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Illumina’s Diagnostic Vision

By Allison Proffitt

January 11, 2022 | Speaking at the 2022 JP Morgan Healthcare Conference—being held virtually again this year—deSouza, the CEO of Illumina, outlined the sequencing giant’s plans for expanding their diagnostic capabilities and business.

GRAIL, the Illumina subsidiary that was spun out of the company in 2016 and then acquired in 2021, has Galleri, a multi-cancer early detection blood test for more than 50 cancers. “GRAIL is working closely with partners throughout healthcare to support access and utilization of Galleri,” deSouza said. “Their goal is to bring this test to as many patients as possible as soon as possible. They’re seeing early success.” deSouza promoted an upcoming GRAIL monitoring test for minimal residual disease, expected in 2023.

For “Core Illumina”, which does not include GRAIL, the company reported revenue in 2021 of more than $5 billion, with records being set for platforms shipped. The current install base of Illumina platforms is more than 20,000 deSouza said and customers number more than 8,000 globally.

More than $1.5B of that revenue was shipments of the NovaSeq 6000. “About 50% of NovaSeq orders in 2021 were to new-to-high throughput customers, a very positive leading indicator,” deSouza said. “There’s growing demand for NovaSeq sequencing in regulated markets,” he continued, announcing that NovaSeq Dx will launch in 2022, including a version specific to China.

Oncology Diagnostics Partnerships

The first market area deSouza highlighted for growth was oncology. Oncology testing is a $75B market that is only 4% penetrated, deSouza believes, and opportunities for genomics lie in early detection, therapy selection, and monitoring.

In particular, deSouza said that Illumina is leading the $14B therapy selection market, highlighting 11 partnerships for the Illumina TruSight oncology comprehensive test including a just-announced partnership with Boehringer Ingelheim, as well as 34 IVD development partnerships including a just-announced partnership with Agendia.

Both of these partnerships were announced yesterday in conjunction with JP Morgan. The Boehringer Ingelheim partnership aims to accelerate the development of therapy selection and precision medicines for patients with advanced cancer. It spans current and future CDx programs, with plans to add CDx claims to an in vitro diagnostic test Illumina is developing that is based on the content of TruSight Oncology 500 (TSO 500). The first program will co-develop a CDx for a Boehringer Ingelheim investigational medicine.

The Agendia partnership will focus on new tests to enhance the care and management of breast cancer patients, utilizing the Illumina MiSeq Dx sequencing platform, expanding the range of gene panels available for solid tumor analysis. Agendia’s flagship test, MammaPrint, which is FDA- cleared and currently offered via Agendia’s central laboratory, is expected to be the first decentralized NGS-based breast cancer recurrence risk test cleared by the FDA.

Diagnostics World spoke with Phillip Febbo, Illumina’s Chief Medical Officer before the announcement to get insight into both new partnerships. “What I’m so excited about is increasingly we’re establishing partnerships with leaders in the oncology field to make sure that their tests or tests that can identify patients for their drugs can be run on our sequencers,” Febbo said. “As we see our install base expand, that really provides an opportunity to enable laboratories to bring the insights of precision medicine to patients.”

Neither type of partnership is new. Several pharma companies have engaged Illumina very early in the drug development process to simultaneously develop companion diagnostics; in addition to Boehringer Ingelheim, deSouza mentioned Merck, Bristol Myer Squibb, and Bayer in his presentation.

“What we are finding is that there’s increasing interest for us to participate earlier in that journey so that we can find the most efficient path forward together,” Febbo explained. While precision medicine offers amazing benefits to patients, there are still significant challenges. From his own experience as a medical oncologist, Febbo listed cost, efficiency, and the overwhelmed healthcare system among the greatest challenges. “By working together early, finding the most efficient path, we can be much better and bring in these novel therapies to identify those patients who will most benefit and where the drug provides the most benefit to the healthcare system,” he said.  

Likewise, Agendia is not the first in vitro diagnostic test maker to work on development and scaling alongside Illumina; others include Roche and Qiagen. These companies have done their own development, but partnership with Illumina helps distribute tests to more patients globally, unhindered by shipping times to a central lab, or issues sending tests out of country.

For Illumina, closely partnering with these companies means pairing the developmental pace of biological research with their own technology innovation development times. “We’re going to stay laser focused on bringing new technologies into sequencing…, increasing the speed, increasing the fidelity, and decreasing the cost of sequencing as we’ve done for the past 22 years,” Febbo said. “We have increased our investment in data science, and our data science group can be an incredible asset in a partnership with these pharma groups because there are very few entities that are as well-positioned to understand how to best glean insights from genomic data as Illumina.”

These partnerships also expand Illumina’s experience and understanding of genetic data challenges that can be incorporated into Illumina Connected Analytics, the company’s bioinformatics solution announced last year at the JP Morgan healthcare conference. “You’ll see us aggressively invest in Illumina Connected Analytics and bring partnerships into that space,” Febbo predicted. “We’ll use the data insights group to help our partners find those targets early, but also to understand what’s the toolkit that any Illumina user needs to generate their own insight.”

Other Diagnostic Areas

In addition to oncology, Illumina is continuing its focus on non-invasive prenatal testing. VeriSeq NIPT v2 received IVDR approval in 2021, and deSouza predicted the first distributable US IVD by 2023, TruSight NIPT IVD. The company is also banking on whole exome and whole genome sequencing gaining ever wide coverage and reimbursement for genetic diseases. Among the efforts deSouza highlighted in his presentation: iHope Genetic Health, launched last November to provide whole-genome sequencing access (WGS) to tens of thousands of patients across the globe impacted by genetic disease

Illumina applications are also growing as well into infectious diseases and other areas, deSouza added. Illumina platforms have been essentially involved in pathogen surveillance throughout the Covid-19 pandemic. deSouza reported that more than 75% of published SARS-CoV-2 sequences were done on an Illumina platform. He also predicted that Illumina platforms will be fundamental to future pan-pathogen surveillance efforts.

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