Early-Warning DNA Sequencing System
21/09/10 15:12 Filed in: GenomeWeb Daily Scan
Submitted by S. Pelech - Kinexus on Tue, 09/21/2010 - 15:12.
This idea is even sillier than sequencing the whole genomes of tens of thousands of people to identify specific genes associated with disease risks. Bacteria and viruses are everywhere and the number of different species of these microbes is likely to exceed a million. Each of our own bodies typically harbor an estimated 10 trillion bacteria representing more than 200 species. The number of total bacteria on the planet has been estimated in the range of five million trillion trillion, that's 5 followed by thirty zero's.
The number of different types of pathogenic bacteria and viruses that have been shown to be harmful in humans is only a couple of hundred. If a new pathogen variant emerged, it would have to be identified from people that are actually sick, not from random samplings of the general environment. Pathogenic bacteria and viruses are always out there undergoing constant mutation and evolution. The vast majority are benign to humans. The actual development of disease depends heavily on the hygienic habits of people and their specific immune systems. Furthermore, only a limited number of viruses possesses the unique ability to gain entry and flourish inside human cells.
Whole genome sequencing is not a quantitative activity. To obtain statistically meaningful data on the abundance of the tiny fractions of bacteria and viruses that are truly pathogenic, it would be necessary to sequence thousands or possibly tens of thousands of the microbes at each location. On top of that, it would also be necessary to monitor hundreds or thousands of sites world-wide to get a sense of how each pathogen was spreading. A cost-benefit analyses of doing this should quickly reveal its impracticality. It is much cheaper to track where and when people are getting sick, and then rapidly identify the culprit.
For local or global monitoring, it would make a lot more sense to have quantitative PCR-based tests that amplify the DNA from specific pathogenic bacteria or viruses. Alternatively, using gene microarrays with oligonucleotide probes that are complimentary to pathogenic bacterial and viral gene sequences is another more cost-effective and efficient strategy.
Link to the original blog post.
This idea is even sillier than sequencing the whole genomes of tens of thousands of people to identify specific genes associated with disease risks. Bacteria and viruses are everywhere and the number of different species of these microbes is likely to exceed a million. Each of our own bodies typically harbor an estimated 10 trillion bacteria representing more than 200 species. The number of total bacteria on the planet has been estimated in the range of five million trillion trillion, that's 5 followed by thirty zero's.
The number of different types of pathogenic bacteria and viruses that have been shown to be harmful in humans is only a couple of hundred. If a new pathogen variant emerged, it would have to be identified from people that are actually sick, not from random samplings of the general environment. Pathogenic bacteria and viruses are always out there undergoing constant mutation and evolution. The vast majority are benign to humans. The actual development of disease depends heavily on the hygienic habits of people and their specific immune systems. Furthermore, only a limited number of viruses possesses the unique ability to gain entry and flourish inside human cells.
Whole genome sequencing is not a quantitative activity. To obtain statistically meaningful data on the abundance of the tiny fractions of bacteria and viruses that are truly pathogenic, it would be necessary to sequence thousands or possibly tens of thousands of the microbes at each location. On top of that, it would also be necessary to monitor hundreds or thousands of sites world-wide to get a sense of how each pathogen was spreading. A cost-benefit analyses of doing this should quickly reveal its impracticality. It is much cheaper to track where and when people are getting sick, and then rapidly identify the culprit.
For local or global monitoring, it would make a lot more sense to have quantitative PCR-based tests that amplify the DNA from specific pathogenic bacteria or viruses. Alternatively, using gene microarrays with oligonucleotide probes that are complimentary to pathogenic bacterial and viral gene sequences is another more cost-effective and efficient strategy.
Link to the original blog post.