Competition I

In April 4, 2001, Genome Canada announced its first investment (Competition I) of $136 million to support 17 large-scale research projects and five science and technology platforms across the country with applications in health, forestry, fisheries, agriculture, the environment as well as the social, legal and ethical aspects of genomics.


Project Descriptions:

Annotation of chromosome 7

Project Leader: Steve Scherer
Institution: The Hospital for Sick Children

Scientists and the medical community have long taken a keen interest in chromosome 7, which contains many genes crucial to development. It also carries the cystic fibrosis gene and is often damaged in some types of leukemia and other cancers.

The overall goal of our project was to complete a gene map and apply it to disease study, as well as to annotate all pertinent biological features contained in the DNA sequence of human chromosome 7. The strategy throughout the effort was to generate and collate all genomic data and to integrate this with every piece of clinical and functional genetic information available. Perhaps the highlight of the project was our publication of a seminal manuscript in Science in 2003, describing an accurate DNA sequence and annotation of the entire human chromosome 7.

This was the first such paper of its kind confirming our group’s worldwide lead studying this portion of the human genome. In collaboration with 90 scientists from 10 countries worldwide and Celera Genomics, 158 million nucleotides of DNA sequence were assembled, 1,917 gene structures identified, and numerous structural features were anchored to the sequence map. At that time we also formally launched the first website and database designed to facilitate community-based annotation of chromosome 7, which continues to be the most relevant site for information on chromosome 7. We also sent the unique molecular reagents from this project to over 240 scientists worldwide to assist their research.

The study of disease was also an important applied goal of this project. We collaborated with many scientists from around the world to further disease gene research and discovered two disease genes that have led to patent filing. The international standing of this project continues to attract outside funds related to spin-off work as well as new trainees from around the world to Canada.

Outcomes: 

  • Publication of a seminal manuscript in Science in 2003, describing an accurate DNA sequence and annotation of the entire human chromosome 7
  • Number of research personnel employed by the project: 23
  • Number of peer reviewed publications published: 38 peer-reviewed manuscripts and 9 book chapters.
  • Resources generated: products of this project have been distributed to over 350 investigators worldwide, many of which were probes sent for patient studies or diagnosis.
  • Number of patents in process or obtained: two disease gene discoveries leading to patent filing.

TOP

Canadian program on genomics and global health

Project Leaders: Peter Singer, Abdallah Daar
Institution: University of Toronto

This is a stand-alone GE3LS project.

In industrialized countries life expectancy is 80 years and rising, but in a number of developing countries, it is at 40 years and falling. While genomics/biotechnology can help address health challenges currently facing both the developed and developing world, there are growing knowledge gaps in the global community. The Canadian Program on Genomics and Global Health (CPGGH) was developed to help close some of those gaps.

Our world-leading program on genomics and global health has influenced federal and foreign policy decisions, increased the opportunity for Canadian genomics and biotechnology companies to internationalize in emerging and developing markets, and increased public awareness on the uses and misuses of genomics to address global health challenges.

Highlights include:

“Health Biotechnology Innovation in Developing Countries”: an in-depth look into biotechnology in seven developing countries, this special Nature Biotechnology report is helping non-industrialized countries develop a biotechnology sector.

“Top 10 Biotechnologies for Improving Health in Developing Countries”: extensively cited in journal articles and presentations by officials from the developing world, this special Nature Genetics report helped shape the Grand Challenges in Global Health program by the Bill and Melinda Gates Foundation.

Genomics and Nanotechnology Working Group – UN Millennium Project: members of our team were invited by the United Nations Science, Technology and Innovation Task Force to form a working group to address the role of genomics and nanotechnology in addressing the UN Millennium Development Goals.

Regulation of Genomics Research: the conference “New Biomedical Research: Regulation, Conflict of Interest and Liability” and resulting book exposed several of the weaknesses of the current regulatory review and provided arguments for a more systematic oversight.

Outcomes: 

  • Reports “Health Biotechnology Innovation in Developing Countries” and “Top Ten Biotechnologies for Improving Health in Developing Countries” have become highly influential with federal and foreign policy makers.
  • Number of research personnel employed by the project: 85
  • Number of peer reviewed publications published: 60 papers, 22 books and monographs, 17 book chapters and contributions to collective work, and 166 invited presentations.

TOP

Functional genomics and proteomics of model organisms

Project Leaders: Janet Rossant, Brenda Andrews, Jack Greenblatt, Andrew Spence
Institutions: The Hospital for Sick Children, University of Toronto

Our project aimed to provide a comprehensive view of protein and genetic interactions in biomedically important model systems – bacteria, yeast, worm, and mouse.

For the bacterial, yeast and worm components, we used a variety of cutting-edge functional genomics approaches to define gene function in model eukaryotic organisms and characterize novel protein complexes in bacteria and yeast. We anticipate that our genetic network and other yeast functional genomics projects will lead to both a better understanding of the basis of genetic disease and also the discovery of new compounds that might be useful in the treatment of proliferative disorders such as cancer.

The Functional Annotation of the Mouse Genome project has moved Canada’s mouse genomics to the forefront of this rapidly growing and increasingly important field. Our team has generated mouse models for human conditions such as kidney disease and osteoporosis, developed new tools to help characterize Canada’s mutant mice, and established new mouse cell lines that are in high demand by academic and industrial investigators worldwide.

The Mammalian Protein-Protein Interactions project team developed high-throughput approaches to quantitatively assess protein-protein interactions in mammalian cell systems. Because most regulated cellular processes are carried out by complex protein-protein interaction networks, the underlying cause of many human diseases can often be traced to mutations that interfere with the assembly or function of these networks. With the successful completion of this program, these approaches now promise to provide major insights into human pathologies and highlight effective targets for therapeutic development.

Outcomes: 

  • Major insights into the molecular causes of a wide range of human diseases and new targets for drug and biomarker development.
  • Number of research personnel employed by the project: 191
  • Number of peer reviewed publications published: 98 referred papers (including Nature and Science), 17 invited reviews, 3 book chapters or contributions to a collective work, and over 385 invited presentations.
  • Patents: 1 provisional patent, 1 patent filed, 2 published patents, 1 commercial license in place, and 4 companies formed (MDSProteomics, Affinium Pharmaceuticals, Virtek Proteomics, and Mycota BioSciences)

TOP