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new Society to focus on Human Genome Variation

  November, 19 2001 4:26
your information resource in human molecular genetics

MELBOURNE, AUSTRALIA, NOV. 13, 2001 -- A new society dedicated to promoting the discovery and free publication of information on the variations in human genes was inaugurated on October 12 at the American Society of Human Genetics annual meeting in San Diego, California. It will be known as the Human Genome Variation Society (HGVS).

Richard Cotton, BAgSc., Ph.D., D.Sc., of the Genomic Disorders Research Centre, Melbourne, a world leader in human genome variation detection, was appointed President of the new society. Other world-renowned medical geneticists, including Victor McKusick, M.D., of Johns Hopkins University, Baltimore, Maryland, and Charles Scriver, M.D., of McGill University, Montreal, Canada, were elected to its Board of Directors. See the new organization's Web site at www.hgvs.org.

"Proper diagnosis and treatment of persons with birth defects and genetic diseases depend very much on understanding the changes in our genes that underlie these disorders," said Prof. Cotton. "These data must be collected and made freely available to physicians, hospitals, and laboratories in every country. Until now, there has been no systematic attempt to do so."

"Scientific journals have stopped publishing reports of single gene variations after the first five or 10," Prof. Cotton said. "Also, diagnostic laboratories often are too busy to report disease-causing variations in their patients so that others may benefit from their experience. Around the world, we have groups of very dedicated scientists creating databases for their own use. This situation is a major obstacle to effective health care today. What's needed is a central repository and coordination of collection of all this information."

One of the most dramatic findings from the study of the human genome has been that specific genes can be faulty in hundreds or even thousands of ways, Prof. Cotton said. "This means that if we have 30,000 genes and each one can be faulty in hundreds of ways, we could have up to tens of millions of ways of causing human disease."

He said a group of the HGVS members will work with the many experts in particular genes and central bioinformatics facilities around the world to set up a system to document and deliver variation data. After review, these data are to be stored and made freely available on the HGVS's online database. Some data passing stringent review may be published by special arrangement with the society's official research journal, Human Mutation (published by Wiley-Liss, Inc., New York).

Prof. Cotton said the HGVS needs the support of those studying mutations in particular genes, especially the diagnostic community. "We are also seeking funding from foundations and industry to set up the necessary bioinformatics infrastructure to support our activities."

The HGVS grew out of the Human Genome Organization (HUGO) Mutation Database Initiative, which was generously supported by grants from the March of Dimes Birth Defects Foundation, White Plains, New York, and substantial assistance from HUGO London.

The mission of the Human Genome Variation Society is to enhance human health through identification and characterization of changes in the genome that lead to susceptibility to illness. To this end, it will collate the genomic information necessary for molecular diagnosis, research on basic mechanisms, and design of treatments of human ailments. Prof. Cotton can be contacted by e-mail at cotton@ariel.ucs.unimelb.edu.au.



MELBOURNE, AUSTRALIA, NOV. 13, 2001 -- Collection of genetic mutations causing thalassaemia began in the 1960s, when such changes were discovered by protein sequencing. The advent of gene cloning and sequencing greatly accelerated not only the accumulation of mutations in the globin genes, but also the rate of discovery of new disease genes and the mutations in them.

Scientists and physicians began to collect data regarding specific gene mutations causing disease to assist them in their clinical, diagnostic, biochemical, and molecular genetics studies. These curators thus created what is now referred to as locus specific databases, e.g., phenylketonuria or PKU

(www.mcgill.ca/pahdb), Fanconi anemia (www.rockefeller.edu/fanconi/mutate/) and cystic fibrosis (www.genet.sickkids.on.ca/cftr/).

