locus-specific databases (LSDBs), LOVD has been developed along the " LSDB-in-a-Box" idea for the creation and maintenance of a fully web-based gene sequence variation database. LOVD is platform-independent, uses PHP and MySQL open source software only, and is freely available.
The LOVD system is currently used to maintain the mutation databases kept at the Leiden Muscular Dystrophy pages ( www.DMD.nl/ ). The LOVD system has dramatically decreased the curator's burden to maintain the 22 locus-specific databases, which con tain nearly 7,893 mutations (3,342 unique) of which more than 1,000 have been submitted via the internet during the past year. To promote the use of LOVD, we currently offer curators the possibility to set up a database on our Leiden server.
The current LOVD system should be con sidered as a basic but expandable framework for LSDBs, mainly focusing on the collection and display of DNA sequence variations . With a minimal effort, the database can be modified to store additional data. Several functional enhancements are under development, but other features like more fancy tools to graphically display the sequence variation data collected still need to be developed. Therefore, we would like to invite (bio)informatics students and other interested individuals to participate in the further development and extension of the current possibilities of the system by writing and adding new scripts .
Reference
Fokkema IF, den Dunnen JT, Taschner PE (2005). LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-Box" approach. Hum Mutation 26:63-68.
Johan T. den Dunnen, LUMC, Wassenaarseweg 72, Leiden 2333 AL, , Nederland ddunnen@lumc.nl
TAZ gene mutation and polymorphism database
Mutations in TAZ (Xq28) are responsible for X-linked Barth syndrome (OMIM 302060), characterized by cardiac manifestations (variously described as dilated cardiomyopathy, left ventricular non-compaction, or endocardial fibroelastosis), neutropenia, early failure to thrive, growth delay, and 3-methylgluta con ic aciduria. The syndrome has been recently reviewed by Barth et al. [X-linked cardioskeletal myopathy and neutropenia (Barth syndrome): an update. Am J Med Genet A. 2004 May 1;126(4):349-54]. Many different mutations have been identified, most of them unpublished, which has prompted the compilation of mutations from the literature and from direct submissions from several testing laboratories. This list has been placed on the Barth Syndrome Foundation web page (http://www.barthsyndrome.org) in the form of an excel file listing the mutations in order along the gene; each mutation listed represents one family. Recurrent mutations reveal several mutational hotspots in the gene. Evolutionary con servation is indicated. Polymorphisms are shown separately. Each case has a numbered reference and a Reference list has been appended.
Database maintained by Iris L. Gonzalez, Ph.D., igonzalez@barthsyndrome.org
5th HUGO Mutation Detection Training Course, Leiden - 2006
This time, this biennial course will be held in Leiden , the Netherlands .
The course will take place from 31st August to 4th September 2006 and is organised by Dr. Johan T. den Dunnen ( Leiden Genome Technology Center ).These popular small courses aim to provide an overview of current technology and applications via a mixture of practical demonstrations, laboratory work and lectures with a combination of top-level speakers and laboratory demonstrations. Participants are from around the world.
See: http://mdtc2006.hugo-international.org/home/index.php
6th Australasian Mutation Detection Meeting - 2006
- Methods, Cancer Gene Analysis and Diagnostic Applications -
2 – 5 August 2006
Couran Cove, South Stradbroke Island, QLD, Australia
This meeting is a satellite to the International the 11th Congress of Human Genetics to be held nearby in Brisbane.
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Coordinator Rania Horaitis horaitis@mail.medstv.unimelb.edu.au |
