Wellcome Trust Genome Campus Inaugural Symposium
HINXTON, UK - Although the Wellcome Trust Genome Campus has been officially opened by HRH Princess Anne last year October, many felt that the three-day Inaugural Symposium held here from 15 to 17 June 1998 was the real (scientific) opening, celebrating the completion of the Campus and its achievements to date.
Organised by the Wellcome Trust and the three institutes that are located on the Campus (Sanger Centre, MRC Human Genome Mapping Project Resource Centre, and the EMBL Outstation - The European Bioinformatics Institute), the symposium was visited by 200 scientists in the fields of bioinformatics, genetics, and molecular biology. Reflecting the mission of the Campus, the organising committee brought together key contributors to the fields of genomics and genetic analysis, new technologies, and ethical and legal implications of genetics.
The first day of the symposium was divided into two sessions: Genomes & Genetics and Bioinformatics, and was topped off with a plenary speech from James Watson.
Major sequencing contributions by Sanger Centre
The session on Genomes & Genetics was chaired by Fred Sanger and gave an overview of the various sequencing and genome efforts. In almost all the sequencing projects that were presented, the Sanger Centre has made major contributions and continues to do so. Except for the Arabidopsis Genome project, the Sanger Centre does extensive work on C. elegans and the Human genome, and a little less so in Drosophila (X-chromosome) and several micro-organisms.
In case of C. elegans, as Robert Waterston (Washington University) presented, the collaboration between the Genome Sequencing Center at the Washington School of Medicine and the Sanger Centre yielded already finished sequences for 80% of the genome with the other 20 Mb expected to be completed at the end of '98.
Sanger Centre's Bart Barrell gave a whirlwind tour on the sequencing efforts in the field of genomes of bacteria and other microorganisms. The Sanger Centre has a large programme in microorganisms, funded by the Wellcome Trust and the Wellcome Trust's spin-off Beowulf Genomics. The latter out-sources the sequencing of pathogens that are of special interest to biomedical research. One of the major successes of the Sanger Centre in this area is the complete genome of M. tuberculosis (see Vol. 393 of Nature), just ahead of a similar effort at TIGR.
On a side-note, the Sanger Centre just reached their first milestone of 100,000,000 base-pairs of finished sequence, totalled over all their sequencing projects.
Towards integrated systems in bioinformatics
The afternoon session on Bioinformatics started with Stephen Bryant (NCBI) on the topic of 'Structure Neighbours and Identification of Homologous Features'. He demonstrated NCBI's effort to make complex information easily accessible to biologists, and exemplified this with Entrez' feature to distinguish look-a-like protein structures from those that are really homologous in function.
From left to right: Stephen Bryant (NCBI), Paolo Zanella (EMBL-EBI), and Terry Gaasterland (University of Chicago)
(c) 1998 BioInformer. All rights reserved.
Terry Gaasterland (University of Chicago) followed with an energetic presentation on the 'Automated Assessment of Genomic Properties: from ORF's to Pathways and Processes'. Setting up systems that allow for automated real-time genome analysis is important in dealing with the ever-growing influx of biological data, but the take-home message is that as of now all these systems still require human supervision to assess or enforce the decisions made by the system.
In 'Discovering Genetics Networks', Gary Stormo (University of Colorado) outlined approaches that combine experimental and computational methods to tackle some of the problems that face bioinformaticians when they look for the regulatory mechanisms and interactions that influence gene expression. He demonstrated this with ongoing work towards defining the specificity of DNA binding proteins.
Chris Sander (Whitehead Institute) presented the work of his previous group at the European Bioinformatics Institute on 'Mapping the Protein Universe', which focuses on describing function and structure to proteins of unknown structure by clustering all protein sequences in multi-dimensional space.
In all the four presentations on bioinformatics, there was a strong sentiment to move on from simple stand-alone applications using a few data sources to integrated systems that use all available data from genomic and protein sequences, protein structure and function, gene expression and metabolic data to mine information and reach understanding by looking at the known biological data as whole.
