Illumina Partners for Development of Next-Gen Sequencing Tests

The one thing you can say for Illumina is that its corporate leaders have chutzpah. For those of you who didn’t grow up with grandparents from Eastern Europe, “chutzpah” is the Yiddish word for guts and nerve. Proceeding with the $8.1 billion Grail acquisition without regulatory approval from the European Community (EC) last August took chutzpah. Nor is Illumina sitting back while it awaits word on whether it will have to unwind the deal. This month, the San Diego-based genetic testing giant made a pair of new strategic deals to develop new next-generation sequencing-based (NGS) diagnostics for decentralized testing.

Illumina & Agendia Collaborate to Create MammaPrint NGS Test

On Jan. 11, Illumina announced it has forged an alliance with Agendia to develop new NGS tests in the oncology space. Under the multi-year collaboration, the firms will use the Illumina MiSeqDx sequencing platform and Agendia’s current MammaPrint test technology to create a decentralized assay aimed at improving breast cancer care. The hope is that the assay, aka, the Agendia MammaPrint NGS test, will become the first decentralized NGS-based breast cancer recurrence risk test to get FDA clearance. “We believe our current FDA-cleared, broadly reimbursed MammaPrint test provides the perfect foundation for incorporation with Illumina’s MiSeqDx platform,” noted Agendia CEO Mark Straley in a statement. Agendia thus becomes the latest addition to Illumina’s list of more than 30 IVD partners that develop sequencing-based solutions for the prognosis of cancer, therapeutic selection, and various other applications.

Illumina Provides NGS Readout Capability to SomaLogic

A week before the Agendia deal became public, Illumina unveiled a new co-development agreement with protein biomarker discovery firm SomaLogic to create and market multiplexed, high-throughput proteomics assays with NGS-based readout. The tests will be based on SomaLogic’s SomaScan platform and will run on Illumina’s NovaSeq and other high-throughput NGS platforms. More broadly, Illumina will seek to integrate SomaLogic's aptamer-based protein counting technology with its own NGS and bioinformatics platforms. This isn’t the first time Illumina has offered its NGS platforms as a readout for assays developed by other companies. Illumina made a similar deal with Olink in 2020, enabling the proteomics firm to add NGS-based readout for its proximity extension assays. That same year, Illumina cut a deal allowing NanoString Technologies to analyze GeoMx Digital Spatial Profiler data on Illumina's Dragen Bio-IT platform. Here’s a summary of some of other key strategic diagnostic deals announced in January 2022:

