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The Next Revolution In Medicine: Genome Scans For Everyone
the_newsbeagle writes "This year, a biotech company called Ion Torrent will introduce a new chip for its genome sequencing machine, which should enable researchers and doctors to scan a complete human genome for $1000 and in just a couple of hours. Compare that to the effort required to complete the first human genome: $3 billion and 13 years. Ion Torrent has nearly reached the $1000-genome milestone by virtue of a process called 'semiconductor sequencing,' and the company's founder says his chip-based sequencing machine benefits from all the efficiencies of the computer industry. At a price point of $1000, genome scans could become a routine part of medicine. And the price could keep dropping. To test out the technology, and to investigate just how useful genome scans are these days for your typical, reasonably healthy person, the IEEE Spectrum reporter got her own genome scanned and analyzed."
Price isn't the only determinant of whether something is a 'routine part of medicine'. For the foreseeable future, there is remarkably little utility that an individual's genome brings to the table. It will become a very important part of medical research, but in terms of an individual's health, not so much.
It will be hyped. It will likely end up like 'full body CT scans" - a bragging tool for the seriously hypochondriac but of no help to the routine patient.
Even the Single Nucleotide Polymorphism (SNP) data which is pretty cheap now (basically what the police use for forensics) helps most people very little. In the context of answering a specific genetic question, perhaps - but not as a routine. When you send someone to a medical geneticist, most of the time and effort revolves around getting the person to understand what you are trying to accomplish and the pros and cons of doing so. Having whole genome sequencing just makes it even harder.
Faster! Faster! Faster would be better!
It would be neat to have a nice, light and portable genome sequencer for when I next go eating meat in the UK
It works great for countries where health is 'free' (through taxes), and their main goal is to make people healthy, not to extract maximum funds from your pocket. It's too bad that you don't live there.
Bye!
I've always considered biology to be hundreds of years behind physics and the other "hard sciences", because they never had the tools to deal with it.The CPU power, the RAM, the hard-disk space, even the cloud infrastructure are all needed to make DNA sequencer efficient. The last instrument I worked on was a low cost DNA sequencer that could yield a sequence in one day. At the end of a run, to do the basecalling and base alignment of the data, you would need significantly more horsepower than what was on the meager instrument. The cloud allows you access to a supercomputer the the short time that you need it, so the customer is not burdened by the huge computational complexity involved.
As the cost sequence drops (and continues to drop), whole new fields of research have opened up. Bioinformatics where biology and computer science meet is a pretty hot topic. We have a deluge of data, but we don't yet have all the good algorithms necessary to unlock all the secrets we wish to solve. The Rosetta stone of the 21st century. This is the biggest complaint I hear about from biochemists.. Making sense of the data. Data leads to knowledge leads to wisdom, but data is not knowledge.
I consider DNA sequencing to be an enabler, just like the steam-engine, or the electric light. It is now possible to look deeply at things we never could, like meta-genomics. Did you know that you have more bacteria in your body then all other cells in your body put together? ..And did you know that you can't grow most of them on a petri dish? We have been to mars, but we don't even know the bacteria in our own gut. Meta-genomics is a form of "shot-gun sequencing" .. In the lab you understand the biology by making millions of replicas of it in the petri dish.Not all bacteria grow on a petri-dsh . With shot-gun sequencing, you sequence enough sample so you can digitally reconstruct what organisms were there to begin with. This has enabled us to [begin to] understand the biochemical messaging between soil bacteria and the roots of plants, understand the biochemistry of food digestion to generate bio-fuels more efficiently, etc .. Interesting times...
I have generally considered biology so far behind the other hard sciences, especially physics, precisely because for a very long time they failed to consult with the chemists, physicists, and engineers. It has largely been self-induced, and almost entirely a process of falling behind. Heck we have some hacks out there in biology using morphological databases (today - with all the genetic tools they have!) to reverse engineer evolution, when the biologists are well aware that morphology is a good categorizing and search tool (it tells you where to start genetically looking), not an extrapolation tool for real data and conclusions.
Physics in particular finally just started going the route of butting in wherever they figured out they could be useful to biologists and clinicians especially. CT and MRI are great examples.
Rothberg's own 6 years of research to sequence 9000 letters of genetic code is a perfect example. After a year or so, a physicist or engineer would have said f--- this, there must be some way of automating this process. I suspect most of the scientists at Ion Torrent are chemists, EEs, and physicists. Probably not too many pure biologists (though some biophysicists are probably around).