Generating solutions

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: The meanings and understandings of terms used in genomics research
GE³LS Project Leaders: Jeff Nisker, University of Western Ontario
Summary
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.