DX Deals: Teaming with Google Leads to WGS Success for PacBio
A strategic partnership with Google enables more accurate whole genome sequencing with machine learning.
Pacific Biosciences (PacBio) is making major inroads into the multibillion global sequencing market thanks in large part to the success of its newest long-read sequencing system, Revio. Though the high-fidelity (HiFi) whole genome sequencing (WGS) technology on which Revio is based is highly accurate to begin with, PacBio has tapped into the machine learning and algorithm development capacities of Google to improve it further. On August 7, the company unveiled a new Revio-related strategic venture with Google to evaluate the system’s capacity for improving diagnosis of genetic conditions in neonatal care.1
The New PacBio-Google Revio Collaboration
Neonatal care could be a major opportunity for PacBio and other developers of WGS technology. A study published in the Journal of the American Medical Association on July 11, 2023, found that WGS outperformed conventional gene panels in diagnosing babies with suspected genetic conditions.2
Under the new deal, PacBio will team with GeneDx, the genome testing and interpretation firm previously known as Sema4, and the University of Washington to perform a study called SeqFirst at Seattle Children’s Hospital. The objective of the project, according to the PacBio press release announcing the collaboration, is to determine “whether whole genome sequencing of children with suspected developmental differences at point-of-diagnosis, as opposed to conventional diagnostic evaluations, will lead to earlier, more rapid diagnoses, reduce costs of these diagnoses, and improve therapeutic outcomes.”1
GeneDx will use the Revio system for the study to perform long-read WGS sequencing and analysis of samples from 350 people, including 120 samples from participants in the SeqFirst study. The researchers will also use short-read sequencing technology to analyze the samples, looking out for novel variants associated with specific genetic conditions, particularly those that are detected with Revio but undetected with short-read sequencing. Google’s role will be to provide an undisclosed amount of funding for reagents and other elements of SeqFirst while also developing informatics methods based on project results.
The Google Advantage
Having Google at its side has been a major boost for PacBio. Previous research between the companies led to the publication of a 2021 paper finding that Google’s DeepConsensus machine learning tool can increase the yield of highly accurate (99.9% accuracy) HiFi reads by as much as 27 percent per instrument run.3 In January 2022, the partners entered into a new research partnership allowing PacBio to implement DeepConsensus on the Revio system and improve overall long-read WGS performance.4
For PacBio, the Revio investment has paid off. On August 2, the firm announced that strong sales of Revio drove a 34 percent increase in overall 2023 second quarter year-over-year earnings.5 PacBio placed 45 Revio instruments and two other sequencers during the quarter, up from 36 instruments in Q2 2022. This momentum enabled the company to raise its 2023 full-year revenue guidance to between $185 million and $190 million, or growth of 44 percent to 48 percent, as opposed to its original forecast of $170 million to $185 million.6,7
Takeaway
Machine learning and artificial intelligence have the potential to improve the performance and accuracy of diagnostics platforms. The PacBio-Google collaboration is an excellent reminder that if your underlying diagnostic technology is sound, you may be able to access the capacities you need to improve it without developing them in-house.
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Here’s a summary of other key strategic diagnostic deals announced in late July through August 2023:
Strategic Alliances, Partnerships, and Collaborations
| Partner 1 | Partner(s) 2+ | Deal Summary |
|---|---|---|
| Agilent Technologies | Element Biosciences | · Objective: Integrate Agilent’s SureSelect target enrichment panels for use with Element’s AVITI™ system · Dynamic: Expansion of co-marketing agreement signed in February 2022 to promote the SureSelect and AVITI products |
| Helix | Nebraska Medicine | · Objective: Broaden access to and improve genetic cancer testing · Dynamic: Launch the Genetic Insights Project, with Helix to provide testing to identify individuals at elevated risk of cancer and other potentially life-threatening diseases while also collecting broader genomic data for research purposes |
| Standigm | Nashville Biosciences | · Objective: Accelerate early-stage drug discovery · Dynamic: South Korea-based Standigm to build customized AI models for drug discovery using de-identified clinical and genomic datasets from Nashville Biosciences |
| Biocartis | Eli Lilly | · Objective: Explore addition of Biocartis’ Idylla™ platform to a molecular diagnostics workflow · Dynamic: Perform study in Spain sponsored by Eli Lilly to examine how Idylla,™ a fully automated and cartridge-based real-time PCR system, might contribute to faster and more comprehensive identification of genetic alterations in non-small cell lung cancer (NSCLC), as compared to current clinical workflows |
| ChromaCode | Protean BioDiagnostics | · Objective: Create early access program to launch new NSCLC test · Dynamic: Test uses ChromaCode’s High Definition PCR(HDPCR™) multiplexing technology to detect all National Comprehensive Cancer Network recommended variants in single assay with turnaround time of under 24 hours |
