As geneticists gather in San Francisco, sequencing companies are strutting their stuff. Oxford Nanopore drew crowds by displaying its sleek, cheap machines that promise to disrupt the market place – but the company remains coy about when exactly it will release data or start taking orders. Pacific Biosciences has announced advances in its sequencing chemistry. And Illumina unveiled cloud-based collaborations to help turn raw data into information.
Sequencing technology from Oxford Nanopore promises the best of everything: quick, cheap sequencing data that can detect variants invisible to other methods. It made a huge splash at the annual meeting of Advances in Genome Biology & Technology (AGBT) in February; five thousand dollars of equipment would reportedly sequence an antire human genome in fifteen minutes, with machines to be ready by the end of the year. Since then, scientists’ wait for Nanopore’s sequencing data has been like waiting for Godot, and no data were forthcoming at today’s meeting of the American Society of Human Genetics.
Chief Executive Officer Gordon Sanghera spent some time telling me how the technology could tag proteins or microRNA with specially-made DNA strands and be used for detection, but he wouldn’t say a word about the company’s timeline for DNA sequencing. Instead, he urged patience. “What we said at AGBT, we will make good.”
Unlike nanopore technology, which reads changes in electrical conductance as DNA strands move through tiny holes, commercially available sequencing techniques work by shredding DNA, and then copying the fragments with chemical reactions that reveal the sequence. The biggest challenge is computationally putting these sequenced fragments, or ‘reads,’ back together.
While small mutations can be detected relatively reliably, larger duplications, deletions and rearrangements are more-or-less invisible. The longer the reads, the easier it is to put the genome back together. Roche 454 announced some software tweaks to lengthen its reads, boasting read lengths of 1000 basepairs and beyond. A customer quoted in the company’s press release says that its most frequent length was 820.
Meanwhile, Pacific Biosciences announced that it had boosted the lengths of its reads from an average of 3,000 basepairs to about 5,000 basepairs, with some reads as long as 20,000. That’s compared to 200 or so basepairs produced by Illumina’s technology. PacBio made these improvements both with software and chemistry. The machine can record data from the sequencing reaction from a longer length of time, and a faster DNA polymerase reads more bases each second. Today, the company described using its technology to sequence single molecules of HIV collected from Zambia.
At $700,000, machines are severalfold more expensive than those of its competitors, and users tell me machines are finicky. PacBio reads also have much higher error rates than its competitors. When I asked director of product management Edwin Hauw about this, he told me the company would soon announce an error-correction technique that uses previously discarded short reads to create a consensus sequence in its standard 5 kb reads. Earlier this year, the company and other research groups described a similar approach using reads from other sequencing technology. Last quarter, revenues at the company were down 73% but the company has booked sales for at least four machines. The company still lags far behind its competitors in market share.
Speaking of market share, Greg Lucier, CEO of Life Technologies, told Bloomberg that he expected his company to take the top sequencing spot next year. (Analysts were skeptical.) The company is focusing on selling benchtop sequencing machines to individual labs. Rather than monitoring a growing DNA strand with light-generating reactions or forcing a single DNA strand through a nanometer scale hole, its technology monitors tiny pH changes as DNA is copied. It launched its latest machine a few months ago; which promises to sequence a human genome in less than a day for $1000, that that metric depends on a chip scheduled for next year. Again, though, researchers are waiting to see sequencing data.
Illumina, for its part, is trying to remove everything that’s burdensome about bioinformatics, says Jordan Stockton, marketing director of computational biology. This week the company is launching applications in BaseSpace. Illumina’s instruments will upload raw sequencing reads to the cloud, where a bevy of apps await. These perform alignment, annotation and more. Illumina announced products from nine partner companies this week and will also let budding bioinformaticians put their own creations in BaseSpace as well, a possibility that should help the scientific community test out new code – in an environment built to support data from Illumina’s instruments.
Besides giving Illumina customers more bioinformatics tools to play with, BaseSpace should start to generate its own revenue stream. Starting in 2013, the company will keep a cut of any fees collected by application providers. Until then, though, BaseSpace and all its applications are free.