Main Menu
Main Menu
Menu

Integrated GE3LS Research: The meanings and understandings of terms used in genomics research

by

Overview

In order to ensure optimal data collection and informed choice, the GE3LS project team’s over-arching goal is to investigate how the understandings of terms used in genomics research by scientists, when translated into the scientists’ meanings on consent forms, information letters, surveys, and demographic forms, may or may not be consistent with the understandings of research participants and their meanings when they respond to such documents. The team will:

  • perform a textual analysis of research grants, information letters and consent forms that are being used in clinical studies of this Genome Canada grant and others funded in the last Genome Canada competition. With interview ‘prompts’ from the results of this research, research participants and researchers involved in the clinical Themes of this Genome Canada grant will be interviewed to provide further insight into the meanings and understandings of terms used in genomics research, particularly related to copy number variations (CNVs);
  • survey other key stakeholders’ views of genomic research (particularly related to CNV), such as health professionals’ (medical geneticists and counselors, physicians) perceptions of the clinical meaning of CNV results (what kinds of results should provoke duty to warn, and child protection obligations);
  • examine the views and experiences of patients and their families as research participants towards furthering informed choice to participate in CNV research;
  • explore the meanings and understandings of terms used in CNV research by studying issues revolving around the interpretation, management and communication of whole genome scanning (WGS) results to patients and their families; and
  • consider the legal issues that are emerging from the methodologies of the aforementioned studies that explore the meanings and understandings of terms used in CNV research, including qualitative content analysis, interviews of researchers and research participants, and electronic surveys.

Structural and functional annotation of the human genome for disease study

by

Overview

Now that the human genome has been sequenced, the next step is to undertake the complete structural and functional annotation of genes associated with diseases, according to Robert Hegele, endocrinologist and scientific director of the London Regional Genomics Centre at the Robarts Research Institute.

Hegele is project leader of Structural and Functional Annotation of the Human Genome for Disease Study, an innovative project which aims to bridge new biological knowledge with medical applications. Any two humans are 99.9% identical at the level of their DNA sequences. But recently, new forms of genomic variation have been appreciated above and beyond single nucleotide polymorphisms. These include large scale variations, such as copy number changes, insertions, deletions, duplications and rearrangements, and they may be much more widespread than was previously appreciated. In this project, collaborator Steve Scherer of the Hospital for Sick Children will define and superimpose these large scale genomic variations over top of the existing “first draft” of the human genome sequence map. Another form of genome variation occurs through a process called “alternative splicing’, which gives rise to multiple versions of a protein encoded by a single gene. Also, some parts of the genome previously thought to be dormant are now known to code for active proteins functioning in the body.

Collaborators Ben Blencowe, Tim Hughes and Brendan Frey of the University of Toronto will define and integrate these new forms of genomic variation into the current human genome sequence map.

The project will therefore deliver a “new improved edition” of the human genome map; one that annotates and characterizes large­scale copy number variants, alternative splicing profiles of genes in selected tissues and previously unknown genes and other functional elements. Hegele and collaborators will then apply the annotated genome map with its rich trove of new biological information to unravel the genetic basis of diseases that extract a huge social and economic toll in Canada, such as diabetes, heart disease and breast cancer.

The data generated from the project will be made available, free of charge, on the Internet, in order to accelerate biomedical discovery, including the diagnosis and treatment of common diseases.

Integrated GE3LS Research: Regulation and monitoring of convergent technologies

by

Overview

The team will systematically address the potential GE³LS issues stemming from the development and commercialization of the quantum dot (Qdot) diagnostic system, a high-throughput diagnostic system capable of detecting multiple global infectious disease threats at point-of-care; in 3 parts:

Public Engagement: The project team will develop and evaluate a public engagement tool for high school students and the general public that encompasses various emergent technologies and their application to infectious disease research.

Regulation of the Convergence of Genomics, Proteomics and Nanotechnology: The project team will identify regulatory issues related to convergent technologies and work with Canadian regulatory authorities to develop regimes and guidelines on implementation of any standards that may be developed. As such, they will

  • survey Canadian and international regulatory regimes for each of the major technologies involved in the project;
  • develop a database of cognate regulatory regimes;
  • identify potential bottlenecks that are likely to slow down the development of convergent technologies;
  • develop recommendations for the federal government on how to streamline the different regimes to develop “smart regulation” for convergent technologies; and
  • work with Canadian regulatory authorities to develop regulatory regimes and guidelines on implementation of any future Canadian standards.

Monitoring of Risks and Benefits of Quantum Dots: The project team will monitor research on toxicity of Qdots and develop an annotated database of research publications and data on the potential risks of Qdots after exposure, and participate in policy discussions with the Canadian federal government on these issues.

Quantum dot diagnostics: Simultaneous Genomic and proteomic profiling of multiple pathogens at point-of-care

by

Overview

Worldwide, infectious diseases cause billions of infections and over 17 million deaths each year. With its well­-traveled population and cultural diversity, Canada is at risk of global diseases such as SARS (severe acute respiratory syndrome), malaria and avian influenza (bird flu). But Canada is developing cutting-edge expertise in the rapid and accurate diagnosis of infectious diseases, based on nanotechnology.