"Keep ethical discussions out of hands of state"
The organising committee was very honoured to have as a plenary speaker the co-discoverer of the structure of DNA: James Watson. He regaled the audience on the research that ultimately led to their important discovery, and went on to discuss topics that are dear to him. Clearly being con-eugenics, he described some of the pitfalls scientists use to step in, and how the state made use of results from eugenics to justify certain decisions. Related to this, studies by the American government showed that every non-English speaking person that applied for immigration was basically stupid, and therefore was not admitted to the US. Of course, the IQ-tests were given in English.
Watson also discoursed on some of the ethical discussions surrounding genetic screening of humans. He was very adamant "to keep these discussions out of the hands of the state". And, although he realised it is an "impopular statement", he said about genetic engineering: "if you think you can do something about it [a disease, affliction you have], go ahead and do it".
The second day started again with a session on Genomes and Genetics, but the focus was now on genetic mechanisms behind diseases and how genetics can be used to improve our understanding and create treatments, if not cures, for diseases.
John Todd (Wellcome Trust Centre for Human Genetics) explained why certain diseases of the immune system are so common, yet at the same time so very complicated. David Porteous (MRC Human Genetics Unit) presented the study of cystic fibrosis, a rare and lethal auto-immune disease, and how encouraging results in genetherapy in mice remove symptoms of the disease. Some clinical trials with a single (nose-spray) dose are going on and show modest results.
In the 'New Technologies' session that afternoon, Patrick Brown (Stanford University) presented preliminary results of the information that has been gleaned from data on gene expression observed via DNA microarrays with the complete yeast genome on it. Tools were demonstrated that clustered genes by functionality and visualised the behaviour of those clusters through time when yeast was inoculated in a limited amount if sugar-rich medium (leading to diauxic shift).
Tea and discussions. In the middle-rear of the picture Dame Bridget Ogilvie.
(c) 1998 BioInformer. All rights reserved.
The last day was dedicated to ethical and legal issues that arise from genetics and in particular the sequencing of the human genome.
Sheila McLean (Glasgow University) focused her talk on the confidentiality issues when genetic tests are involved. Basically, she pleaded that with genetic information, 'confidentiality' should be upgraded to 'privacy'. Confidentiality has a long list of professional and legal exceptions, and especially where insurance companies or employers are involved, individuals need absolute privacy. On a similar topic, Bruce Ponder (University of Cambridge) explained how genetic testing in oncology, especially in breast and ovarian cancer, can greatly influence a patient's life, and that of the family, both for the better or the worse. Medical dilemmas also extend to family doctors and to the health system as a whole.
Dean Hamer (National Cancer Institute, US) presented results from the study of behavioural genes, and how evidence has been found that a number of behaviours have a strong genetic background, environmental influence only playing a minor role in shaping certain behaviours. Knowledge about these genes can be used for diagnosis and drug development for mental illnesses, but unfortunately also for other, less savoury, applications. How knowledge like this will be used, is up to the society.
Dame Bridget Ogilvie, Director of the Wellcome Trust, in her closing speech stressed the importance of centres such as the Genome Campus, where data production, collection, and use go hand in hand. Furthermore, "to make use of this massive amount of information, we need the skills of computational biologists, bioinformaticians (I am not quite sure what is what these days) and of course those skills are fundamental to our hope to manipulate, manage, and mine this massive amount of biological data, which is already available."
"So, realising that this area of biology is important for the future, the Wellcome Trust has already been told firmly that they have to invest even more money in the training of people in this area."
Article by: Jean-Jack M. Riethoven
Resources and further information
European Bioinformatics Institute (EMBL-EBI)
DALI 3D protein structure searches
The Sanger Centre
MRC Human Genome Mapping Project Resource Centre (MRC HGMP-RC)
The Wellcome Trust
National Center for Biotechnology Information (NCBI)
Entrez 3D structure search
Argonne National Laboratory
Mathematics and Computer Science Division
Multipurpose Automated Genome Project Investigation Environment (MAGPIE)
External sites are not endorsed by EMBL-EBI