Virus cells and DNA strand. Picture by Shutterstock/ Kjpargeter
I recently spoke with Dr. Suneil Malik about genomics and outbreak preparedness.
This is the second part of our conversation, in which we were discussing the benefits and potential downsides of the so-called “omics”-revolution, which consists of new technologies such as transcriptomics and proteomics that are changing the field of medicine.
Dr. Malik is a Manager and Team Leader for Toxicology at Health Canada, a government agency directed by the Canadian Minister of Health. He is based in Ottawa, Ontario, Canada.
About Dr. Malik:
- He was a Biologist at the Office of Biotechnology, Genomics, and Population Health at the Public Health Agency of Canada (PHAC).
- He is an investigator at the McGill International Tuberculosis Centre in Ottawa.
- He is the author of numerous publications in the field of genomics, including the highly regarded article “Genomics Research: The Underpinning of Infectious Disease Prevention and Control Strategies” (2013) and a landmark paper on the association of the NRAMP1 gene with pediatric tuberculosis [1].
- He currently works as a Manager for the Mechanistic Studies Division and the Hazard Identification Division in the Environmental Health and Science Research Bureau at Health Canada, a department of the Government of Canada focused on promoting and maintaining the health of Canadians.
Q: Which new technologies are being used in addition to genomics to make diagnoses easier and find cures?
The “omics revolution” – an integrated comprehensive “omics” approach combining genomics, transcriptomics, proteomics, metabolomics, and fluxomics for advancement of systemic sciences and for human disease diagnostics and treatment. After Nielsen and Oliver (1). Courtesy of US National Library of Medicine (https://openi.nlm.nih.gov/)
Dr. Malik: There are technologies that are being used and they are being given the name “omics”. We already talked about genomics, but there are other technologies, too. The study of genes is called “genomics”, the study of the transcript is called “transcriptomics”, the study of proteins is called “proteomics”, and the study of metabolites is called “metabolomics”. Together these technologies can give us a more comprehensive understanding of disease mechanism. Once we understand the disease mechanism we can develop diagnostic tests and, yes, potentially find cures.
Q: When will we see practical tools coming from this research? Will there be quick, non-invasive tests that help doctors decide who is most at risk of an infection or illness?
Dr. Malik: That is what the medical community is focusing on and has been for a while. One of the biggest advances is being able to rapidly sequence infectious agents to promptly treat. Traditionally many infections were diagnosed by taking a biological sample from an individual to try and grow the pathogen in a petri dish. Once pathogen colonies formed, then analyses can be undertaken to identify pathogens. This can be a very time consuming process (several days in some cases) and delays prompt treatment that could mean life or death. However, sequencing a biological sample takes only a day and is very accurate. In my opinion, there will be a wide range of non-invasive tests that will be emerging in the near future.
Q: Are there certain types of infection where genomics work is having the best results? Or is it useful for all types of infectious disease?
Dr. Malik: Genomics can have utility for all infectious diseases. Remember, genomics is a tool to help understand the biology underlying infectious diseases or chronic diseases for that matter. We focus on infections that represent the highest burden of disease. This can be tuberculosis in sub-Saharan Africa or in the Canadian northern communities. Influenza is the greatest killer of Canadians due to infection. These are infections for which we need a better understanding of their biology in order to mitigate severe outcomes and genomics may provide critical information in this regard.
Q: How important do you think personalized medicine will become to public health in general?
Dr. Malik: Extremely important! What we have learned over the decades is that individuals do not respond equally to infections or illnesses. In every aspect of our being, genetics play a role. We see this now in cancer. Not everyone should be treated the same way for the same cancer. If there are two people with lung cancer, and you sequence their DNA, there can be important differences that would influence the type of treatment they receive. Personalized medicine is incredibly important, for both infectious as well as chronic diseases.
Just to add, we have gone beyond the one gene, one disease paradigm (for the most part). Most diseases are complex meaning that they involve multiple genes interacting with the environment. There are a small number of diseases that are almost exclusively genetic, like Huntington’s and cystic fibrosis but there is still an environmental factor involved i.e. not all cystic fibrosis patients progress at the same rate. On the opposite side of the spectrum, there are for example motor vehicle accidents, which are almost exclusively environmental, but there can be a genetic component, maybe your reflexes are influenced by your genes. Those are the extremes. Most illnesses are caused by a more equal contribution of gene and environment. This suggests that genes do not necessarily control our fate. For example, if you have a gene associated with elevated cholesterol you may modify the risk of heart disease through a healthy diet and exercise. If an individual carries a gene that increases their risk of colon cancer, they would likely receive colonoscopies at an earlier age and/or more frequently than those that do not carry that gene variant. Cancer treatments are often tailored to the genetic profile of an individual’s cancer.
Q: Are there concerns about privacy? For example, if companies discover that certain people are more vulnerable to certain diseases, could it get harder for them to get medical insurance?
Dr. Malik: Yes, that is a huge problem but Canada has its own genetic discrimination laws in place.
Q: Are there other downsides to genomics that you can think of?
Dr. Malik: I’m not sure there are downsides. Genomics is a tool that helps our understanding of disease mechanisms. It is not a stand-alone approach however. We need to employ other technologies to get a more fulsome understanding of a disease mechanism.
Q: Thank you so very much for this interview!
Dr. Malik: Anytime, Mia!
[1]“Alleles of the NRAMP1 gene are risk factors for pediatric tuberculosis disease”. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1189316/
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