Kevin C. Kain, Director of the McLaughlin­ Rotman Center for Global Health and Senior Scientist in the division of genomic medicine at the Toronto General Research Institute, and Michael Greenberg, FIO Corp, are project leaders of Quantum dot diagnostics: simultaneous genomic and proteomic profiling of multiple pathogens at point­ of­ care.

They have assembled a research team that will incorporate advances in nanotechnology with pathogen genomics and proteomics, in order to create a high­ throughput diagnostic system capable of detecting multiple global infectious diseases within minutes. The system is based on quantum dots ­ tiny fluorescent probes that can be used as biomarkers to tag organic molecules and track them during biological processes. The research team plans to develop this diagnostic system specifically for use at point of care, in order to detect or exclude the presence of pathogens related to five major infectious diseases ­ SARS, HIV/AIDS, malaria, hepatitis B and hepatitis C. The social and economic potential of this innovative system is underscored by the fact that these five diseases account for over 2 billion infections and 5 million deaths worldwide each year.

The project is organized into a continuous discovery pipeline, making it possible to accelerate discovery of diagnostic tools, commercialize them and translate them into clinical use. According to Kain, “the ability to definitively detect or exclude multiple pathogens at point of care within minutes would be a breakthrough with impact on our healthcare system, the quality of life of Canadians as well as global communities.”

Integrative Biology

by

Overview

The genomes of more than two hundred organisms have been sequenced, from microscopic earthworms to humans. The function of thousands of individual genes is attracting the attention of scientists. But integrative biology is revealing that genes work not individually but as physical or functional assemblies to perform their functions.

Brenda Andrews is Director of the Terrence Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto and she is project leader of Integrative Biology. According to Andrews, genes perform their functions not individually, but in assemblies or groups. In turn, these gene assemblies work with each other to allow the cell to function and respond to its environment. The value of integrative biology is underlined by the fact that some medications are highly specific, binding to one protein and one protein alone – but these medications can have unexpected and unpredictable effects when they impact on gene assemblies.

The project led by Andrews will develop an integrated view of Saccharomyces cerevisiae (baker’s yeast) – a leading model organism, which has conserved many of the same genes and pathways as humans, and is amenable to experimentation. By investigating cells and functional sub-components in baker’s yeast, the project is expected to yield valuable intellectual property. Examples of IP include new instrumentation, reagents (substances used in chemical analysis or synthesis), methodologies for human and veterinary therapeutics, and reagents for industrial processes and for basic and applied research.

Based at the newly opened Terrence Donnelly Centre for Cellular and Biomolecular Research, this project will help develop a world-leading platform for functional genomics and proteomics, drawing on multidisciplinary approaches and research strengths in Toronto and across Canada.

Identification of genetic pathways that regulate the survival and development of cancer and cancer stem cells

by

Overview

Breast cancer, leukemia and brain tumours are among the most common and lethal tumors that affect Canadians. Because these cancers frequently affect young women and children, many patients are given very aggressive treatments to improve their chances of survival. But these treatments often have serious side effects, and they are not effective in fighting the most serious forms of these cancers.

According to Cynthia Guidos, a Senior Scientist at the Hospital for Sick Children Research Institute in Toronto and a Professor of Immunology at the University of Toronto, treatment failure might occur if the therapy does not target the rare cancer stem cells which can re­initiate tumour growth and thus function as the “roots” of the tumour.

Guidos’ research focuses on the development of normal and leukemic immune cells. She is leader of a project entitled “Identification of Genetic Pathways that Regulate the Survival and Development of Cancer and Cancer Stem Cells”. Her team also includes experts in leukemia, breast cancer, brain tumors, and cancer stem cells. Their project will study human tumors and mouse cancer models in order to address two crucial issues: what genetic alterations distinguish very aggressive from more benign tumors, and what genetic and biological malfunctions lead to the development of cancer stem cells.

By dissecting the cellular signals that govern abnormal survival of tumor cells and cancer stem cells, the project is expected to develop new “biomarkers” that may help to reserve the most aggressive cancer treatments for patients with the highest risk of failing conventional therapies. Ultimately, the project may lead to development of new and more effective therapies specifically targeted to cancer stem cells. The project team hopes that their research will eventually increase survival rates and improve quality of life for survivors of breast cancer, leukemia and brain tumours.

GE3LS Summary

Although no specific GE3LS project has been outlined as part of this Cancer Stem Cell project, the long-term outcomes of the project’s scientific research may have the potential to alter diagnosis and management of cancer, with important ramifications for both pediatric and adult cancer patients and their families. Thus, it is important to have an ongoing GE3LS component to this project. As such, a GE³LS Advisory Committee (consisting of Stuart Howe, Randi Zlotnik-Shaul, and Aideen Moore) meets bi-annually to review research developments, focusing on two main areas:

Identifying new GE³LS  issues.

