Test the Waters
27/03/12 13:20 Filed in: GenomeWeb Daily Scan
Submitted by S. Pelech - Kinexus on Tue, 03/27/2012 - 01:20.
The GenomeBC- and GenomeCanada-funded project to create a metagenomics-based test for detection of bacterial contaminants in community drinking water seems rather ill-conceived. The central objective appears to be the development of a tool kit consisting of field-ready testing procedures that can be conducted on basic equipment common to labs all over the province of British Columbia (BC) and software that can be used to quickly detect the presence of unhealthy conditions. It is difficult to imagine that this could be achieved with the proposed funding of $3.2 million, and that it would be the most cost-effective solution for this problem.
Metagenomics is a very effective strategy to identify new species of organisms; field samples can contain thousands of diverse types of microbes, including viruses, bacteria and protozoa. However, only a few hundred dangerous pathogens are known to harm humans and livestock. The contemplated project would really be about monitoring the presence of known pathogenic microbes and viruses based on the presence of traces of their DNA. To isolate sufficient DNA from water specimens, sample concentration and PCR-amplification steps would be required. This would be followed up by either high throughput gene sequencing or more likely with gene microarray analyses with specific complementary oligonucleotide probes. This requires equipment that are not basic instruments commonly found in laboratories across the province of BC.
Although such approaches are likely to be inherently noisy and error-prone, the information provided is really limited to detection of the presence of the DNA or RNA of pathogens of specific interest. They are not very quantitative, and more importantly dead and live organisms and viruses would be hard to distinguish. It would seem much more sensible to develop methods such as mass spectrometry and antibody-based microarrays for the quantification of specific toxins and biomarker proteins that are more reflective of actual disease potential.
Interestingly, the announcement of the GenomeBC and GenomeCanada-funded water metagenomics project comes after an earlier call at the end of January this year for new multi-million dollar proposals for projects that use genomics to advance personalized health care delivery. The Government of Canada has proposed to provide up to $40 million to GenomeCanada and up to $22.5 million to the Canadian Institutes for Health Research (CIHR) for this initiative. It would appear that the Canadian federal government wants to be seen to be promoting more applied research. At the same time, basic biomedical research funding in Canadian universities and hospitals has been continuing to erode, and recent proposals to fix problems in how grant proposals are reviewed by CIHR have incurred even further wrath from Canadian researchers. Moreover, now the funding for industrial research in successful programs like the Industrial Research Assistance Program of the National Research Council (NRC-IRAP) and the Scientific Research and Economic Development (SRED) program is also threatened.
Over the last 12 years, GenomeCanada has received over $915 million from the federal government in Canada in support of its mega-projects that have also received comparable funding from provincial governments and other sources. While a few genomes were sequenced, some of which are still not in the public domain, there has been extremely poor translation of this research into tangible benefits for the health and welfare of Canadians. Even the production of resultant scientific research publications has been pathetic in view of the amount of funding awarded to these mega-projects. I see no reason to believe that the future performance of GenomeCanada will be any different.
Link to the original blog post.
The GenomeBC- and GenomeCanada-funded project to create a metagenomics-based test for detection of bacterial contaminants in community drinking water seems rather ill-conceived. The central objective appears to be the development of a tool kit consisting of field-ready testing procedures that can be conducted on basic equipment common to labs all over the province of British Columbia (BC) and software that can be used to quickly detect the presence of unhealthy conditions. It is difficult to imagine that this could be achieved with the proposed funding of $3.2 million, and that it would be the most cost-effective solution for this problem.
Metagenomics is a very effective strategy to identify new species of organisms; field samples can contain thousands of diverse types of microbes, including viruses, bacteria and protozoa. However, only a few hundred dangerous pathogens are known to harm humans and livestock. The contemplated project would really be about monitoring the presence of known pathogenic microbes and viruses based on the presence of traces of their DNA. To isolate sufficient DNA from water specimens, sample concentration and PCR-amplification steps would be required. This would be followed up by either high throughput gene sequencing or more likely with gene microarray analyses with specific complementary oligonucleotide probes. This requires equipment that are not basic instruments commonly found in laboratories across the province of BC.
Although such approaches are likely to be inherently noisy and error-prone, the information provided is really limited to detection of the presence of the DNA or RNA of pathogens of specific interest. They are not very quantitative, and more importantly dead and live organisms and viruses would be hard to distinguish. It would seem much more sensible to develop methods such as mass spectrometry and antibody-based microarrays for the quantification of specific toxins and biomarker proteins that are more reflective of actual disease potential.
Interestingly, the announcement of the GenomeBC and GenomeCanada-funded water metagenomics project comes after an earlier call at the end of January this year for new multi-million dollar proposals for projects that use genomics to advance personalized health care delivery. The Government of Canada has proposed to provide up to $40 million to GenomeCanada and up to $22.5 million to the Canadian Institutes for Health Research (CIHR) for this initiative. It would appear that the Canadian federal government wants to be seen to be promoting more applied research. At the same time, basic biomedical research funding in Canadian universities and hospitals has been continuing to erode, and recent proposals to fix problems in how grant proposals are reviewed by CIHR have incurred even further wrath from Canadian researchers. Moreover, now the funding for industrial research in successful programs like the Industrial Research Assistance Program of the National Research Council (NRC-IRAP) and the Scientific Research and Economic Development (SRED) program is also threatened.
Over the last 12 years, GenomeCanada has received over $915 million from the federal government in Canada in support of its mega-projects that have also received comparable funding from provincial governments and other sources. While a few genomes were sequenced, some of which are still not in the public domain, there has been extremely poor translation of this research into tangible benefits for the health and welfare of Canadians. Even the production of resultant scientific research publications has been pathetic in view of the amount of funding awarded to these mega-projects. I see no reason to believe that the future performance of GenomeCanada will be any different.
Link to the original blog post.