Diagnostics Partnerships, New Sequencers, Technical Advances From Illumina
By Allison Proffitt
January 13, 2020 | Francis deSouza, CEO of Illumina, gave his report this morning at the annual JP Morgan Healthcare Conference. Just days after terminating the planned merger between Illumina and Pacific Biosciences, deSouza was positive about Illumina’s outlook for 2020, announcing agreements with Roche and Genomics England as well as new sequencers and technical advances. “I have never been more excited about the opportunity for Illumina as we enter 2020,” he said.
Roche Diagnostics Partnership
In 2012 Roche launched a hostile takeover bid for Illumina but was successfully rebuffed by Illumina, then under the leadership of Jay Flatley. Today deSouza announced what he called a “groundbreaking partnership” with Roche to accelerate the adoption of distributable NGS-based testing in oncology. The 15-year, non-exclusive collaboration agreement includes Roche IVD kits for both the NextSeq DX and NovaSeqDX platforms and could include CDx claims for current and pipeline Roche medicines for Illumina’s TruSight Oncology 500 panel.
Under the IVD terms of the agreement, Roche will develop, manufacture and commercialize AVENIO IVD tests for both tissue and blood for use on Illumina’s NextSeq 550Dx System. Illumina will continue to sell the NextSeq 550Dx Systems and core sequencing consumables. Under the CDx terms of the agreement, Illumina and Roche will develop tests and pursue CDx claims on TSO 500 for both existing and pipeline oncology targeted therapies on the NextSeq 550Dx System. Illumina will lead the development and regulatory approval process, and will continue to manufacture, supply and commercialize TSO 500. Roche will support the development of the claims and regulatory filings.
“By partnering closely, we expect to accelerate the demand for NGS-based tests in pursuit of our shared goal of enabling as many cancer patients as possible to have access to these potentially life-impacting IVD tests and therapies,” deSouza said.
Population Research to Population Health
deSouza outlined three areas of focus for Illumina in the coming year: enabling genomics research, accelerating clinical adoption of genomics, and technology innovation. Among the genomics research advances, deSouza highlighted population health efforts including Genomics England, All Of Us, and others. There are more than 50 programs similar to Genomics England worldwide, deSouza said, though many are in early planning stages. “These program plan to genotype or sequence more than 10 million people,” he said.
The programs that are more advanced are already generating data, and deSouza emphasized that these results must now be integrated into clinical care. Broad application of clinical sequencing will most likely begin in therapy selection tests for cancer and genomic diseases, deSouza believes, and points to developments in the UK’s National Health Services as evidence. “Once again the UK is charting new territory: 21 rare diseases and four cancer groups have been added to the national test directory. Which means patients in the UK will be offered whole genome sequencing as a standard of care,” deSouza said.
He announced a new contract with Genomics England to provide sequencing lab testing services for the NHS. “We expect testing services to begin ramping around the middle of this year in support of the NHS ambitions to sequence between 300,000 and 500,000 patients by the end of 2025.”
“Our goal is to make the benefits of clinical sequencing accessible to everyone with a multi-pronged strategy to accelerate clinical adoption.”
NextSeq Family Expansion
deSouza announced two new members of the NextSeq family: the NextSeq 1000 and the NextSeq 2000. Both launched today not at JP Morgan, but at an Illumina sales meeting, deSouza said.
“We believe that these are among our most innovative systems releases ever,” he said. “NextSeq 2000 offers higher output, greater ease of use, greater breadth of applications, and all at lower sequencing costs.”
deSouza described the NextSeq 1000 and 2000 platforms as flexible, enabling higher intensity applications that have previously been limited to high throughput systems. The 2000 has 2.5x the output of the NextSeq 550, deSouza reports. Cartridges are much smaller, decreasing storage and waste footprint by four times. The 2000 is listed at $335,000 and limited quantities will ship later this quarter.
Among the “more than 75 breakthrough innovations and more than 60 associated patent applications filed” powering the NextSeq 1000 and 2000, deSouza highlighted improved data density, and thus cost.
“As we’ve pushed density to the nanometer scale, a fundamental challenge has been accurately resolving DNA clusters when adjacent clusters are only a few hundred nanometers away,” he said. Illumina developers are addressing that challenge by new blue/green SBS chemistry and implementing “super resolution optics”. “These breakthroughs allow us to more than double the theoretical density of our technology by leveraging shorter wavelengths and pushing the boundaries of physics to image below the diffraction limit of light.”
The developments reduce the flow cell area needed to sequence a 30x genome 30-fold, deSouza said.
Onboard Analytics
The platforms also have analytics on board. In May 2018, Illumina acquired Edico Genomics and its DRAGEN bio-IT platform for $100 million. DRAGEN uses field programmable gate array (FPGA) technology in conjunction with algorithms to reduce both data footprint and time to results. At the time of the acquisition, Susan Tousi, Senior Vice President of Product Development at Illumina, told Bio-IT World that Edico’s ability to build the DRAGEN platform into a solution for the acceleration of secondary analysis played a key role in Illumina’s interest in the company. Integrating DRAGEN into the new NextSeq platforms enables a 3x reduction in data touchpoints and 6x faster secondary analysis, deSouza said.
A Decade of Sequencing By the Numbers
2020 also marks a milestone: ten years since Illumina introduced the HiSeq 2000. Compared to 2010, the company has ten times more customers and 50x the data that it had in 2010, deSouza said. The largest Illumina customers can sequence a whole genome for $800, he emphasized. In 2010, Flatley raved that the HiSeq was “unmatched in cost effectiveness” and would “drive the cost of a genome under $10,000 and a transcriptome under $200.”
Illumina shipped 2,400 sequencing systems, an all-time high, which included a record number of NovaSeq and NextSeq systems. The new sequencers bring Illumina’s “cumulative install base” to more than 15,000 systems. Illumina serves 6,600 sequencing customers in 115 countries.
Customers generated more than 150 petabases of data in 2019, a 50% year of year increase—the equivalent, deSouza said, of more than 500 years of continuous video recording in HD. More than 110 petabases of data came from NovaSeq platforms, deSouza said—more than double what that platform generated in 2018.
NovaSeq launched in 2017, and of the 850 HiSeq and HiSeq X customers at that time, about 1/3 have begun their transition to NovaSeq. “We continue to believe that a majority of the remaining active HiSeq customers will transition to newer Illumina sequencing system over time,” deSouza said.
Illumina shipped 620 NextSeq platforms in 2019, more than half of them to clinical customers. NextSeq DX netted more than 100 new customers, and the low throughput systems brought in about 700 new customers, “many of whom we expect to eventually scale up to NextSeq or NovaSeq,” deSouza said. They are unlikely to turn in their low throughput systems though. deSouza said 85% of all Illumina customers have an active low throughput system that they use for on-demand sequencing.