Sunday, March 4, 2012

Portable Units Could Ease the Sequencer's Move to Clinical Labs

 A sequencing device that is the size of a USB memory stick and that costs under $1,000.  Right now, it sounds like science fiction.  According to a recent New York Times article, this development is possible if a company named Oxford Nanopore is able to produce a very different kind of DNA sequencer as promised by the end of the year.  
Sequencing currently requires samples to be sent to one of a few central labs with a sequencing device.  The instruments are large and costly.  Price varies, but top models can cost more than half a million dollars.  A few companies, among them Roche, Illumina and Applied Biosystems compete in this market.  Price is not the only competitive factor - as cheaper models such as Polanator that use open-source technology and bring the price down to 170K have not made a dent in the market for the higher end systems; Kalorama's surveys of this market show  throughput and accuracy win out here.  Though the proposed price is much lower for the portable sequencer, its unclear that a nanopore or 'strand sequencing,' which Oxford relies on, has the accuracy/resolution of the next-generation sequencers.  
If it does it is not only the price but the portability that could disrupt the market.  Such a device might bring dna sequencing into the point of care (POC) diagnostics market, and as the article details, may help doctors to sequence genes at a patient’s bedside, wildlife biologists to study genes in the field, or food inspectors to identify pathogens.
Kalorama Information's latest report on personalized medicine diagnostics details the increasing role and potential of sequencing in clinical use.  The introduction of a portable unit with the capability to present results on a standard laptop could increase the penetration of sequencing.

A hurdle remains even if a portable unit is developed -- data analysis.  It's one thing to sequence a tumor or a pathogens in food, its another to inspect the office physician or hospital lab tech to be able to crunch very large data sets analyze the meaning of dna sequences to a preciseness that makes it relevant to treatment decisions.  Well-designed  computer software will be needed to get from the taking of a sample to a diagnosis that can impact treatment.