If the twitter feeds from Marco Island are blowing up, its because our friends at Oxford Nanopore have lit the fuse. They have finally made public the crucial information about 2 new nanopore-based sequencing instruments to be generally available the second half of 2012. There are some great summaries of the technology that have already appeared, see especially:
The capsule review: staggering long read lengths (50kbp or more), minimal sample prep, uniform error rate, extremely high throughput, eventual direct reading of RNA (no cDNA required).
All very impressive and impactful on their own...
But the kicker is the MinION: a USB-stick disposable sequencing instrument for less than $1000.
Let that sink in for a moment. A sequencing instrument that you can carry in your pocket, that plugs right into your laptop, provides results within hours, and costs less than $1000 with no other instrument required. I had to pick my jaw off the floor when ONT first briefed us…
As we announced some time ago, ONT will be distributing Pipeline Pilot and the NGS Collection as their preferred bioinformatics solution for the GridION and MinION systems. Combining Pipeline Pilot with ONTs real-time sequencing technology is enabling some amazing capabilities. You no longer need to run an instrument for days or longer and blindly hope for usable results. Now, your analysis can control the experiment: run until polymorphisms are found in locations of interest, run until you achieve a desired level of exome coverage, you can even parallelize sequencing experiments, with results from one sample controlling sequencing performed on other samples. And with the MinION "stick", you can sequence anywhere you can take a laptop.
A few brief videos on the ONT site highlight how Pipeline Pilot is being used to work with and analyze the data from these remarkable instruments:
“Why do drugs affect some people more than others?” This was a question posed to me by one of my coworkers in the midst of our 6 mile after-office run last week. I was thinking, “why is it so easy for you to talk while running after 5 ½ miles?!” After numerous postulations, our meeting of the minds came to the conclusion that genetic diversity was at least part of the answer.
Have you ever wondered if you’ve taken drugs that have actually had no positive effect? In a recent article in the New York Times, author Andrew Pollack describes how various drugs on the market don’t work as intended in, often times, all too much of the population. “Pfizer’s Xalkori for lung cancer, works wonders — but only for the roughly 5 percent of patients whose tumors have a particular chromosomal abnormality”.
Pollack goes on to describe the regulatory and payer pressures on the drug companies to come up with a measurable test for determining which patients are benefiting from the drugs and which ones may be subjected to harmful side effects with no chance of benefit.
Regulatory authorities have spoken and given guidance on the subject and may even be helping drug companies get their drugs to market faster and get to peak sales faster. They may also be helping companies reduce cost by failing drugs earlier and by enabling the selection of patients more suitable for successful clinical trials. But some argue that this cost cutting will pale in comparison to the enormous losses that the drug companies will face by limiting their products only to those who will benefit from its use (reading statements like the ones found here make me really glad that regulatory authorities exist).
Biomarkers are often the corner stone of these diagnostic tests and can be found in areas of research like next generation sequencing (NGS), molecular modeling and imaging. For example, a test done to sequence a particular region of your DNA could tell you whether or not you had the “chromosomal abnormality” that would render the drug effective. The cost of sequencing has dropped tremendously since the worldwide effort of sequencing the human genome that began in the 1990’s - estimated in the $3 Billion dollar range. Today new technologies in this area have the industry expecting that we will see the cost of a full human genome drop below $1000 in this decade. But sequencing alone doesn’t provide answers.
Today the cost of analysis and interpretation of results will play a role in determining the total cost and implied benefit of tests that rely on sequencing. What if the patient and the payer shared in the cost of development of the diagnostic test? I, for one, look forward to the day I can pay a few hundred dollars and determine my best course of action. I was at a recent conference where one of my coworkers spoke on how after extensive genetic testing the attending team was able to offer her a few options with assigned success probabilities. Personalized medicine had arrived.
Imagine the impact if even our over the counter supplements could be linked to personalized benefit through a companion diagnostic more immediate than weight loss or muscle tone. It will be here sooner than you think, just like mile 6 was for me.