Bioinformatics--Role in Future of Science and Medicine in Canada
Dr. Jamie Cuticchia is the Head of the Bioinformatics program at the Hospital for Sick Children in Toronto. Since 1997, Dr. Cuticchia has actively and successfully developed this program, which is designed to turn trillions of pieces of biological information into usable knowledge. In the June issue of Geriatrics & Aging, Dr. Cuticchia shared his thoughts on the Human Genome Project and Canada's role in this project. This month he has shared his thoughts on the field of bioinformatics and its role in the future of science and medicine in Canada.
Q: What is meant by the term 'bioinformatics'?
A: Bioinformatics is the joining together of hardware, software, and communications devices with the objective of solving a biological question.
Q: What are the origins of bioinformatics and what have been some of the critical milestones in the development of this field?
A: The origins of the field are rooted in the human genome project. Most of the funding for bioinformatics has been attained for purposes of collecting, disseminating, assembling, and analyzing human genomic data (and those of model organisms). There have been several milestones to date. These include: The creation of large databases, such as GenBank and the Genome Database (GDB); the production of rapid-comparison tools, such as BLAST, which is used to determine sequence homology; the current milestone is that phase of bioinformatics which looks to co-ordinate data from hundreds of widely distributed biological databases.
Q: Do you see biology and medicine becoming increasingly driven by computation?
A: The position of biology today is similar to where physics stood over a decade ago. The field of physics underwent a shift, splitting research into two directions. There were the large centres that acted as the providers of massive amounts of data (the light sources) and the smaller research groups who pooled information from them and worked on analysis and theories. In the field of biology, the independent, small research lab with a technician, a post-doc, and a student, will no longer be competitive research-wise. There will have to be either larger groups, such as the genome centres in the US, with hundreds of researchers, or, alternatively, smaller groups that will rely on the Internet data and software tools to make new discoveries.
Q: How did the Supercomputing Centre for Bioinformatics come to be established here in Toronto? What has your role in all of this been?
A: Luck. I came to Toronto in August, 1997 to form a small group whose mandate was to set up an infrastructure enabling the hospital researchers to handle more effectively scientific data and to use bioinformatic tools. Canada was very far behind the US in acknowledging the importance of this field, and after a few attempts at fund-raising it became clear that bioinformatics programs couldn't be funded through any traditional granting programs in Canada. However, the philanthropists of the hospital's foundation, and members of the information technology industry, had enough vision to see the important role bioinformatics would play in the future of research. With the first endowments coming in from companies like SGI, IBM, and Oracle we were off to the races. Eventually infrastructure monies from the Federal and Provincial governments of Canada were awarded and I went from $200,000 of funding to $50,000,000 in about 2 years.
Q: Did the prominence of the role of Canada and Toronto (and in particular, that of The Hospital for Sick Children) in genetic research play a part in the establishment of the Centre? How significant is this genetic work in the international context?
A: HSC has been recognized worldwide as a place for discovery of genetic information. Given its level of funding, it is probably the most efficiently run genetic group in the world. However, with groups in the US and Europe getting $10 or even $20 for every $1 the Canadian genomics group receives, it is only a matter of time before its reputation drops unless significant Canadian funding is provided.
Q: What is the capacity of the Supercomputer facility? Why is bioinformatics so computationally intensive?
A: We have a 128 cpu Origin 2800 supercomputer and an IBM-SP3 supercomputer. The combined performance of these systems is about the same as having 3000 desktop PCs working in unison. An example: We recently performed a clustering of DNA sequences (1.5 million) and it took over 5 days using the entire supercomputer. If we tried to do this on a PC the program would still be running long after the genome project was completed!
Q: How much information is being generated by the Human Genome Project? Are the means of organizing this data sufficient to meet the demands and the complexity of the task?
A: Right now, very little "information" is being generated; however, it is generating a great deal of data. We generated over 1 billion bases of DNA in one year and, in the end, we will have over 3 billion in total. The organization of this data is not particularly complex when compared to the analysis of this data, which will be going on for the next 5-15 years.
Q: The Supercomputer Centre was established to house the GDB. What function does the GDB serve in the overall Genome project?
A: There has always been some confusion about GDB. GenBank is a database of raw sequences of all sequenced organisms and is merely a listing of the nucleotide bases. GDB is the repository for biological knowledge and maps about the human genome. Using the GDB, researchers can see what probes are available for a gene or region of the genome, what mutations exists, and what polymorphisms have been studied. Best of all, unlike MOST biological databases, GDB is curated by a group of nearly 100 leading researchers in the genome field. Our data are high quality.
Q: What database source is of greatest value to physicians and clinicians?
A: That would probably be OMIM, the online version of Victor McKusick's Mendelian Inheritance in Man. It is a free text version of the catalogue, which has been a staple for medical geneticists for decades. GDB provides links to OMIM where appropriate.
Q: What role do you see Canada playing in Genomics and bioinformatics ten years down the road?
A: I fear that Canada will take its investments in these areas and, because of the enforced socialism within research, dilute them so much that we will have a greater number of 2nd class scientists. The body of research will be bigger, but will not necessarily improve. Unless the funding agencies, or the venture capitalists, see that the "big science" requires significant investment, we will continue to plod along. However, if investments are made in select groups with significant intellectual capital, I have no doubt Canada could be a worldwide leader in both of these fields.