Identifying GE³LS research questions for the future: Possible GE³LS issues to consider when clinical testing begins:

  • Knowledge transfer
  • Dissemination of research findings
  • Language and cultural barriers for patient recruitment

Integrated GE3LS Research: Genome-environment interactions in Type 1 diabetes: Attitudes of Adults and Adolescents to Predictive Genetic Testing for Diabetes

by

Overview

Recent research advances mean that Research Ethics Boards (REBs) are now reviewing protocols that involve predictive genetic testing in children. While issues surrounding predictive genetic testing are clear in adults, there remain significant problems regarding the ethics of predictive testing in children. Further information on the acceptability and impact of predictive testing in children and adolescents and their families is required so as to allow REBs to better quantify risks and benefits of such studies.

Objectives

The objectives of our research study include:

  • Examine the views of first-degree relatives of diabetics to predictive testing for type 1 diabetes as compared to the nondiabetic population.
  • Determine the views of first degree relatives of diabetics as compared to the general population, relating to studies on gene-environment interaction for Type 1 Diabetes (T1D).
  • Examine the views of children and young adolescents who are able to provide assent.
  • Determine the effect of having a child with T1D on parent’s perceived risk to other children and impact on anxiety levels and family functioning.

This information should help to guide investigators, REB members and research participants on the key elements that need to be included in consent forms for research in T1D that includes predictive testing. Many other childhood diseases, including asthma and Crohn’s disease, are now understood to involve genome-environment interactions. Information gained in the GE3LS component of our project will be generalisable to many other disorders and will be very important as other large population-based predictive studies are undertaken.

Integrated GE3LS Research: Exploring the Impacts of DNA Barcoding

by

Overview

The project is collaborating with the “Taxonomy at a Crossroads” project, a major study being led by social science researchers at Lancaster University who are probing the impacts of DNA barcoding on taxonomy.

The project team is also combining educational outreach initiatives with GE3LS research by engaging high school students in research projects relevant to consumer fraud and food safety (e.g., market surveys of fish labeling).

In addition, the project team acknowledges that there are policy implications that arise from DNA barcoding, and as such, the GE3LS committee is continuously monitoring opportunities and discussing strategies for policy recommendations and implementation.

Canadian Barcode of Life Network

by

Overview

DNA barcodes use a small fragment of an organism’s DNA – a portion of a single gene – to identify the species to which an organism belongs. They are powerful tools, which can be used to help catalogue biodiversity. DNA barcoding began in Canada, and Canadian scientists continue to lead international work aimed at developing a complete catalogue of the Earth’s life forms.

Paul Hebert, an evolutionary biologist and Director of the Biodiversity Institute of Ontario at the University of Guelph, is project leader of the Canadian Barcode of Life Network. It has taken 250 years to catalogue some 15% of the world’s biodiversity. But with many species now under threat, the Canadian Barcode of Life Network seeks to develop comprehensive DNA barcode libraries for all the world’s birds and fishes, and then of other animals, fungi, plants and protists (these are often single-celled organisms).

This project seeks to develop a DNA-based identification system which can be used to catalogue all species. Given that this and other barcoding projects are expected to generate a flood of new data, the Network will also create an advanced databasing system to aid the storage and analysis of barcode records.

It is hoped that the barcoding project will provoke the development of hand-held barcoders. These devices could then be used by bioprospectors in the rapid identification of thousands of species with the potential to yield lifesaving drugs, or to signal the presence of animal and plant organisms in food even after processing.

The Network will initially barcode groups of particular economic and social interest in Canada, before moving on to examine environmental samples from a wide range of other species. The project is a vital step toward the creation of a complete inventory of Canadian biodiversity – the first inventory of its kind in the world.

Integrated GE3LS Research: The communication of genomics research results to research participants

by

Overview

Genomic research on the autism spectrum disorders (ASD) raises a number of social and ethical issues. These include issues in human subjects research more generally, and in the ethics of research on a medically and social complex child-onset disorder more specifically.

Most of our research has concerned the issue of communicating genetic research results to research participants. Recent commentaries argue that researchers bear an obligation to report genetic research findings to study participants. Others contend that while the principles of respect for persons, reciprocity, and beneficence indeed apply to the research context, they may neither be well served if results are disclosed nor denied if they are not disclosed. This issue is particularly challenging in the context of autism genomics, given the intensity of the relationship between researchers and the participant community, the complexity of the scientific information generated, and the multifaceted ways in which this information may be interpreted and used by research participants and families. The communication of genetic research results also bears on issues of health and social service delivery, and the extent to which research can or should serve a compensatory function.

We have pursued research on these issues through a review of relevant sub-national, national and supra-national policy guidance, and a set of qualitative interviews with researchers and research participants. We are currently mounting a survey of ASD genomics researchers using an experimental design, to understand the myriad factors influencing professional judgments regarding the disclosure of genetic research results.

Related publications:
Miller, F.A.; Giacomini, M.; Ahern, C.; Robert, J.S.; de Laat, S. 2008. When research seems like clinical care: A qualitative study of the communication of cancer genetic research results. BMC Medical Ethics, Vol 9: 4.
Miller, F.A.; Giacomini, M.; Robert, J.S.; Christensen, R. 2008. Duty to disclose what? Querying the putative obligation to return research results to participants. Journal of Medical Ethics, Vol 34: 210-213.