STRATEGIC ALLIANCES, PARTNERSHIPS, & COLLABORATIONS

Partner 1	Partner(s) 2+	Deal Summary
Single Cell Discoveries	BioTuring	Objective: Integrate firms’ respective single-cell sequencing products Dynamic: Single Cell Discoveries to offer BioTuring’s BBrowser single-cell multiomics analysis platform as part of its single-cell sequencing services
Thermo Fisher Scientific	Oncocyte	Objective: Clinically validate Thermo Fisher's Oncomine Comprehensive Assay Plus and develop Oncocyte’s DetermaIO assay on Ion Torrent Genexus system  Dynamic: Under comarketing agreement running through 2035, Thermo subsidiary Life Technologies to retain exclusive right to partner with pharma companies to develop its Oncomine test as a companion diagnostic, HealthPulse@home into lab systems using LumiraDx’s SARS-CoV-2 RNA Star Complete test Oncocyte keeps exclusive right to partner with therapeutics companies to develop DetermaIO as a companion diagnostic Thermo Fisher to pay Oncocyte a low- to mid-20s percentage of revenue it receives on worldwide sales of a resulting Oncomine IVD test and on sales of DetermaIO IVD outside US
Illumina	Agendia	Objective: Develop IVD tests for oncology testing Dynamic: Multi-year collaboration to leverage the Illumina MiSeqDx sequencing platform to create new diagnostics to improve breast patient cancer care and management
Illumina	SomaLogic	Objective: Create multiplexed, high-throughput proteomics assays with NGS-based readout Dynamic: Codevelopment agreement with Illumina to develop and market protein detection assays based on SomaLogic's SomaScan platform that run on Illumina's high-throughput NGS platforms, including NovaSeq
Illumina	Syapse	Objective: Assess uptake and actionability of comprehensive genomic profiling in community oncology health system setting Dynamic: Do study using data from Syapse Learning Health Network data aggregation platform to identify trends in testing approaches over time and actionability of results
Scienion	Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA)	Objective: Develop multiplexed, lateral-flow diagnostic platform for bladder cancer Dynamic: Leverage IPA’s knowledge of biomarkers and biobank 500 urine samples to create test and Scienon’s automated precision dispensing technology to print biomarkers on the lateral flow immunoassay
Yourgene	EKF Diagnostics	Objective: Offer noninvasive prenatal and other genomic testing services in US Dynamic: 5-year deal with Yourgene to provide EKF subsidiary and CLIA lab Advanced Diagnostics Laboratory with proprietary reagents and NGS analysis software for use in creating noninvasive prenatal testing service providing results within 48 hours ADL to also offer Yourgene's PCR tests for cystic fibrosis, aneuploidy, and DPYD deficiency in chemotherapy toxicity
Veranome	Cold Spring Harbor Laboratories (CSHL)	Objective: Develop new applications using CSHL's BARseq platform  Dynamic: Collaboration and licensing agreement bringing CSHL’s in situ sequencing and data analytics technologies into Veranome's spatial omics portfolio
Cardea Bio	Siemens Healthineers Center for Innovation in Diagnostics	Objective: Assess feasibility of developing biosensor testing applications for Cardea's BPU Platform Dynamic: Optimize and test a next-generation SARS-CoV-2 immunoassay Hardware, software, wetware, and know-how to be transferred to Siemens Healthineers' facilities to enable use of and experimentation with BPU Platform
Becton Dickinson	Pfizer + Wellcome (charitable foundation)	Objective: Study the role of diagnostics in supporting antimicrobial stewardship practices Dynamic: Survey existing diagnostic practices to understand the benefits and gaps in diagnostic testing in antimicrobial resistance stewardships
Caris Life Sciences	HotSpot Therapeutics	Objective: Develop HotSpot's precision medicine products and potential companion diagnostic tests Dynamic: Strategic collaboration to initially focus on therapeutic programs using HotSpot's E3 ubiquitin ligase immunotherapy program from pre-first-in-human trials to potential CDx tests and product launch Caris has negotiation rights for CDx tests resulting from partnership
NeoGenomics	Biomarker Collaborative	Objective: Expand cancer patient access to biomarkers testing Dynamic: Biomarker to prepare resource page to be provided to patients whose lung cancer biomarker is identified with NeoGenomics' tests
Grail	PINC AI	Objective: Identify patients who may benefit from early cancer detection using Galleri, Grail's multi-cancer early detection blood test Dynamic: PINC AI plans to augment its artificial intelligence-enabled clinical decision support platform to alert doctors to patients with higher risks of cancer who may benefit from early testing using Galleri
C2i Genomics	OncoDNA	Objective: Pair C2i's AI-based whole-genome sequencing and minimal residual disease cancer monitoring platform with OncoDNA's European network of cancer clinician-researchers Dynamic: Support interventional clinical trial led by Paris' Gustave Roussy Institute to test the clinical utility of escalating metastatic treatments in over 750 patients with high risk of cancer recurrence
Exagen	Queen Mary University of London	Objective: Develop patented molecular signatures for rheumatoid arthritis therapy selection Dynamic: Exagen gets exclusive global license from Queen Mary University to patent-pending tests that use RNA expression patterns to predict patient response to commonly prescribed therapeutics for rheumatoid arthritis
Acon Laboratories	AusDiagnostics	Objective: Launch Acon’s over-the-counter Flowflex COVID-19 Home Test in Australia Dynamic: Acon's Flowflex test is a lateral flow assay to detect SARS-CoV-2 nucleocapsid protein antigen in self-collected anterior nasal swab specimens
Qiagen	Actome	Objective: Develop protein analysis applications for the QIAcuity digital PCR system  Dynamic: Comarketing agreement giving Qiagen a co-exclusive license for digital PCR applications to use Actome's patented protein-interaction-coupling (PICO)-technology on QIAcuity Qiagen also makes undisclosed investment in German startup
Singular Genomics Systems	Broad Institute	Objective: Connect Singular’s G4 next-generation sequencing platform to the Terra data platform Dynamic: Partnership giving researchers who use the Singular G4 access to cloud-based data storage and analytical tools optimized for genomic data
Twist Bioscience	Artisan Development Labs (Artisan Bio)	Objective: Discover new antibodies against 5 undisclosed targets Dynamic: Apply Twist’s Library of Libraries to discover novel antibodies directed against Artisan Bio's immunotherapy targets, and leverage Artisan’s Immune Cell Engineering Foundry and STAR Guides to develop custom cell therapeutics  Twist to receive upfront technology access and project fees for each program, milestone payments and royalties on product sales
Bio-Techne	Akoya Biosciences	Objective: Develop a single-cell, spatial multiomics workflow for analysis of tissue samples Dynamic: Combine Akoya’s PhenoCycler-Fusion workflow with Bio-Techne’s RNAScope HiPlex v2 assay
Pacific Biosciences	Care4Rare Canada Consortium	Objective: Study complex cases of rare disease with whole-genome sequencing Dynamic: Use PacBio's HiFi long-read sequencing technology to study rare disease samples that have been sequenced with short-read technology, but for which no causative genetic variants were identified
Alamar Biosciences	Abcam	Objective: Further proteomics research  Dynamic: Combine Alamar's NUcleic acid-Linked Immuno-Sandwich Assay (NULISA) proteomics platform and Abcam's antibody portfolio
Mission Bio	SequMed	Objective: Create new single-cell assays for early cancer detection Dynamic: Combine Mission Bio's Tapestri platform with SequMed's clinical assay development and data analysis capabilities

