We truly are living in the age of technology, but not as we know it. Machines will no longer be developed through scientific knowledge; scientific knowledge will be developed through machines.
Science Writer Sumaya Anwar interviews Dr Eugene SchusterÂ to find out more about the Archon Genomics X prize. The $10 million prize competition, which awaits a team capable of sequencing 100 genomes, at a cost of $1000 per genome, in 30 days or less with no more than 1 error in 1,000,000 bases!
It seems surprising to see head-to-head competition in the scientific world, is this something you have come across often or is the vision of scientists working fully together and sharing their findings more realistic?
There is a growing movement in the scientific community for this type of competition â€“ another example is https://www.innocentive.com and shows that the crowdsourcing movement has entered into the scientific community. I think the impact of these types of competitions will be limited and focused to very particular research areas and will not greatly expand as a funding source for academic research. This is because research is very expensive to conduct and you need funding from the beginning. Only an extremely well funded lab or company could undertake such a project and most likely would already have funding in place to do this type of research â€“ so winning the X prize would only be a bonus. However, I think it is much more likely that crowdfunding â€“ when someone proposes to build or do something and ask the public for funds to accomplish the task â€“ will become a bigger part of scientific funding in the future.
The 100 genomes to be sequenced have been donated from centenarians; as a researcher within the aging field how would this genomic database benefit you?
Although, my group studies ageing in a tiny worm called Caenorhabditis elegans, we are interested in identifying evolutionarily conserved mechanisms that can affect lifespans. We would clearly benefit by this research because when human genes are discovered that might help humans to live past 100 we can immediately test if the equivalent genes in worms also affect lifespan. For example, we study a gene called daf-16 in worms and almost 20 years ago the scientist Cynthia Kenyon discovered that this gene plays an important role in extending the lifespan of worms. In the past few years the equivalent gene in humans (called FOXO3A) has been implicated in helping humans to live past 100. We believe that by understanding the role of this gene in worms we can start to understand what it does in humans.
Which standard of the competition do you think is going to be most difficult to meet: 98% completeness of the sequences, the time restriction of 30 days or less, the cost restriction of $1,000 per genome or achieving complete haplotype phasing of the chromosomes?
Complete haplotype phasing will be the most difficult to achieve. It is very difficult to predict inheritance without sequencing the parents or related individuals. To do this probably requires the ability to sequence very long stretches of single strands of DNA with very little error â€“ which is probably beyond current methods.
The process of aging is no doubt complex; research tends to be conducted on model organisms, would the development of genomic sequencing technology mean the end of model organism use?
No because having genomic information does not mean the end of experiments. Large sequencing studies in human will only provide weak evidence that a gene may be involved in a disease or the prevention of a disease. Experiments will have to be done to show a definitive link between the disease and the gene and it is much easier to test these links in model organisms. In worms, you can do an aging experiment in a few weeks. If I started a study in humans, it is likely that the study would out live me.
Steve Jobs had his genome sequenced for $100,000; $1,000 seems much more commercially viable for the general public. What does the current price stand at?
To get a high quality genome with very few errors it would cost about $10,000 today. Once the price gets near $1000 (approximately the cost of an MRI scan) then it can become reasonable for insurance companies or the NHS to sequence a genome if there is good reason to suspect that there is a genetic basis for a disease or symptom. However, this does not include the cost of making sense of that genome and including analysis and interpretation costs may significantly add to the price.
Which technologies are currently at the forefront in terms of cost-efficient sequencing and how do they achieve this?
Two companies that have recently announced low cost genome sequencing are Ion Torrent and Oxford Nanopore Technologies. Both companies will use a semiconductor based technology â€“ Ion Torrent bases the technology on detecting ion charges during the sequencing process and Oxford Nanopore detects changes to the electrical current as a strand of DNA is passed through a nanopore. The major cost savings of these technologies is that they do not rely on optics (i.e. expensive lasers and scanners) nor on labelled samples (older technology typically relies on costly fluorescent labels to detect sequence).
This competition was first proposed in October 2006, what date would you estimate the commercialisation of the $1000 genome?
I would estimate that it will take 2 years before the first commercial $1000 genome (including the cost of interpretation) is available.
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