| Pacific Biosciences | GeneDx (formerly called Sema4) + University of Washington + Google | · Objective: Study capabilities of PacBio’s HiFi long-read sequencing technology to increase diagnostic rates in pediatric patients with genetic conditions · Dynamic: GeneDx to use PacBio’s new Revio instrument to perform whole-genome sequencing and analysis of samples from 350 people, including from 120 SeqFirst study participants at Seattle Children’s Hospital · Google to develop informatics methods and provide undisclosed amount of funding for reagents and certain other aspects of project |
| Curetis (subsidiary of OpGen) | FIND | · Objective: Develop antimicrobial resistance (AMR) assay and a cartridge for Curetis’s Unyvero A30 platform for AMR detection from commonly used blood culture bottles · Dynamic: Extension of R&D collaboration after successful completion of feasibility phase of original deal with companies to also develop corresponding software plug-in, and analytical performance evaluation · Development phase is expected to last 10 months with expected total project investment of about $1.5 million |
| Amoy Diagnostics | AstraZeneca | · Objective: Develop AmoyDx® Essential NGS panel as a companion diagnostic for use in China with AstraZeneca’s ENHERTU® (trastuzumab deruxtecan) antibody-drug conjugate for treatment of NSCLC · Dynamic: Assay to be used to identify patients that can benefit from ENHERTU®, which is approved in China to treat patients who’ve received previous treatments for HER2-low and HER2-positive metastatic breast cancer |
| Amoy Diagnostics | AstraZeneca | · Objective: Develop AmoyDx® HRD Complete Panel as companion diagnostic for Astra Zeneca’s PARP inhibitor LYNPARZA® (olaparib) · Dynamic: Panel to be used to identify patients that can benefit from olaparib for treating HRD-positive advanced epithelial ovarian, fallopian tube, or primary peritoneal cancer in patients who have a complete or partial response to first-line chemotherapy in combination with bevacizumab |
| MetaSight Diagnostics | Kahn-Sagol-Maccabi (KSM), the research and innovation center of Israel’s HMO Maccabi Health Services | · Objective: Create comprehensive metabolomics dataset consisting of hundreds of thousands of de-identified serum samples to support development of liquid biopsy tests · Dynamic: Develop liquid biopsy platform for oncology and other disease areas, with early development targets in chronic liver disease, cancer, cardiovascular disease, and neurological diseases |
| QuidelOrtho | BYG4lab® | · Objective: Expand and improve QuidelOrtho’s diagnostic system informatics offerings · Dynamic: Expansion of current collaboration to promote wider use of proprietary tools that allow auto-verification, i.e., use of computers to verify clinical lab test results without manual intervention, enabling labs to overcome workflow and labor challenges |
| Zymo Research | Opentrons Labworks | · Objective: Develop and commercialize automated workflow for cell-free DNA (cfDNA) isolation and library preparation · Dynamic: Combine Zymo’s chemistries with automation capabilities of Opentrons’ Flex platform to enable superior cfDNA yields and reduced processing time, as compared to current extraction methods |
| DiaCarta | Hopkins MedTech Compliance/Hopkins MedTech Lab Services | · Objective: Offer validation and regulatory compliance services for lab test and in vitro diagnostic developers in US · Dynamic: Service currently unmet need of companies that have developed novel IVD tests for help to advance their products for FDA approval or to establish them as laboratory developed tests |
| One Codex | 4bases | · Objective: Offer sample-to-report microbiome analysis solutions to clinicians in the EU · Dynamic: One Codex to integrate its cloud-based SaaS platform, designed for identifying bacteria, viruses, protists, and fungi, with 4bases’ clinically validated microbial analysis panels using short- and long-read sequencing, with integrated solution to be validated to CE-IVD standards |
Distribution, Sales, and Marketing Agreements
| Product Owner | Distributor | Deal Summary |
|---|---|---|
| Sysmex | Roche | · Products: Sysmex’s hematology products · Territories: Global · Nonexclusive · Renewal and expansion of current partnership agreement |
| LumiraDx | Axonlab | · Products: LumiraDx platform for point-of-care testing · Territories: Europe · Exclusive in Switzerland · Nonexclusive in Germany and other unnamed European countries |
| Pillar Biosciences | Illumina | · Products: Pillar’s oncology assays · Territories: Global · Illumina to make Pillar’s targeted NGS assays available as part of its own portfolio of oncology products |
| Renalytix | Vector Pharma | · Products: Renalytix’s kidneyintelX.dkd™ test · Territories: The Gulf Cooperation Council (GCC) countries of Saudi Arabia, Bahrain, Qatar, Oman, Kuwait, UAE |
Licenses
| Licensor | Licensee | Deal Summary |
|---|---|---|
| ERS Genomics | Transomic Technologies | ERS Genomics grants gene editing company nonexclusive license to its foundational CRISPR-Cas9 patent portfolio |
| Johns Hopkins University | DELFI Diagnostics | DELFI exclusively licenses GEMINI (GEnome-wide Mutational Incidence for Non Invasive detection of cancer), a method for identifying somatic genomic alterations in cell-free DNA |
Government Contracts
| Contractor | Govt. Agency | Contract Summary |
|---|---|---|
| Cue Health | U.S. Department of Health and Human Services’ Biomedical Advanced Research and Development Authority (BARDA) | $28 million contract to develop multiplex, molecular respiratory test to simultaneously detect and differentiate among influenza A/B, RSV, and COVID-19 run on the Cue Health Monitoring System with results returned in about 25 minutes for over-the-counter and point-of-care use |
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