DISTRIBUTION, SALES, & MARKETING AGREEMENTS

Product Owner	Distributor	Deal Summary
SDI Labs	Medi-Wheels Diagnostics	Products: SDI’s over-the counter rapid antigen test kits Territory: Global Kits to be sold under Medi-Wheels Diagnostics brand name in packs of two
Purigen	Institute of Applied Biotechnologies	Products: Purigen’s Ionic Purification System benchtop instrument for extracting, purifying, and concentrating genomic RNA and DNA from cells and formalin-fixed, paraffin-embedded tissues Territory: Czech Republic, Hungary, Poland, Romania, Slovakia Exclusive
Parse Biosciences	Research Instruments	Products: Parse's Evercode Whole Transcriptome, Cell Fixation, and Nuclei Fixation kits  Territory: Singapore, Thailand, Malaysia, Vietnam
XPhyto Therapeutics	TechUnit	Products: XPhyto's COVID-ID Lab test  Territory: Czech Republic Non-exclusive
OraSure Technologies	Eurobio Scientific	Products: OraSure Technologies' OraQuick saliva-based HIV self-test Territory: France Exclusive

LICENSES

Licensor	Licensee	Deal Summary
OncXerna	Exact Sciences	Exclusive license allows Exact to offer OncXerna's Xerna tumor microenvironment panel to identify patients likely to respond to anti-angiogenic and immunotherapies to CUT&RUN and CUT&Tag chromatin profiling technologies as part of its own GEM ExTra test
Socpra Sciences Santé Et Humaines	Mainz Biomed	Mainz gets exclusive option to globally license portfolio of 5 novel mRNA biomarkers

GOVERNMENT CONTRACTS

Contractor	Govt. Agency	Contract Summary
Abbott Rapid Dx North America	US Department of Defense	$306 million firm-fixed-price contract for COVID-19 rapid antigen test kits