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Next generation Sequencing – Roche and IBM join forces

10.07.2010

Third-generation DNA sequencers seem likely to hit the US$1bn sequencing market in 3-5 years, and insiders predict the new machines will bring down sequencing costs for a full human genome to a mere one hundred euros. Diagnostics and IT giants Roche and IBM are now throwing their hats into a ring that until now has been dominated by small high-tech firms like Oxford Nanopore. At the start of July, the companies announced that they are co-developing a nanopore-based DNA-sequencer based on IBM’s “DNA Transistor” technology.

Unlike current second-generation DNA sequencing technologies, nanopore sequencing does not require PCR amplification, but instead reads the DNA code directly as a single strand of the DNA double helix is threaded through a nanometer-sized pore in a silicon chip. Nanopore sequencing, which has also been commercialised by Oxford Nanopore, is expected to significantly improve speed, costs and read lengths compared to current sequencing machines. Experts say that these third-generation sequencing technologies will open up the molecular diagnostics market for ultra-high-throughput sequencing, making the dream of patient stratification before medication a reality. “Sequencing is an increasingly critical tool for personalised healthcare. It can provide the individual genetic information necessary for the effective diagnosis and targeted treatment of disease,” says Manfred Baier, Head of Roche Applied Science (Penz­berg, Germany), which is funding the development of IBM’s technology.

A demanding task

However, there are quite a few technological challenges left to master. Perfecting a technique for threading a long, fragile DNA molecule through a three-nanometer wide hole in a silicon chip will not be easy. Neither will it be simple to optimise the electrical sensor that determines which of the four bases is being detected. One problem is to control exactly how the DNA strand is passed through the nanopore . The rapidly-occurring process also has to be slowed down in a controlled way in order to give the sensor time to read each individual base.
To control the speed at which the DNA flows through the nanopore, IBM researchers have developed a device consisting of a multilayer metal/dielectric nano-structure. A membrane containing the functionalised nanopore divides a reservoir into an upper part containing an ionic solution with a high concentration of single-stranded DNA, and a lower part where the translocated DNA collects after the read. A biasing voltage induces the DNA in the top reservoir to move through the passage to the bottom reservoir. These voltage biases also modulate the electric field inside the pore. The technique utilises the interaction of discrete charges along the backbone of a DNA molecule with the modulated electric field to trap DNA in the nanopore. By cyclically turning these gate voltages on and off, the researchers have already simulated the movement of DNA through the nanopore at a rate of one

nucleotide per cycle.
It’s clear the diagnostics market for sequencing applications would be significantly larger than the current research market, and more than one company sees nanopore technology as promising. Roche’s competitor Illumina last year also secured marketing of Oxford Nanopore’s BASETM Technology. But molecules of DNA are not passed through as a whole in this approach. Instead, an exonuclease cuts a base from the DNA strand and directs it to the nanopore.

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