By Julia Karow
This article was originally published Sept. 24.
Illumina is plowing ahead with an internal cancer-sequencing project that is part of its diagnostic initiative, but has found it difficult to procure suitable patient samples, CEO Jay Flatley said during a recent investor conference.
He also said that the company continues to be confident about Oxford Nanopore Technologies, in which it invested $18 million earlier this year, and is "pleased with" the progress of the startup.
Flatley, who spoke last week at the UBS Global Life Sciences Conference in New York, said that as part of its diagnostics initiative, the company has collected a number of tumor/normal sample pairs for sequencing, which it will analyze over the next three to six months.
However, he said the company has found it difficult to track down suitable patient samples, especially for ovarian and gastric cancer. For ovarian cancer, for example, it is looking for early-stage samples from non-smoking patients with no variants in the BRCA genes, he explained.
As a result, Illumina now plans to sequence 75 to 80 cancer samples, or up to 40 tumor-normal pairs, instead of 50 pairs, as it had stated earlier. The project, Flatley pointed out, "is sample-limited, not sequencing-capacity-limited."
The firm has already conducted a proof-of-concept study on cancer sequencing, using a melanoma patient sample, and presented results from that project earlier this month at a conference at Cold Spring Harbor Laboratory this month (see In Sequence 9/22/2009).
Flatley also made a few remarks about the company's investments in future sequencing technologies.
Earlier this year, Illumina invested $18 million in Oxford Nanopore Technologies, which has been developing a label-free single-molecule sequencing technology that harnesses an exonuclease to chop off individual nucleotides and feed them into a protein nanopore for detection.
"If this technology works, which we expect it to, it has the potential to be the fastest and cheapest way to sequence DNA in the near term," Flatley said, adding later that Illumina has been "pleased with" Oxford Nanopore's progress to date.
Further investment by Illumina in the company, however, is contingent on "one very important technical milestone," he said: Oxford must demonstrate that it can reliably pass nucleotides cleaved by an exonuclease down the nanopore. Until this process is "very far along to prove it works robustly," he said, Illumina will not provide further details about the technology.
Earlier this year, Oxford Nanopore published a paper showing that the alpha-hemolysin nanopore can accurately identify single nucleotides, including methylated cytosine (see In Sequence 2/24/2009), but that research did not involve an exonuclease.
In addition to its investment in Oxford Nanopore, Illumina last year acquired sequencing startup Avantome for $25 million and up to $35 in contingent payments. However, during his UBS presentation, Flatley provided scant information about that technology, noting only that it will be targeted at "long-read diagnostically oriented sequencing" and provide reads on the order of several hundred bases in length.
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In the meantime, Illumina believes its Genome Analyzer platform will continue to be viable for several more years. Flatley said the platform's sequencing technology "has continued to surprise us" and has already delivered a higher throughput than what Illumina had hoped for when it acquired Solexa in early 2007. The Genome Analyzer is still expected to produce on the order of 95 gigabases per run by the end of the year, "and I don't see any end to that anytime soon," Flatley said.
The GA's sequencing-by-synthesis technology, he predicted, will "still be around three to four years from now."
Also at the UBS conference, Flatley commented on the replacement of array technology by sequencing, noting that more than half of its Genome Analyzer customers are currently using the platform in part for transcriptome sequencing. He said that while arrays are still cheaper for whole-genome transcriptome studies today, he expects sequencing will reach parity in about a year, at which point the market will begin to shift quickly.
Targeted resequencing, he said, will be a significant market for Illumina over the next few years, with customized projects dominating all-exon sequencing. However, he added that it will be a "market with a limited life." As the cost of sequencing drops below $5,000 per genome, he explained, the added up-front cost of preparing DNA for targeted sequencing will make targeted approaches less compelling.
Asked whether Illumina sees opportunities in the sequencing service business — embraced, for example, by Complete Genomics — Flatley said that for now, its customers seem to prefer purchasing their own Genome Analyzers instead of outsourcing sequencing to Illumina’s existing service.
However, he noted that five years from now, the sequencing service market might look very different, and the company is "prepared to play in this service market as we need to." It already has certain infrastructure in place, he said, for example its recently CLIA-certified laboratory that it uses for the personal genome sequencing service that Illumina launched in June (see In Sequence 6/16/2009).