IBM joins race for $1000 genome with nanopore electronics
Computer maker IBM is joining the race to build a cheap DNA sequencer, using transistors buried inside silicon nanopores to detect the individual nucleic acid bases electrostatically as the DNA threads through. The approach is similar to the one being taken by UK startup Oxford Nanopore and colleagues at US universities Harvard and Santa Cruz.
IBM Research is among a number of companies to have been awarded grants totalling almost $6m by the US National Human Genome Research Institute (NHGRI) to investigate technologies able to provide personalised genome sequencing for less than $1000. The TJ Watson Research Center will receive just over $0.5m for its nanopore-sequencing programme.
In constrast to the first-generation nanopore demonstrated by Oxford Nanopore, which places a ring-shaped protein at the top of the pore to cut and pass individual bases through, the IBM design will use a naked nanopore with transistors to control the movement of intact DNA strands. Oxford plans to move to a naked nanopore design once its first machines have been commercialised that will be able to handle continuous strands. So far, IBM has only demonstrated the technique computationally and is working on the first prototypes.
Although nanopores promise the ability to deal with intact strands of DNA, which will improve overall accuracy versus methods that rely on sequencing very short lengths of DNA combined with statistical processing, the speed at which the molecule passes through a nanopore is a major problem. A million bases can pass through a pore in one second, according to Gordon Sanghera, CEO and co-founder of Oxford Nanopore with Professor Hagan Bailey.
A further problem with artificial nanopores is consistency, experts say. It is hard to etch holes that are consistently the same size. Inserting a protein provides more consistency and the pores have proved to be very resilient. Some researchers have said they have working biological nanopores that are close to 20 years old.
Researchers in nanopore-based genetic sequencing have formed coalitions to try to push the work ahead more quickly than if they worked individually. Although a spokesperson for Oxford Nanopore refused to say whether the company is working with IBM, she added: “Oxford Nanopore has relationships with the world’s leading nanopore researchers for current and future generations of nanopore-sensing technology. The company has leadership in expertise and intellectual property in this area.”
Oxford Nanopore has disclosed a technology-sharing partnership with Harvard University – which has expertise in solid-state nanopores – and the University of California at Santa Cruz. The company signed a deal with another DNA-sequencing company, Illumina, at the start of the year.