Others were interested in documenting mutations in genes and in the pattern of mutation in genes and began collecting data on the published mutations in all genes. Victor McKusick, M.D., of Johns Hopkins

University, Baltimore, Maryland, who first catalogued inherited syndromes, began collecting the first and subsequent interesting mutations in genes, but not all of them (OMIM: www.ncbi.nlm.nih.gov/omim/). The Human Gene Mutation Database at the Institute of Medical Genetics, Cardiff, http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html also collected published mutations in all genes. Much later, databases were established in the private sector and public sector by deliberate funding of SNP discovery programs and sequencing efforts, (e.g., HGBASE: http://hgbase.cgb.ki.se/ dbSNP: www.ncbi.nlm.nih.gov/SNP/) to receive polymorphisms referred to as SNPs..

However, three major problems prevented the complete collection of and public access to particular mutations causing single-gene disorders:
1) As some genes can be inactivated by hundreds -- even thousands -- of mutations, the task of collecting the perhaps tens of millions of mutations causing disease is daunting. It would be almost impossible for this task to be achieved by a single entity and requires co-ordination of scientists worldwide.
2) Many mutations remain unpublished because many journals will not accept reports of mutations after the first 5, 10 or 15. In addition, diagnostic laboratories that identify important disease-causing mutations are often too busy to report them consistently in the literature or databases.
3) There was no central body promoting complete collection of mutations, but only groups of very dedicated scientists creating central databases and locus-specific database for use in their own research.

The necessity to unify the world's gene mutation data led in 1994 to the creation of the Mutation Database Initiative (MDI) of the Human Genome Organization (HUGO). This group grew out of a meeting of leading geneticists in Montreal, with the encouragement of HUGO and the American Society of Human Genetics.

The MDI, generously supported by HUGO and grants from the March of Dimes Birth Defects Foundation, White Plains, New York, has presented at meetings and published widely on the problems described above and succeeded in solving some of them. An account of some of this progress can be found in the freely available January 2000 special issue of the journal Human Mutation at www.wiley.com/genetics/HUMUMDI.

The greatest recent obstacle for the HUGO MDI has been lack of funding to put in place a system to capture, document, store and display variation data. After a concerted effort to obtain funding from industry, MDI is now attempting to obtain grant funding to allow development and a suitable structure.

This structure will involve a receiving unit called the WayStation in Toronto, Canada, (see prototype at www.centralmutations.org), the Administrative/Review office in Melbourne, and the WareHouse, an adapted version of HGBASE (http://hgbase.cgr.ki.se/), to store and display the data in Stockholm, Sweden.

The current plan is that mutation data and related information will be submitted by investigators at the WayStation (see www.genomic.unimelb.edu.au/mdi/entry.html for description of the type of data). Then, the mutations will be reviewed by scientists and, if accepted, a report of the data will be assigned a

reference in the society journal Human Mutation and made freely available to the public. Data will also be sent to the WareHouse and any other interested databases for public distribution. We are currently accumulating a series of gene editors for the purpose of review.

It had been thought for some time that an organized society should be formed by the 600 or so members of the HUGO MDI residing in 33 countries of the HUGO MDI worldwide. Such a society was created on October 12 at the annual meeting of the American Society of Human Genetics in San Diego and named the Human Genome Variation Society (HGVS). Richard Cotton of the Genomic Disorders Research Centre, at St. Vincent's Hospital and the University of Melbourne, the HUGO MDI convener, was elected President of the HGVS. The journal Human Mutation has become the HGVS journal after the company showed considerable support for the initiative in recent years. Details of HGVS office bearers and membership can be seen at: www.hgvs.org.

The most urgent tasks for the HGVS at this time are to obtain funding to set up the necessary infrastructure for the system and create a strategy to collect mutations from diagnostic laboratories, create simple software for experts to use to curate data on their gene of interest, and to obtain assistance from relevant companies to support these activities and individuals with informatics skills as well as gene editors.

Membership details and history are available from the HGVS Web site or Rania Horaitis at:
Human Genome Variation Society Office
Genomic Disorders Research Centre,
St. Vincent's Hospital Melbourne
PO Box 2900
Fitzroy VIC 3065, Australia
E-mail: horaitis@medstv.unimelb.edu.au
URL: www.hgvs.org

Message posted by: Kai Garlipp

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